Starting phenix.real_space_refine on Mon Apr 8 00:21:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2u_32971/04_2024/7x2u_32971_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2u_32971/04_2024/7x2u_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2u_32971/04_2024/7x2u_32971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2u_32971/04_2024/7x2u_32971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2u_32971/04_2024/7x2u_32971_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2u_32971/04_2024/7x2u_32971_neut_updated.pdb" } 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 Residue "A GLU 48": "OE1" <-> "OE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A GLU 492": "OE1" <-> "OE2" Residue "A GLU 630": "OE1" <-> "OE2" Residue "A GLU 646": "OE1" <-> "OE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B GLU 433": "OE1" <-> "OE2" Residue "B GLU 477": "OE1" <-> "OE2" Residue "B GLU 492": "OE1" <-> "OE2" Residue "B GLU 630": "OE1" <-> "OE2" Residue "B GLU 646": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D ARG 111": "NH1" <-> "NH2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D GLU 186": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 6.89, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.94 Conformation dependent library (CDL) restraints added in 1.9 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... running ksdssp... Secondary structure from input PDB file: 74 helices and 0 sheets defined 68.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 54 through 74 removed outlier: 3.659A pdb=" N LEU A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 79 No H-bonds generated for 'chain 'A' and resid 76 through 79' Processing helix chain 'A' and resid 84 through 101 Processing helix chain 'A' and resid 112 through 115 No H-bonds generated for 'chain 'A' and resid 112 through 115' Processing helix chain 'A' and resid 120 through 129 Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 149 through 168 Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 193 through 202 removed outlier: 4.967A pdb=" N ALA A 198 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 200 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU A 201 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 237 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 244 through 278 removed outlier: 3.593A pdb=" N ARG A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 303 removed outlier: 3.674A pdb=" N GLU A 286 " --> pdb=" O ARG A 283 " (cutoff:3.500A) Proline residue: A 287 - end of helix removed outlier: 3.598A pdb=" N PHE A 291 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE A 293 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 294 " --> pdb=" O PHE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 317 Processing helix chain 'A' and resid 329 through 359 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 368 through 396 removed outlier: 3.623A pdb=" N ARG A 382 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 417 through 424 Processing helix chain 'A' and resid 434 through 463 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 494 removed outlier: 3.661A pdb=" N ASP A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 513 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 536 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 630 No H-bonds generated for 'chain 'A' and resid 628 through 630' Processing helix chain 'A' and resid 646 through 660 Processing helix chain 'B' and resid 54 through 74 removed outlier: 3.658A pdb=" N LEU B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 79 No H-bonds generated for 'chain 'B' and resid 76 through 79' Processing helix chain 'B' and resid 84 through 101 Processing helix chain 'B' and resid 112 through 115 No H-bonds generated for 'chain 'B' and resid 112 through 115' Processing helix chain 'B' and resid 120 through 129 Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 149 through 168 Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 193 through 202 removed outlier: 4.967A pdb=" N ALA B 198 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 200 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 237 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 244 through 278 removed outlier: 3.593A pdb=" N ARG B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 303 removed outlier: 3.675A pdb=" N GLU B 286 " --> pdb=" O ARG B 283 " (cutoff:3.500A) Proline residue: B 287 - end of helix removed outlier: 3.598A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE B 293 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER B 294 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 317 Processing helix chain 'B' and resid 329 through 358 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 368 through 396 removed outlier: 3.622A pdb=" N ARG B 382 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 417 through 424 Processing helix chain 'B' and resid 434 through 463 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 494 removed outlier: 3.661A pdb=" N ASP B 493 " --> pdb=" O SER B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 513 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 522 through 536 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 628 through 630 No H-bonds generated for 'chain 'B' and resid 628 through 630' Processing helix chain 'B' and resid 646 through 660 Processing helix chain 'C' and resid 13 through 21 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 25 through 38 Processing helix chain 'C' and resid 48 through 52 Processing helix chain 'C' and resid 63 through 70 Processing helix chain 'C' and resid 80 through 90 removed outlier: 4.061A pdb=" N HIS C 89 " --> pdb=" O ARG C 85 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N PHE C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 98 No H-bonds generated for 'chain 'C' and resid 95 through 98' Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 132 through 142 Processing helix chain 'C' and resid 149 through 163 Processing helix chain 'C' and resid 173 through 182 removed outlier: 5.031A pdb=" N LYS C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 188 No H-bonds generated for 'chain 'C' and resid 185 through 188' Processing helix chain 'D' and resid 13 through 21 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 25 through 38 Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 63 through 70 Processing helix chain 'D' and resid 80 through 90 removed outlier: 4.062A pdb=" N HIS D 89 " --> pdb=" O ARG D 85 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N PHE D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 No H-bonds generated for 'chain 'D' and resid 95 through 98' Processing helix chain 'D' and resid 111 through 122 Processing helix chain 'D' and resid 132 through 142 Processing helix chain 'D' and resid 149 through 163 Processing helix chain 'D' and resid 173 through 182 removed outlier: 5.031A pdb=" N LYS D 182 " --> pdb=" O LYS D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 188 No H-bonds generated for 'chain 'D' and resid 185 through 188' 643 hydrogen bonds defined for protein. 1839 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: 3.04 Time building geometry restraints manager: 5.37 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: 98.73 - 105.91: 153 105.91 - 113.09: 6899 113.09 - 120.27: 4786 120.27 - 127.45: 4388 127.45 - 134.63: 110 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: 313 2.69 - 3.24: 12516 3.24 - 3.79: 20087 3.79 - 4.35: 27311 4.35 - 4.90: 44338 Nonbonded interactions: 104565 Sorted by model distance: nonbonded pdb=" OH TYR A 146 " pdb=" OG1 THR A 390 " model vdw 2.138 2.440 nonbonded pdb=" OH TYR B 146 " pdb=" OG1 THR B 390 " model vdw 2.138 2.440 nonbonded pdb=" NH1 ARG D 65 " pdb=" O LEU D 121 " model vdw 2.175 2.520 nonbonded pdb=" NH1 ARG C 65 " pdb=" O LEU C 121 " model vdw 2.175 2.520 nonbonded pdb=" OH TYR A 625 " pdb=" OE2 GLU A 651 " model vdw 2.210 2.440 ... (remaining 104560 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 4.040 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 34.230 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.720 ------------------------------------------------------------------------------- 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= 0.664 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 *********************** 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 fitting. rotamer outliers: 12 poor density : 174 time to evaluate : 1.556 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: 0.3148 time to fit residues: 79.0727 Evaluate side-chains 155 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 150 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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: 3.9990 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS A 139 ASN B 76 HIS B 139 ASN C 109 ASN C 195 HIS D 195 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12107 Z= 0.223 Angle : 0.531 7.421 16336 Z= 0.280 Chirality : 0.040 0.190 1881 Planarity : 0.004 0.048 2020 Dihedral : 9.192 59.130 1815 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.47 % Allowed : 9.95 % Favored : 89.58 % 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: 0.13 (0.22), residues: 1435 helix: 0.52 (0.16), residues: 1025 sheet: None (None), residues: 0 loop : -0.82 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 507 HIS 0.011 0.001 HIS B 76 PHE 0.016 0.002 PHE C 90 TYR 0.012 0.001 TYR A 298 ARG 0.002 0.000 ARG A 283 *********************** 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 185 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 179 time to evaluate : 1.371 Fit side-chains REVERT: C 56 GLU cc_start: 0.7752 (pm20) cc_final: 0.7314 (pm20) REVERT: D 56 GLU cc_start: 0.7941 (pm20) cc_final: 0.7509 (pm20) REVERT: D 135 LEU cc_start: 0.7974 (tp) cc_final: 0.7736 (tp) outliers start: 6 outliers final: 0 residues processed: 182 average time/residue: 0.2705 time to fit residues: 68.8672 Evaluate side-chains 169 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 141 optimal weight: 8.9990 chunk 116 optimal weight: 0.0370 chunk 129 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12107 Z= 0.218 Angle : 0.503 7.282 16336 Z= 0.265 Chirality : 0.040 0.129 1881 Planarity : 0.003 0.045 2020 Dihedral : 8.165 58.209 1808 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.64 % Allowed : 11.82 % Favored : 86.53 % 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: 0.44 (0.22), residues: 1435 helix: 0.75 (0.16), residues: 1030 sheet: None (None), residues: 0 loop : -0.70 (0.32), residues: 405 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 0.014 0.002 PHE B 200 TYR 0.011 0.001 TYR A 322 ARG 0.002 0.000 ARG A 637 *********************** 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 193 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 172 time to evaluate : 1.338 Fit side-chains REVERT: C 56 GLU cc_start: 0.7737 (pm20) cc_final: 0.7408 (pm20) REVERT: C 142 MET cc_start: 0.8807 (ptm) cc_final: 0.8563 (ptp) REVERT: C 168 ASP cc_start: 0.6055 (OUTLIER) cc_final: 0.5682 (t0) REVERT: D 56 GLU cc_start: 0.7729 (pm20) cc_final: 0.7208 (pm20) REVERT: D 135 LEU cc_start: 0.7980 (tp) cc_final: 0.7739 (tp) outliers start: 21 outliers final: 15 residues processed: 181 average time/residue: 0.2796 time to fit residues: 71.4956 Evaluate side-chains 179 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 93 ILE 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 129 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 131 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12107 Z= 0.269 Angle : 0.517 7.221 16336 Z= 0.271 Chirality : 0.041 0.174 1881 Planarity : 0.003 0.045 2020 Dihedral : 7.991 58.443 1808 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.51 % Allowed : 12.92 % Favored : 84.57 % 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: 0.51 (0.22), residues: 1435 helix: 0.79 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -0.63 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 366 HIS 0.008 0.001 HIS A 76 PHE 0.017 0.002 PHE B 200 TYR 0.011 0.001 TYR A 322 ARG 0.002 0.000 ARG A 637 *********************** 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 192 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 160 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 56 GLU cc_start: 0.7634 (pm20) cc_final: 0.7431 (pm20) REVERT: D 13 GLU cc_start: 0.4627 (pm20) cc_final: 0.4396 (pm20) REVERT: D 56 GLU cc_start: 0.7509 (pm20) cc_final: 0.7256 (pm20) REVERT: D 135 LEU cc_start: 0.7986 (tp) cc_final: 0.7731 (tp) outliers start: 32 outliers final: 23 residues processed: 177 average time/residue: 0.2834 time to fit residues: 70.0061 Evaluate side-chains 183 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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 217 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 327 ILE 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 217 SER Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 489 SER Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 136 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 103 optimal weight: 0.0770 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12107 Z= 0.207 Angle : 0.483 7.539 16336 Z= 0.253 Chirality : 0.039 0.149 1881 Planarity : 0.003 0.043 2020 Dihedral : 7.511 56.228 1808 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.90 % Allowed : 13.31 % Favored : 83.79 % 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: 0.70 (0.22), residues: 1435 helix: 0.93 (0.16), residues: 1030 sheet: None (None), residues: 0 loop : -0.57 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 507 HIS 0.009 0.001 HIS A 76 PHE 0.013 0.001 PHE B 200 TYR 0.010 0.001 TYR B 322 ARG 0.002 0.000 ARG A 637 *********************** 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 211 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 174 time to evaluate : 1.380 Fit side-chains REVERT: B 348 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8669 (m) REVERT: C 56 GLU cc_start: 0.7360 (pm20) cc_final: 0.7151 (pm20) REVERT: C 123 ASP cc_start: 0.6282 (t0) cc_final: 0.5881 (t0) REVERT: C 168 ASP cc_start: 0.5995 (OUTLIER) cc_final: 0.5640 (t0) REVERT: D 56 GLU cc_start: 0.7481 (pm20) cc_final: 0.7210 (pm20) REVERT: D 123 ASP cc_start: 0.6327 (t0) cc_final: 0.5859 (t0) REVERT: D 128 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7061 (tp30) REVERT: D 135 LEU cc_start: 0.7974 (tp) cc_final: 0.7731 (tp) outliers start: 37 outliers final: 26 residues processed: 195 average time/residue: 0.2761 time to fit residues: 76.0463 Evaluate side-chains 198 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 170 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 327 ILE 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 54 ASP Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 327 ILE 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 639 GLU Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 168 ASP Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 136 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 115 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 134 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1806 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= 0.248 Angle : 0.517 9.598 16336 Z= 0.268 Chirality : 0.040 0.149 1881 Planarity : 0.003 0.043 2020 Dihedral : 7.519 57.745 1808 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.82 % Allowed : 14.64 % Favored : 82.54 % 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: 0.70 (0.22), residues: 1435 helix: 0.93 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -0.57 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 507 HIS 0.007 0.001 HIS A 76 PHE 0.016 0.001 PHE B 200 TYR 0.010 0.001 TYR A 322 ARG 0.002 0.000 ARG B 283 *********************** 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 194 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 158 time to evaluate : 1.472 Fit side-chains REVERT: B 339 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8380 (mtt) REVERT: B 348 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8694 (m) REVERT: C 56 GLU cc_start: 0.7379 (pm20) cc_final: 0.7156 (pm20) REVERT: C 123 ASP cc_start: 0.6374 (t0) cc_final: 0.5988 (t0) REVERT: C 168 ASP cc_start: 0.5973 (m-30) cc_final: 0.5686 (t0) REVERT: D 56 GLU cc_start: 0.7500 (pm20) cc_final: 0.7208 (pm20) REVERT: D 123 ASP cc_start: 0.6321 (t0) cc_final: 0.5833 (t0) REVERT: D 128 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7046 (tp30) REVERT: D 135 LEU cc_start: 0.7902 (tp) cc_final: 0.7698 (tp) outliers start: 36 outliers final: 27 residues processed: 178 average time/residue: 0.2739 time to fit residues: 68.1112 Evaluate side-chains 191 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 327 ILE 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 54 ASP Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 339 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 64 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 160 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 15 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 101 optimal weight: 0.3980 chunk 78 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS B 76 HIS C 195 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1953 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= 0.208 Angle : 0.495 8.170 16336 Z= 0.257 Chirality : 0.039 0.140 1881 Planarity : 0.003 0.042 2020 Dihedral : 7.234 58.086 1808 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.82 % Allowed : 15.19 % 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: 0.82 (0.22), residues: 1435 helix: 1.08 (0.16), residues: 1018 sheet: None (None), residues: 0 loop : -0.66 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 507 HIS 0.008 0.001 HIS A 76 PHE 0.013 0.001 PHE B 200 TYR 0.010 0.001 TYR B 322 ARG 0.002 0.000 ARG A 637 *********************** 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 210 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 174 time to evaluate : 1.649 Fit side-chains REVERT: A 348 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8642 (m) REVERT: B 339 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8349 (mtt) REVERT: B 348 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8691 (m) REVERT: C 56 GLU cc_start: 0.7426 (pm20) cc_final: 0.7221 (pm20) REVERT: C 123 ASP cc_start: 0.6227 (t0) cc_final: 0.5800 (t0) REVERT: C 168 ASP cc_start: 0.5919 (m-30) cc_final: 0.5618 (t0) REVERT: D 56 GLU cc_start: 0.7415 (pm20) cc_final: 0.7142 (pm20) REVERT: D 123 ASP cc_start: 0.6325 (t0) cc_final: 0.5876 (t0) REVERT: D 128 GLU cc_start: 0.7567 (tm-30) cc_final: 0.7109 (tp30) REVERT: D 135 LEU cc_start: 0.7903 (tp) cc_final: 0.7631 (tp) outliers start: 36 outliers final: 28 residues processed: 190 average time/residue: 0.2669 time to fit residues: 71.5560 Evaluate side-chains 197 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 166 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 327 ILE 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 A residue 649 ASP Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 339 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 64 ASP Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 160 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.4980 chunk 82 optimal weight: 0.3980 chunk 41 optimal weight: 0.0070 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.5802 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2091 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= 0.190 Angle : 0.493 7.890 16336 Z= 0.255 Chirality : 0.039 0.132 1881 Planarity : 0.003 0.042 2020 Dihedral : 6.987 58.616 1808 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.82 % Allowed : 15.35 % Favored : 81.83 % 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: 0.90 (0.22), residues: 1435 helix: 1.14 (0.16), residues: 1024 sheet: None (None), residues: 0 loop : -0.65 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 507 HIS 0.008 0.001 HIS B 76 PHE 0.013 0.001 PHE A 484 TYR 0.010 0.001 TYR B 322 ARG 0.002 0.000 ARG A 637 *********************** 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 210 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 174 time to evaluate : 1.353 Fit side-chains revert: symmetry clash REVERT: A 348 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8643 (m) REVERT: B 48 GLU cc_start: 0.7626 (tp30) cc_final: 0.7366 (tp30) REVERT: B 339 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8346 (mtt) REVERT: B 348 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8693 (m) REVERT: C 56 GLU cc_start: 0.7390 (pm20) cc_final: 0.7185 (pm20) REVERT: C 168 ASP cc_start: 0.5968 (m-30) cc_final: 0.5632 (t0) REVERT: D 123 ASP cc_start: 0.6328 (t0) cc_final: 0.5876 (t0) REVERT: D 135 LEU cc_start: 0.7943 (tp) cc_final: 0.7673 (tp) outliers start: 36 outliers final: 27 residues processed: 192 average time/residue: 0.2581 time to fit residues: 70.2714 Evaluate side-chains 198 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 168 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 327 ILE 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 A residue 649 ASP Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 339 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 64 ASP Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 93 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.0370 chunk 121 optimal weight: 0.2980 chunk 129 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS A 618 HIS B 76 HIS B 618 HIS C 195 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2221 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= 0.179 Angle : 0.487 8.040 16336 Z= 0.254 Chirality : 0.038 0.131 1881 Planarity : 0.003 0.042 2020 Dihedral : 6.837 58.948 1808 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.58 % Allowed : 16.13 % Favored : 81.28 % 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: 1.09 (0.22), residues: 1435 helix: 1.31 (0.16), residues: 1005 sheet: None (None), residues: 0 loop : -0.57 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 507 HIS 0.008 0.001 HIS A 76 PHE 0.014 0.001 PHE A 484 TYR 0.009 0.001 TYR B 322 ARG 0.002 0.000 ARG B 336 *********************** 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 fitting. rotamer outliers: 33 poor density : 176 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: A 348 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8634 (m) REVERT: B 48 GLU cc_start: 0.7638 (tp30) cc_final: 0.7373 (tp30) REVERT: B 339 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8350 (mtt) REVERT: B 348 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8694 (m) REVERT: C 56 GLU cc_start: 0.7386 (pm20) cc_final: 0.7162 (pm20) REVERT: C 168 ASP cc_start: 0.5922 (m-30) cc_final: 0.5573 (t0) REVERT: D 123 ASP cc_start: 0.6270 (t0) cc_final: 0.5806 (t0) REVERT: D 135 LEU cc_start: 0.7936 (tp) cc_final: 0.7653 (tp) outliers start: 33 outliers final: 24 residues processed: 190 average time/residue: 0.2652 time to fit residues: 71.1471 Evaluate side-chains 199 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 172 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 368 THR 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 217 SER Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 368 THR 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 64 ASP Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 64 ASP 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 136 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 chunk 132 optimal weight: 0.0020 chunk 114 optimal weight: 0.0770 chunk 11 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 overall best weight: 0.4746 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12107 Z= 0.175 Angle : 0.483 8.951 16336 Z= 0.251 Chirality : 0.038 0.153 1881 Planarity : 0.003 0.042 2020 Dihedral : 6.715 59.659 1808 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.82 % Allowed : 15.82 % Favored : 81.36 % 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: 1.18 (0.22), residues: 1435 helix: 1.37 (0.16), residues: 1005 sheet: None (None), residues: 0 loop : -0.54 (0.31), residues: 430 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 D 90 TYR 0.009 0.001 TYR B 322 ARG 0.001 0.000 ARG B 336 ********************** 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 212 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 176 time to evaluate : 1.350 Fit side-chains revert: symmetry clash REVERT: A 348 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8630 (m) REVERT: B 48 GLU cc_start: 0.7628 (tp30) cc_final: 0.7364 (tp30) REVERT: B 339 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8343 (mtt) REVERT: B 348 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8677 (m) REVERT: C 56 GLU cc_start: 0.7393 (pm20) cc_final: 0.7167 (pm20) REVERT: C 168 ASP cc_start: 0.5918 (m-30) cc_final: 0.5573 (t0) REVERT: D 123 ASP cc_start: 0.6182 (t0) cc_final: 0.5852 (t0) REVERT: D 135 LEU cc_start: 0.7963 (tp) cc_final: 0.7661 (tp) outliers start: 36 outliers final: 25 residues processed: 192 average time/residue: 0.2862 time to fit residues: 77.6464 Evaluate side-chains 197 residues out of total 1277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 169 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 327 ILE 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 621 GLN Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain B residue 339 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 64 ASP Chi-restraints excluded: chain D residue 59 ILE 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 121 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 0.0670 chunk 47 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.139860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.098145 restraints weight = 13220.895| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.55 r_work: 0.2784 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2371 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= 0.181 Angle : 0.493 8.561 16336 Z= 0.255 Chirality : 0.039 0.170 1881 Planarity : 0.003 0.042 2020 Dihedral : 6.723 59.676 1808 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.27 % Allowed : 16.29 % Favored : 81.44 % 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: 1.23 (0.22), residues: 1435 helix: 1.41 (0.16), residues: 1007 sheet: None (None), residues: 0 loop : -0.53 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 507 HIS 0.006 0.001 HIS A 76 PHE 0.017 0.001 PHE D 90 TYR 0.009 0.001 TYR B 322 ARG 0.001 0.000 ARG A 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2756.35 seconds wall clock time: 51 minutes 8.65 seconds (3068.65 seconds total)