Starting phenix.real_space_refine on Wed Jul 30 14:29:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x2u_32971/07_2025/7x2u_32971_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x2u_32971/07_2025/7x2u_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7x2u_32971/07_2025/7x2u_32971.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x2u_32971/07_2025/7x2u_32971.map" model { file = "/net/cci-nas-00/data/ceres_data/7x2u_32971/07_2025/7x2u_32971_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x2u_32971/07_2025/7x2u_32971_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.06, per 1000 atoms: 0.68 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: 3.57 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.04 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: 3.44 Time building geometry restraints manager: 3.81 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.290 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.730 ------------------------------------------------------------------------------- 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 : 11.43 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (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 TRP 0.009 0.001 TRP B 364 HIS 0.013 0.002 HIS B 76 PHE 0.033 0.002 PHE B 653 TYR 0.013 0.002 TYR A 322 ARG 0.004 0.001 ARG B 650 Details of bonding type rmsd hydrogen bonds : bond 0.17432 ( 761) hydrogen bonds : angle 7.73515 ( 2253) covalent geometry : bond 0.01028 (12107) covalent geometry : angle 0.91957 (16336) *********************** 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 : 1.390 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: 0.2841 time to fit residues: 71.5242 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 : 1.302 ------------------------------------------------------------------------------- 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 121 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.136722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.093037 restraints weight = 13281.836| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 1.56 r_work: 0.2702 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2573 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1337 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= 0.166 Angle : 0.577 7.028 16336 Z= 0.304 Chirality : 0.042 0.197 1881 Planarity : 0.004 0.050 2020 Dihedral : 9.347 59.667 1815 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.30 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.22), residues: 1435 helix: 0.60 (0.16), residues: 1023 sheet: None (None), residues: 0 loop : -0.96 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 507 HIS 0.010 0.001 HIS B 76 PHE 0.022 0.002 PHE A 200 TYR 0.012 0.001 TYR A 322 ARG 0.004 0.000 ARG A 637 Details of bonding type rmsd hydrogen bonds : bond 0.04863 ( 761) hydrogen bonds : angle 5.10691 ( 2253) covalent geometry : bond 0.00389 (12107) covalent geometry : angle 0.57657 (16336) *********************** 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 : 1.741 Fit side-chains REVERT: C 56 GLU cc_start: 0.7962 (pm20) cc_final: 0.7465 (pm20) REVERT: C 188 LYS cc_start: 0.8537 (ptmt) cc_final: 0.8145 (ptmt) REVERT: D 56 GLU cc_start: 0.8297 (pm20) cc_final: 0.7859 (pm20) REVERT: D 135 LEU cc_start: 0.7701 (tp) cc_final: 0.7361 (tp) outliers start: 6 outliers final: 0 residues processed: 171 average time/residue: 0.3763 time to fit residues: 91.0802 Evaluate side-chains 155 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 90 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 69 optimal weight: 0.1980 chunk 40 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.141376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.098382 restraints weight = 13350.163| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.52 r_work: 0.2792 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1862 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= 0.131 Angle : 0.512 6.585 16336 Z= 0.270 Chirality : 0.040 0.134 1881 Planarity : 0.003 0.048 2020 Dihedral : 7.928 58.593 1808 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.41 % Allowed : 11.75 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.22), residues: 1435 helix: 1.00 (0.16), residues: 1026 sheet: None (None), residues: 0 loop : -0.92 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 366 HIS 0.005 0.001 HIS A 76 PHE 0.017 0.001 PHE B 200 TYR 0.011 0.001 TYR B 322 ARG 0.002 0.000 ARG A 637 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 761) hydrogen bonds : angle 4.62910 ( 2253) covalent geometry : bond 0.00295 (12107) covalent geometry : angle 0.51245 (16336) *********************** 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 202 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 1.398 Fit side-chains REVERT: A 208 VAL cc_start: 0.8742 (t) cc_final: 0.8520 (t) REVERT: A 381 TYR cc_start: 0.9194 (m-80) cc_final: 0.8927 (m-10) REVERT: A 621 GLN cc_start: 0.7564 (tm-30) cc_final: 0.7225 (pt0) REVERT: B 208 VAL cc_start: 0.8756 (t) cc_final: 0.8548 (t) REVERT: B 339 MET cc_start: 0.8966 (mtt) cc_final: 0.8757 (mtt) REVERT: B 621 GLN cc_start: 0.7595 (tm-30) cc_final: 0.7254 (pt0) REVERT: C 56 GLU cc_start: 0.8067 (pm20) cc_final: 0.7595 (pm20) REVERT: C 135 LEU cc_start: 0.7766 (tp) cc_final: 0.7478 (tp) REVERT: D 56 GLU cc_start: 0.8127 (pm20) cc_final: 0.7658 (pm20) REVERT: D 135 LEU cc_start: 0.7667 (tp) cc_final: 0.7251 (tp) outliers start: 18 outliers final: 11 residues processed: 192 average time/residue: 0.2683 time to fit residues: 73.3401 Evaluate side-chains 182 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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 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 136 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 20 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 135 optimal weight: 0.0570 chunk 23 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 49 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.141540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.098688 restraints weight = 13183.897| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.49 r_work: 0.2797 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2101 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= 0.131 Angle : 0.499 6.229 16336 Z= 0.263 Chirality : 0.040 0.160 1881 Planarity : 0.003 0.048 2020 Dihedral : 7.629 59.682 1808 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.64 % Allowed : 12.45 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.22), residues: 1435 helix: 1.18 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -0.88 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 366 HIS 0.005 0.001 HIS A 76 PHE 0.016 0.001 PHE A 200 TYR 0.010 0.001 TYR B 322 ARG 0.003 0.000 ARG D 65 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 761) hydrogen bonds : angle 4.48424 ( 2253) covalent geometry : bond 0.00302 (12107) covalent geometry : angle 0.49878 (16336) *********************** 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 206 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 1.261 Fit side-chains REVERT: A 208 VAL cc_start: 0.8734 (t) cc_final: 0.8516 (t) REVERT: A 380 VAL cc_start: 0.9016 (t) cc_final: 0.8700 (m) REVERT: A 621 GLN cc_start: 0.7522 (tm-30) cc_final: 0.7169 (pt0) REVERT: B 208 VAL cc_start: 0.8733 (t) cc_final: 0.8511 (t) REVERT: B 339 MET cc_start: 0.8974 (mtt) cc_final: 0.8772 (mtt) REVERT: B 621 GLN cc_start: 0.7547 (tm-30) cc_final: 0.7209 (pt0) REVERT: C 56 GLU cc_start: 0.7975 (pm20) cc_final: 0.7526 (pm20) REVERT: C 135 LEU cc_start: 0.7675 (tp) cc_final: 0.7332 (tp) REVERT: C 168 ASP cc_start: 0.6172 (m-30) cc_final: 0.5540 (t0) REVERT: D 45 THR cc_start: 0.7934 (t) cc_final: 0.7680 (m) REVERT: D 56 GLU cc_start: 0.7959 (pm20) cc_final: 0.7526 (pm20) REVERT: D 124 LEU cc_start: 0.7505 (mt) cc_final: 0.7135 (pt) REVERT: D 141 MET cc_start: 0.7502 (ttt) cc_final: 0.7131 (ttt) REVERT: D 168 ASP cc_start: 0.5817 (m-30) cc_final: 0.5459 (t0) outliers start: 21 outliers final: 15 residues processed: 194 average time/residue: 0.2598 time to fit residues: 71.2246 Evaluate side-chains 189 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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 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 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 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 31 optimal weight: 1.9990 chunk 67 optimal weight: 0.0470 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.7484 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.140560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.097103 restraints weight = 13203.316| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 1.53 r_work: 0.2757 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2148 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= 0.145 Angle : 0.516 9.071 16336 Z= 0.269 Chirality : 0.040 0.146 1881 Planarity : 0.003 0.048 2020 Dihedral : 7.584 59.276 1808 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.96 % Allowed : 13.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.22), residues: 1435 helix: 1.17 (0.16), residues: 1044 sheet: None (None), residues: 0 loop : -0.96 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 366 HIS 0.005 0.001 HIS A 76 PHE 0.016 0.001 PHE B 200 TYR 0.010 0.001 TYR B 322 ARG 0.006 0.000 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 761) hydrogen bonds : angle 4.46861 ( 2253) covalent geometry : bond 0.00343 (12107) covalent geometry : angle 0.51623 (16336) *********************** 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 214 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 1.475 Fit side-chains REVERT: A 621 GLN cc_start: 0.7497 (tm-30) cc_final: 0.7190 (pt0) REVERT: B 348 THR cc_start: 0.9093 (OUTLIER) cc_final: 0.8829 (m) REVERT: B 380 VAL cc_start: 0.9011 (t) cc_final: 0.8693 (m) REVERT: B 621 GLN cc_start: 0.7579 (tm-30) cc_final: 0.7248 (pt0) REVERT: C 56 GLU cc_start: 0.7826 (pm20) cc_final: 0.7420 (pm20) REVERT: C 93 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7405 (tp) REVERT: C 135 LEU cc_start: 0.7650 (tp) cc_final: 0.7326 (tp) REVERT: C 168 ASP cc_start: 0.6191 (m-30) cc_final: 0.5732 (t0) REVERT: D 11 ASP cc_start: 0.5454 (p0) cc_final: 0.5250 (p0) REVERT: D 45 THR cc_start: 0.7933 (t) cc_final: 0.7700 (m) REVERT: D 56 GLU cc_start: 0.7866 (pm20) cc_final: 0.7459 (pm20) REVERT: D 124 LEU cc_start: 0.7481 (mt) cc_final: 0.7125 (pt) REVERT: D 168 ASP cc_start: 0.5875 (m-30) cc_final: 0.5507 (t0) outliers start: 25 outliers final: 18 residues processed: 199 average time/residue: 0.2591 time to fit residues: 73.2381 Evaluate side-chains 194 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 1.385 ------------------------------------------------------------------------------- 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 A residue 649 ASP 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 649 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 64 ASP 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 143 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 113 optimal weight: 0.0870 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 50 optimal weight: 0.1980 chunk 3 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 overall best weight: 0.5160 ------------------------------------------------------------------------------- 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 = 0.3548 r_free = 0.3548 target = 0.147451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.105975 restraints weight = 13119.299| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.47 r_work: 0.2802 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12107 Z= 0.127 Angle : 0.516 9.465 16336 Z= 0.268 Chirality : 0.039 0.134 1881 Planarity : 0.003 0.047 2020 Dihedral : 7.333 58.445 1808 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.11 % Allowed : 13.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.22), residues: 1435 helix: 1.40 (0.16), residues: 1032 sheet: None (None), residues: 0 loop : -0.98 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 507 HIS 0.005 0.001 HIS A 76 PHE 0.017 0.001 PHE A 484 TYR 0.009 0.001 TYR B 322 ARG 0.003 0.000 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 761) hydrogen bonds : angle 4.37548 ( 2253) covalent geometry : bond 0.00292 (12107) covalent geometry : angle 0.51604 (16336) *********************** 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: 27 poor density : 180 time to evaluate : 1.280 Fit side-chains REVERT: A 48 GLU cc_start: 0.8087 (tp30) cc_final: 0.7794 (tp30) REVERT: B 348 THR cc_start: 0.9097 (OUTLIER) cc_final: 0.8860 (m) REVERT: B 621 GLN cc_start: 0.7535 (tm-30) cc_final: 0.7208 (pt0) REVERT: C 56 GLU cc_start: 0.7863 (pm20) cc_final: 0.7431 (pm20) REVERT: C 93 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7363 (tp) REVERT: C 135 LEU cc_start: 0.7738 (tp) cc_final: 0.7396 (tp) REVERT: C 168 ASP cc_start: 0.5886 (m-30) cc_final: 0.5459 (t0) REVERT: D 56 GLU cc_start: 0.7902 (pm20) cc_final: 0.7488 (pm20) REVERT: D 93 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7384 (tp) REVERT: D 123 ASP cc_start: 0.6335 (t0) cc_final: 0.5871 (t70) REVERT: D 124 LEU cc_start: 0.7401 (mt) cc_final: 0.7058 (pt) REVERT: D 142 MET cc_start: 0.8817 (ttp) cc_final: 0.8519 (ttp) REVERT: D 168 ASP cc_start: 0.5865 (m-30) cc_final: 0.5510 (t0) outliers start: 27 outliers final: 19 residues processed: 193 average time/residue: 0.2698 time to fit residues: 73.9655 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 : 1.368 ------------------------------------------------------------------------------- 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 A residue 649 ASP 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 B residue 649 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 64 ASP 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 64 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 74 optimal weight: 0.0060 chunk 126 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 51 optimal weight: 0.0970 chunk 119 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 overall best weight: 0.3594 ------------------------------------------------------------------------------- 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 = 0.3499 r_free = 0.3499 target = 0.143779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.100693 restraints weight = 13268.935| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.55 r_work: 0.2815 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12107 Z= 0.116 Angle : 0.506 7.573 16336 Z= 0.263 Chirality : 0.039 0.134 1881 Planarity : 0.003 0.047 2020 Dihedral : 7.053 58.739 1808 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.04 % Allowed : 14.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.22), residues: 1435 helix: 1.53 (0.16), residues: 1031 sheet: None (None), residues: 0 loop : -0.92 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 366 HIS 0.005 0.001 HIS A 76 PHE 0.016 0.001 PHE A 200 TYR 0.009 0.001 TYR B 322 ARG 0.004 0.000 ARG D 65 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 761) hydrogen bonds : angle 4.34598 ( 2253) covalent geometry : bond 0.00256 (12107) covalent geometry : angle 0.50612 (16336) *********************** 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 223 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.7966 (tp30) cc_final: 0.7646 (tp30) REVERT: A 501 ASN cc_start: 0.7493 (t0) cc_final: 0.7135 (t0) REVERT: A 621 GLN cc_start: 0.7463 (tm-30) cc_final: 0.7157 (pt0) REVERT: B 48 GLU cc_start: 0.8046 (tp30) cc_final: 0.7672 (tp30) REVERT: B 348 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8862 (m) REVERT: B 501 ASN cc_start: 0.7513 (t0) cc_final: 0.7147 (t0) REVERT: B 621 GLN cc_start: 0.7504 (tm-30) cc_final: 0.7178 (pt0) REVERT: C 93 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7296 (tp) REVERT: C 135 LEU cc_start: 0.7579 (tp) cc_final: 0.7201 (tp) REVERT: C 149 ASP cc_start: 0.7105 (m-30) cc_final: 0.6295 (p0) REVERT: D 13 GLU cc_start: 0.5048 (pm20) cc_final: 0.4656 (pm20) REVERT: D 16 GLU cc_start: 0.7550 (mp0) cc_final: 0.7181 (mp0) REVERT: D 93 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7392 (tp) REVERT: D 123 ASP cc_start: 0.5933 (t0) cc_final: 0.5495 (t70) REVERT: D 124 LEU cc_start: 0.7363 (mt) cc_final: 0.7049 (pt) REVERT: D 142 MET cc_start: 0.8831 (ttp) cc_final: 0.8580 (ttp) REVERT: D 168 ASP cc_start: 0.5905 (m-30) cc_final: 0.5572 (t0) outliers start: 26 outliers final: 17 residues processed: 209 average time/residue: 0.2599 time to fit residues: 77.1139 Evaluate side-chains 204 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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 A residue 629 GLN Chi-restraints excluded: chain B residue 93 LEU 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 629 GLN 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 93 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 112 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 114 optimal weight: 0.2980 chunk 28 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 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 ** 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 = 0.3479 r_free = 0.3479 target = 0.142028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.098678 restraints weight = 13373.667| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.57 r_work: 0.2786 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2514 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= 0.133 Angle : 0.521 8.468 16336 Z= 0.270 Chirality : 0.040 0.134 1881 Planarity : 0.003 0.047 2020 Dihedral : 7.129 58.767 1808 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.04 % Allowed : 15.19 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.22), residues: 1435 helix: 1.55 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -0.94 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 507 HIS 0.005 0.001 HIS A 76 PHE 0.016 0.001 PHE A 200 TYR 0.010 0.001 TYR A 322 ARG 0.006 0.000 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 761) hydrogen bonds : angle 4.37756 ( 2253) covalent geometry : bond 0.00311 (12107) covalent geometry : angle 0.52077 (16336) *********************** 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 212 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8911 (m) REVERT: A 501 ASN cc_start: 0.7477 (t0) cc_final: 0.7118 (t0) REVERT: A 621 GLN cc_start: 0.7541 (tm-30) cc_final: 0.7254 (pt0) REVERT: B 48 GLU cc_start: 0.8118 (tp30) cc_final: 0.7729 (tp30) REVERT: B 348 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8881 (m) REVERT: B 501 ASN cc_start: 0.7519 (t0) cc_final: 0.7138 (t0) REVERT: B 621 GLN cc_start: 0.7452 (tm-30) cc_final: 0.7237 (pt0) REVERT: C 93 ILE cc_start: 0.7562 (OUTLIER) cc_final: 0.7348 (tp) REVERT: C 128 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7403 (tp30) REVERT: C 135 LEU cc_start: 0.7587 (tp) cc_final: 0.7161 (tp) REVERT: C 149 ASP cc_start: 0.7185 (m-30) cc_final: 0.6312 (p0) REVERT: D 93 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7420 (tp) REVERT: D 123 ASP cc_start: 0.6140 (t0) cc_final: 0.5685 (t70) REVERT: D 124 LEU cc_start: 0.7397 (mt) cc_final: 0.7075 (pt) REVERT: D 149 ASP cc_start: 0.7174 (m-30) cc_final: 0.6479 (p0) REVERT: D 168 ASP cc_start: 0.5872 (m-30) cc_final: 0.5521 (t0) outliers start: 26 outliers final: 15 residues processed: 199 average time/residue: 0.2619 time to fit residues: 74.0371 Evaluate side-chains 198 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 1.393 ------------------------------------------------------------------------------- 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 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 C residue 33 SER Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain D residue 93 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 24 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 87 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.146027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.104224 restraints weight = 13162.357| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.49 r_work: 0.2808 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2527 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 : 0.527 8.124 16336 Z= 0.273 Chirality : 0.040 0.142 1881 Planarity : 0.003 0.047 2020 Dihedral : 7.113 59.998 1808 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.27 % Allowed : 15.74 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.22), residues: 1435 helix: 1.50 (0.16), residues: 1044 sheet: None (None), residues: 0 loop : -0.84 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 507 HIS 0.006 0.001 HIS A 76 PHE 0.016 0.001 PHE A 200 TYR 0.009 0.001 TYR B 322 ARG 0.004 0.000 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 761) hydrogen bonds : angle 4.39687 ( 2253) covalent geometry : bond 0.00318 (12107) covalent geometry : angle 0.52689 (16336) *********************** 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 209 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8912 (m) REVERT: A 501 ASN cc_start: 0.7479 (t0) cc_final: 0.7118 (t0) REVERT: A 621 GLN cc_start: 0.7521 (tm-30) cc_final: 0.7288 (pt0) REVERT: B 48 GLU cc_start: 0.8087 (tp30) cc_final: 0.7883 (tp30) REVERT: B 348 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8881 (m) REVERT: C 135 LEU cc_start: 0.7566 (tp) cc_final: 0.7145 (tp) REVERT: C 149 ASP cc_start: 0.7251 (m-30) cc_final: 0.6413 (p0) REVERT: C 158 ARG cc_start: 0.6141 (mtm180) cc_final: 0.5928 (ttm170) REVERT: C 188 LYS cc_start: 0.8332 (ptmt) cc_final: 0.8096 (ptmt) REVERT: D 93 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7407 (mt) REVERT: D 123 ASP cc_start: 0.6020 (t0) cc_final: 0.5300 (t0) REVERT: D 124 LEU cc_start: 0.7350 (mt) cc_final: 0.7144 (pt) REVERT: D 149 ASP cc_start: 0.7209 (m-30) cc_final: 0.6527 (p0) REVERT: D 168 ASP cc_start: 0.5886 (m-30) cc_final: 0.5530 (t0) REVERT: D 188 LYS cc_start: 0.8293 (ptmt) cc_final: 0.7851 (ptmt) outliers start: 29 outliers final: 17 residues processed: 195 average time/residue: 0.2717 time to fit residues: 75.3330 Evaluate side-chains 192 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 1.245 ------------------------------------------------------------------------------- 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 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 14 LEU Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 45 THR 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 19 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 120 optimal weight: 0.4980 chunk 111 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.140134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.096582 restraints weight = 13205.235| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 1.56 r_work: 0.2764 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2482 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= 0.151 Angle : 0.540 7.823 16336 Z= 0.280 Chirality : 0.041 0.160 1881 Planarity : 0.003 0.047 2020 Dihedral : 7.196 59.580 1808 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.11 % Allowed : 16.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.22), residues: 1435 helix: 1.46 (0.16), residues: 1044 sheet: None (None), residues: 0 loop : -0.84 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 507 HIS 0.006 0.001 HIS A 76 PHE 0.017 0.001 PHE A 200 TYR 0.010 0.001 TYR B 322 ARG 0.003 0.000 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 761) hydrogen bonds : angle 4.44371 ( 2253) covalent geometry : bond 0.00359 (12107) covalent geometry : angle 0.53982 (16336) ********************** 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 201 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8909 (m) REVERT: A 380 VAL cc_start: 0.8971 (t) cc_final: 0.8682 (m) REVERT: A 621 GLN cc_start: 0.7512 (tm-30) cc_final: 0.7250 (pt0) REVERT: B 48 GLU cc_start: 0.8090 (tp30) cc_final: 0.7867 (tp30) REVERT: B 348 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8881 (m) REVERT: B 380 VAL cc_start: 0.8969 (t) cc_final: 0.8684 (m) REVERT: C 135 LEU cc_start: 0.7535 (tp) cc_final: 0.7118 (tp) REVERT: C 149 ASP cc_start: 0.7243 (m-30) cc_final: 0.6420 (p0) REVERT: C 158 ARG cc_start: 0.6155 (mtm180) cc_final: 0.5948 (ttm170) REVERT: D 93 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7359 (tp) REVERT: D 123 ASP cc_start: 0.6026 (t0) cc_final: 0.5454 (t0) REVERT: D 124 LEU cc_start: 0.7378 (mt) cc_final: 0.7069 (pt) REVERT: D 149 ASP cc_start: 0.7231 (m-30) cc_final: 0.6538 (p0) REVERT: D 168 ASP cc_start: 0.6086 (m-30) cc_final: 0.5619 (t0) REVERT: D 188 LYS cc_start: 0.8432 (ptmt) cc_final: 0.7955 (ptmt) outliers start: 27 outliers final: 16 residues processed: 189 average time/residue: 0.2579 time to fit residues: 68.9792 Evaluate side-chains 190 residues out of total 1277 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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 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 14 LEU Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 45 THR 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 127 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 D 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.141530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.101220 restraints weight = 13171.373| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.47 r_work: 0.2781 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12107 Z= 0.173 Angle : 0.560 8.184 16336 Z= 0.290 Chirality : 0.042 0.171 1881 Planarity : 0.003 0.048 2020 Dihedral : 7.427 58.926 1808 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.80 % Allowed : 16.21 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.22), residues: 1435 helix: 1.28 (0.16), residues: 1044 sheet: None (None), residues: 0 loop : -0.76 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 507 HIS 0.006 0.001 HIS B 76 PHE 0.017 0.001 PHE A 200 TYR 0.010 0.001 TYR B 381 ARG 0.002 0.000 ARG C 65 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 761) hydrogen bonds : angle 4.55402 ( 2253) covalent geometry : bond 0.00419 (12107) covalent geometry : angle 0.55954 (16336) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7175.56 seconds wall clock time: 126 minutes 56.71 seconds (7616.71 seconds total)