Starting phenix.real_space_refine on Thu Mar 14 22:54:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xr4_33407/03_2024/7xr4_33407.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xr4_33407/03_2024/7xr4_33407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xr4_33407/03_2024/7xr4_33407.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xr4_33407/03_2024/7xr4_33407.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xr4_33407/03_2024/7xr4_33407.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xr4_33407/03_2024/7xr4_33407.pdb" } resolution = 3.4 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 6717 2.51 5 N 1539 2.21 5 O 1695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 65": "NH1" <-> "NH2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A ARG 311": "NH1" <-> "NH2" Residue "A ARG 373": "NH1" <-> "NH2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A ARG 476": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B ARG 311": "NH1" <-> "NH2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B ARG 387": "NH1" <-> "NH2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C GLU 275": "OE1" <-> "OE2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C ARG 311": "NH1" <-> "NH2" Residue "C ARG 373": "NH1" <-> "NH2" Residue "C GLU 376": "OE1" <-> "OE2" Residue "C ARG 387": "NH1" <-> "NH2" Residue "C GLU 405": "OE1" <-> "OE2" Residue "C ARG 476": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10026 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3185 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 14, 'TRANS': 410} Chain breaks: 2 Chain: "B" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3185 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 14, 'TRANS': 410} Chain breaks: 2 Chain: "C" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3185 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 14, 'TRANS': 410} Chain breaks: 2 Chain: "A" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 157 Unusual residues: {'PC1': 8, 'Y01': 1} Classifications: {'peptide': 1, 'undetermined': 9} Modifications used: {'COO': 1} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 392 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PC1:plan-2': 8, 'PC1:plan-1': 8} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 157 Unusual residues: {'PC1': 8, 'Y01': 1} Classifications: {'peptide': 1, 'undetermined': 9} Modifications used: {'COO': 1} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 392 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PC1:plan-2': 8, 'PC1:plan-1': 8} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 157 Unusual residues: {'PC1': 8, 'Y01': 1} Classifications: {'peptide': 1, 'undetermined': 9} Modifications used: {'COO': 1} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 392 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PC1:plan-2': 8, 'PC1:plan-1': 8} Unresolved non-hydrogen planarities: 48 Time building chain proxies: 6.01, per 1000 atoms: 0.60 Number of scatterers: 10026 At special positions: 0 Unit cell: (111.28, 114.4, 85.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 75 16.00 O 1695 8.00 N 1539 7.00 C 6717 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: 4.14 Conformation dependent library (CDL) restraints added in 1.8 seconds 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 3 sheets defined 87.2% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 37 through 44 removed outlier: 4.328A pdb=" N ASN A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 65 Processing helix chain 'A' and resid 71 through 92 Proline residue: A 81 - end of helix removed outlier: 3.757A pdb=" N LEU A 92 " --> pdb=" O MET A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 107 Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 114 through 143 Processing helix chain 'A' and resid 163 through 176 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 241 through 260 removed outlier: 3.825A pdb=" N GLY A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 303 removed outlier: 3.604A pdb=" N TYR A 287 " --> pdb=" O MET A 283 " (cutoff:3.500A) Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 305 through 330 Processing helix chain 'A' and resid 330 through 341 Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.536A pdb=" N ALA A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 367 through 379 Processing helix chain 'A' and resid 382 through 394 Proline residue: A 391 - end of helix Processing helix chain 'A' and resid 398 through 416 removed outlier: 3.577A pdb=" N ASN A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 439 Processing helix chain 'A' and resid 445 through 458 removed outlier: 4.117A pdb=" N LEU A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEU A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 470 removed outlier: 4.159A pdb=" N LEU A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 497 removed outlier: 3.912A pdb=" N LEU A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 507 Processing helix chain 'B' and resid 38 through 44 removed outlier: 4.329A pdb=" N ASN B 44 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 65 Processing helix chain 'B' and resid 71 through 92 Proline residue: B 81 - end of helix removed outlier: 3.758A pdb=" N LEU B 92 " --> pdb=" O MET B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 107 Processing helix chain 'B' and resid 109 through 114 Processing helix chain 'B' and resid 114 through 143 Processing helix chain 'B' and resid 163 through 176 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 241 through 260 removed outlier: 3.825A pdb=" N GLY B 260 " --> pdb=" O MET B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 303 removed outlier: 3.604A pdb=" N TYR B 287 " --> pdb=" O MET B 283 " (cutoff:3.500A) Proline residue: B 289 - end of helix Processing helix chain 'B' and resid 305 through 330 Processing helix chain 'B' and resid 330 through 341 Processing helix chain 'B' and resid 343 through 351 removed outlier: 3.536A pdb=" N ALA B 349 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 367 through 379 Processing helix chain 'B' and resid 382 through 394 Proline residue: B 391 - end of helix Processing helix chain 'B' and resid 398 through 416 removed outlier: 3.577A pdb=" N ASN B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 439 Processing helix chain 'B' and resid 445 through 458 removed outlier: 4.117A pdb=" N LEU B 451 " --> pdb=" O LEU B 447 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEU B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 463 through 470 removed outlier: 4.158A pdb=" N LEU B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 497 removed outlier: 3.911A pdb=" N LEU B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET B 477 " --> pdb=" O LEU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 507 Processing helix chain 'C' and resid 38 through 44 removed outlier: 4.329A pdb=" N ASN C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 65 Processing helix chain 'C' and resid 71 through 92 Proline residue: C 81 - end of helix removed outlier: 3.758A pdb=" N LEU C 92 " --> pdb=" O MET C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 107 Processing helix chain 'C' and resid 109 through 114 Processing helix chain 'C' and resid 114 through 143 Processing helix chain 'C' and resid 163 through 176 Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 241 through 260 removed outlier: 3.825A pdb=" N GLY C 260 " --> pdb=" O MET C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 303 removed outlier: 3.603A pdb=" N TYR C 287 " --> pdb=" O MET C 283 " (cutoff:3.500A) Proline residue: C 289 - end of helix Processing helix chain 'C' and resid 305 through 330 Processing helix chain 'C' and resid 330 through 341 Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.537A pdb=" N ALA C 349 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 367 through 379 Processing helix chain 'C' and resid 382 through 394 Proline residue: C 391 - end of helix Processing helix chain 'C' and resid 398 through 416 removed outlier: 3.577A pdb=" N ASN C 416 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 439 Processing helix chain 'C' and resid 445 through 458 removed outlier: 4.118A pdb=" N LEU C 451 " --> pdb=" O LEU C 447 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU C 452 " --> pdb=" O VAL C 448 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE C 453 " --> pdb=" O THR C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 470 removed outlier: 4.159A pdb=" N LEU C 467 " --> pdb=" O ASP C 463 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 497 removed outlier: 3.912A pdb=" N LEU C 474 " --> pdb=" O VAL C 470 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET C 477 " --> pdb=" O LEU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 507 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 193 removed outlier: 3.854A pdb=" N LYS A 231 " --> pdb=" O LYS A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 186 through 193 removed outlier: 3.854A pdb=" N LYS B 231 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 186 through 193 removed outlier: 3.854A pdb=" N LYS C 231 " --> pdb=" O LYS C 193 " (cutoff:3.500A) 793 hydrogen bonds defined for protein. 2379 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 4.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1807 1.33 - 1.45: 2021 1.45 - 1.57: 6195 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 10155 Sorted by residual: bond pdb=" CAX Y01 A 602 " pdb=" OAH Y01 A 602 " ideal model delta sigma weight residual 1.248 1.343 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" CAX Y01 C 602 " pdb=" OAH Y01 C 602 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" CAX Y01 B 602 " pdb=" OAH Y01 B 602 " ideal model delta sigma weight residual 1.248 1.341 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" CAX Y01 C 602 " pdb=" OAF Y01 C 602 " ideal model delta sigma weight residual 1.247 1.207 0.040 2.00e-02 2.50e+03 3.92e+00 bond pdb=" CAX Y01 A 602 " pdb=" OAF Y01 A 602 " ideal model delta sigma weight residual 1.247 1.208 0.039 2.00e-02 2.50e+03 3.89e+00 ... (remaining 10150 not shown) Histogram of bond angle deviations from ideal: 96.90 - 104.31: 168 104.31 - 111.73: 5454 111.73 - 119.14: 3111 119.14 - 126.55: 4827 126.55 - 133.96: 93 Bond angle restraints: 13653 Sorted by residual: angle pdb=" CAM Y01 C 602 " pdb=" CAY Y01 C 602 " pdb=" OAW Y01 C 602 " ideal model delta sigma weight residual 111.19 120.24 -9.05 3.00e+00 1.11e-01 9.09e+00 angle pdb=" CAM Y01 B 602 " pdb=" CAY Y01 B 602 " pdb=" OAW Y01 B 602 " ideal model delta sigma weight residual 111.19 120.21 -9.02 3.00e+00 1.11e-01 9.04e+00 angle pdb=" CAM Y01 A 602 " pdb=" CAY Y01 A 602 " pdb=" OAW Y01 A 602 " ideal model delta sigma weight residual 111.19 120.18 -8.99 3.00e+00 1.11e-01 8.98e+00 angle pdb=" CBB Y01 C 602 " pdb=" CBE Y01 C 602 " pdb=" CBI Y01 C 602 " ideal model delta sigma weight residual 119.27 111.67 7.60 3.00e+00 1.11e-01 6.42e+00 angle pdb=" CBB Y01 A 602 " pdb=" CBE Y01 A 602 " pdb=" CBI Y01 A 602 " ideal model delta sigma weight residual 119.27 111.67 7.60 3.00e+00 1.11e-01 6.42e+00 ... (remaining 13648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.07: 5922 25.07 - 50.14: 276 50.14 - 75.21: 57 75.21 - 100.28: 15 100.28 - 125.35: 3 Dihedral angle restraints: 6273 sinusoidal: 2670 harmonic: 3603 Sorted by residual: dihedral pdb=" CBC Y01 A 602 " pdb=" CAR Y01 A 602 " pdb=" CAT Y01 A 602 " pdb=" CBH Y01 A 602 " ideal model delta sinusoidal sigma weight residual -57.13 68.22 -125.35 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" CBC Y01 C 602 " pdb=" CAR Y01 C 602 " pdb=" CAT Y01 C 602 " pdb=" CBH Y01 C 602 " ideal model delta sinusoidal sigma weight residual -57.13 68.19 -125.32 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" CBC Y01 B 602 " pdb=" CAR Y01 B 602 " pdb=" CAT Y01 B 602 " pdb=" CBH Y01 B 602 " ideal model delta sinusoidal sigma weight residual -57.13 68.19 -125.32 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 6270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1599 0.093 - 0.187: 90 0.187 - 0.280: 6 0.280 - 0.373: 3 0.373 - 0.466: 3 Chirality restraints: 1701 Sorted by residual: chirality pdb=" CBG Y01 C 602 " pdb=" CAQ Y01 C 602 " pdb=" CBD Y01 C 602 " pdb=" CBI Y01 C 602 " both_signs ideal model delta sigma weight residual False -2.33 -2.80 0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" CBG Y01 B 602 " pdb=" CAQ Y01 B 602 " pdb=" CBD Y01 B 602 " pdb=" CBI Y01 B 602 " both_signs ideal model delta sigma weight residual False -2.33 -2.80 0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" CBG Y01 A 602 " pdb=" CAQ Y01 A 602 " pdb=" CBD Y01 A 602 " pdb=" CBI Y01 A 602 " both_signs ideal model delta sigma weight residual False -2.33 -2.80 0.46 2.00e-01 2.50e+01 5.37e+00 ... (remaining 1698 not shown) Planarity restraints: 1611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 372 " -0.018 2.00e-02 2.50e+03 1.80e-02 5.70e+00 pdb=" CG PHE C 372 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE C 372 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 372 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 372 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 372 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 372 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 372 " -0.018 2.00e-02 2.50e+03 1.80e-02 5.69e+00 pdb=" CG PHE A 372 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 372 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 372 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 372 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 372 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 372 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 372 " -0.018 2.00e-02 2.50e+03 1.80e-02 5.69e+00 pdb=" CG PHE B 372 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 372 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 372 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 372 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 372 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 372 " -0.001 2.00e-02 2.50e+03 ... (remaining 1608 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2868 2.82 - 3.34: 10651 3.34 - 3.86: 16733 3.86 - 4.38: 19300 4.38 - 4.90: 33588 Nonbonded interactions: 83140 Sorted by model distance: nonbonded pdb=" O THR A 503 " pdb=" NE2 GLN A 507 " model vdw 2.304 2.520 nonbonded pdb=" O THR C 503 " pdb=" NE2 GLN C 507 " model vdw 2.305 2.520 nonbonded pdb=" O THR B 503 " pdb=" NE2 GLN B 507 " model vdw 2.305 2.520 nonbonded pdb=" O LEU C 430 " pdb=" OG1 THR C 433 " model vdw 2.321 2.440 nonbonded pdb=" O LEU B 430 " pdb=" OG1 THR B 433 " model vdw 2.321 2.440 ... (remaining 83135 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' selection = chain 'B' selection = chain 'C' } 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: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.930 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 29.770 Find NCS groups from input model: 0.570 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 10155 Z= 0.429 Angle : 0.944 9.047 13653 Z= 0.420 Chirality : 0.052 0.466 1701 Planarity : 0.004 0.042 1611 Dihedral : 15.583 125.349 3957 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.29 % Allowed : 0.86 % Favored : 98.86 % 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: 1.68 (0.24), residues: 1257 helix: 1.68 (0.16), residues: 1029 sheet: -0.79 (0.64), residues: 60 loop : -1.58 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 286 HIS 0.003 0.002 HIS B 495 PHE 0.042 0.002 PHE A 372 TYR 0.007 0.002 TYR C 287 ARG 0.002 0.000 ARG B 384 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 176 time to evaluate : 1.153 Fit side-chains REVERT: A 387 ARG cc_start: 0.8277 (mmm-85) cc_final: 0.8073 (mmm160) REVERT: B 287 TYR cc_start: 0.9199 (t80) cc_final: 0.8902 (t80) REVERT: C 285 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8202 (mmt) REVERT: C 368 LEU cc_start: 0.8402 (tp) cc_final: 0.8156 (tp) outliers start: 3 outliers final: 1 residues processed: 176 average time/residue: 0.1865 time to fit residues: 48.3489 Evaluate side-chains 153 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 151 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain C residue 285 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 64 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 114 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN B 397 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10155 Z= 0.185 Angle : 0.536 5.673 13653 Z= 0.270 Chirality : 0.039 0.119 1701 Planarity : 0.004 0.040 1611 Dihedral : 9.803 58.511 1809 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.10 % Allowed : 9.05 % Favored : 90.86 % 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: 2.54 (0.25), residues: 1257 helix: 2.20 (0.16), residues: 1047 sheet: -0.45 (0.66), residues: 60 loop : -1.11 (0.60), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 286 HIS 0.002 0.001 HIS B 143 PHE 0.025 0.002 PHE B 372 TYR 0.018 0.002 TYR A 287 ARG 0.001 0.000 ARG B 119 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.017 Fit side-chains REVERT: A 377 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7934 (mt-10) REVERT: B 334 LEU cc_start: 0.8146 (tp) cc_final: 0.7867 (tp) REVERT: C 368 LEU cc_start: 0.8411 (tp) cc_final: 0.8180 (tp) outliers start: 1 outliers final: 1 residues processed: 166 average time/residue: 0.1761 time to fit residues: 44.2310 Evaluate side-chains 153 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 123 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 378 ASN C 397 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10155 Z= 0.216 Angle : 0.511 5.685 13653 Z= 0.263 Chirality : 0.039 0.122 1701 Planarity : 0.004 0.036 1611 Dihedral : 8.826 59.814 1803 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.67 % Allowed : 11.05 % Favored : 88.29 % 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: 2.72 (0.25), residues: 1257 helix: 2.29 (0.16), residues: 1047 sheet: -0.24 (0.67), residues: 60 loop : -0.89 (0.61), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 286 HIS 0.002 0.001 HIS C 143 PHE 0.014 0.001 PHE B 249 TYR 0.022 0.002 TYR B 287 ARG 0.002 0.000 ARG B 478 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 161 time to evaluate : 1.083 Fit side-chains REVERT: B 287 TYR cc_start: 0.9238 (t80) cc_final: 0.8895 (t80) REVERT: B 322 ILE cc_start: 0.8666 (mm) cc_final: 0.8429 (mm) REVERT: B 334 LEU cc_start: 0.8188 (tp) cc_final: 0.7885 (tp) REVERT: B 368 LEU cc_start: 0.8433 (tp) cc_final: 0.8192 (tp) REVERT: C 334 LEU cc_start: 0.8139 (tp) cc_final: 0.7880 (tp) outliers start: 7 outliers final: 5 residues processed: 164 average time/residue: 0.1674 time to fit residues: 41.9822 Evaluate side-chains 161 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 156 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 434 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10155 Z= 0.188 Angle : 0.498 5.612 13653 Z= 0.257 Chirality : 0.039 0.123 1701 Planarity : 0.004 0.042 1611 Dihedral : 8.124 58.576 1803 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.24 % Allowed : 11.71 % Favored : 87.05 % 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: 2.90 (0.25), residues: 1257 helix: 2.38 (0.16), residues: 1050 sheet: 0.04 (0.69), residues: 60 loop : -0.76 (0.63), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 286 HIS 0.002 0.001 HIS B 143 PHE 0.016 0.001 PHE C 411 TYR 0.013 0.002 TYR B 287 ARG 0.001 0.000 ARG A 478 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 1.081 Fit side-chains REVERT: B 285 MET cc_start: 0.8167 (mmt) cc_final: 0.7946 (mmt) REVERT: B 322 ILE cc_start: 0.8710 (mm) cc_final: 0.8457 (mm) REVERT: C 334 LEU cc_start: 0.8122 (tp) cc_final: 0.7852 (tp) outliers start: 13 outliers final: 10 residues processed: 168 average time/residue: 0.1727 time to fit residues: 44.2003 Evaluate side-chains 161 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 434 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 109 optimal weight: 0.0970 chunk 30 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10155 Z= 0.185 Angle : 0.493 5.876 13653 Z= 0.254 Chirality : 0.039 0.130 1701 Planarity : 0.004 0.043 1611 Dihedral : 7.839 57.736 1803 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.71 % Allowed : 13.05 % Favored : 85.24 % 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: 2.99 (0.25), residues: 1257 helix: 2.46 (0.16), residues: 1044 sheet: 0.22 (0.70), residues: 60 loop : -0.77 (0.61), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 286 HIS 0.002 0.001 HIS C 143 PHE 0.017 0.001 PHE C 388 TYR 0.028 0.002 TYR B 287 ARG 0.001 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 1.073 Fit side-chains REVERT: B 231 LYS cc_start: 0.6751 (ttpt) cc_final: 0.6085 (ttpt) REVERT: B 285 MET cc_start: 0.8172 (mmt) cc_final: 0.7949 (mmt) REVERT: B 322 ILE cc_start: 0.8720 (mm) cc_final: 0.8462 (mm) REVERT: C 334 LEU cc_start: 0.8094 (tp) cc_final: 0.7834 (tp) outliers start: 18 outliers final: 13 residues processed: 167 average time/residue: 0.1780 time to fit residues: 44.7203 Evaluate side-chains 167 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 154 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 507 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 121 optimal weight: 0.0970 chunk 101 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10155 Z= 0.191 Angle : 0.503 6.153 13653 Z= 0.257 Chirality : 0.039 0.155 1701 Planarity : 0.004 0.044 1611 Dihedral : 7.745 58.857 1803 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.24 % Allowed : 15.52 % Favored : 83.24 % 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: 3.02 (0.25), residues: 1257 helix: 2.47 (0.16), residues: 1044 sheet: 0.28 (0.71), residues: 60 loop : -0.77 (0.61), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 286 HIS 0.002 0.001 HIS C 143 PHE 0.015 0.001 PHE C 388 TYR 0.031 0.002 TYR B 287 ARG 0.001 0.000 ARG A 478 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 1.035 Fit side-chains REVERT: B 231 LYS cc_start: 0.6855 (ttpt) cc_final: 0.6171 (ttpt) REVERT: B 322 ILE cc_start: 0.8758 (mm) cc_final: 0.8484 (mm) REVERT: C 334 LEU cc_start: 0.8105 (tp) cc_final: 0.7832 (tp) outliers start: 13 outliers final: 13 residues processed: 159 average time/residue: 0.1733 time to fit residues: 41.5471 Evaluate side-chains 164 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 507 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10155 Z= 0.196 Angle : 0.505 6.950 13653 Z= 0.258 Chirality : 0.039 0.148 1701 Planarity : 0.004 0.045 1611 Dihedral : 7.712 57.842 1803 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.43 % Allowed : 16.00 % Favored : 82.57 % 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: 3.01 (0.25), residues: 1257 helix: 2.52 (0.16), residues: 1032 sheet: 0.29 (0.72), residues: 60 loop : -0.86 (0.57), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 286 HIS 0.002 0.001 HIS C 143 PHE 0.014 0.001 PHE B 388 TYR 0.033 0.002 TYR B 287 ARG 0.001 0.000 ARG C 387 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 154 time to evaluate : 1.061 Fit side-chains REVERT: B 231 LYS cc_start: 0.6849 (ttpt) cc_final: 0.6486 (tmmt) REVERT: B 287 TYR cc_start: 0.9177 (t80) cc_final: 0.8935 (t80) REVERT: B 322 ILE cc_start: 0.8773 (mm) cc_final: 0.8494 (mm) REVERT: C 334 LEU cc_start: 0.8105 (tp) cc_final: 0.7847 (tp) outliers start: 15 outliers final: 15 residues processed: 160 average time/residue: 0.1763 time to fit residues: 42.6105 Evaluate side-chains 166 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 151 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 507 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.6980 chunk 36 optimal weight: 0.1980 chunk 23 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10155 Z= 0.199 Angle : 0.514 7.540 13653 Z= 0.262 Chirality : 0.040 0.179 1701 Planarity : 0.004 0.045 1611 Dihedral : 7.678 56.029 1803 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.52 % Allowed : 16.00 % Favored : 82.48 % 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: 3.04 (0.25), residues: 1257 helix: 2.54 (0.16), residues: 1029 sheet: 0.31 (0.72), residues: 60 loop : -0.80 (0.55), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 286 HIS 0.002 0.001 HIS C 143 PHE 0.016 0.001 PHE C 388 TYR 0.027 0.002 TYR B 287 ARG 0.001 0.000 ARG C 387 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 153 time to evaluate : 1.151 Fit side-chains REVERT: B 231 LYS cc_start: 0.6855 (ttpt) cc_final: 0.6483 (tmmt) REVERT: B 322 ILE cc_start: 0.8772 (mm) cc_final: 0.8485 (mm) REVERT: C 334 LEU cc_start: 0.8127 (tp) cc_final: 0.7860 (tp) outliers start: 16 outliers final: 15 residues processed: 160 average time/residue: 0.1793 time to fit residues: 43.3965 Evaluate side-chains 165 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 507 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 88 optimal weight: 0.0670 chunk 34 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 112 optimal weight: 0.1980 chunk 74 optimal weight: 0.8980 chunk 119 optimal weight: 0.2980 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10155 Z= 0.155 Angle : 0.490 7.116 13653 Z= 0.251 Chirality : 0.039 0.176 1701 Planarity : 0.004 0.044 1611 Dihedral : 7.304 52.815 1803 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.14 % Allowed : 16.76 % Favored : 82.10 % 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: 3.25 (0.25), residues: 1257 helix: 2.62 (0.16), residues: 1047 sheet: 0.38 (0.73), residues: 60 loop : -0.68 (0.61), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 355 HIS 0.002 0.001 HIS C 143 PHE 0.013 0.001 PHE C 388 TYR 0.034 0.002 TYR B 287 ARG 0.001 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 166 time to evaluate : 1.017 Fit side-chains REVERT: B 231 LYS cc_start: 0.6797 (ttpt) cc_final: 0.6447 (tmmt) REVERT: B 322 ILE cc_start: 0.8689 (mm) cc_final: 0.8418 (mm) REVERT: C 231 LYS cc_start: 0.6712 (tttm) cc_final: 0.6263 (tmmt) outliers start: 12 outliers final: 12 residues processed: 170 average time/residue: 0.1738 time to fit residues: 44.2931 Evaluate side-chains 169 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 157 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 507 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 83 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 79 optimal weight: 0.0570 chunk 106 optimal weight: 0.2980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10155 Z= 0.179 Angle : 0.501 6.937 13653 Z= 0.254 Chirality : 0.039 0.179 1701 Planarity : 0.004 0.046 1611 Dihedral : 7.368 59.303 1803 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.24 % Allowed : 16.76 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.19 (0.25), residues: 1257 helix: 2.62 (0.16), residues: 1035 sheet: 0.43 (0.74), residues: 60 loop : -0.81 (0.57), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 286 HIS 0.002 0.001 HIS C 143 PHE 0.012 0.001 PHE C 249 TYR 0.027 0.002 TYR C 287 ARG 0.001 0.000 ARG A 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 156 time to evaluate : 1.059 Fit side-chains REVERT: B 231 LYS cc_start: 0.6814 (ttpt) cc_final: 0.6448 (tmmt) REVERT: B 322 ILE cc_start: 0.8737 (mm) cc_final: 0.8460 (mm) REVERT: C 231 LYS cc_start: 0.6726 (tttm) cc_final: 0.6287 (tmmt) outliers start: 13 outliers final: 13 residues processed: 161 average time/residue: 0.1736 time to fit residues: 41.9974 Evaluate side-chains 164 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 507 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.5980 chunk 92 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 102 optimal weight: 0.1980 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.124888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.103094 restraints weight = 12171.328| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.52 r_work: 0.2910 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10155 Z= 0.182 Angle : 0.504 7.111 13653 Z= 0.256 Chirality : 0.039 0.170 1701 Planarity : 0.004 0.046 1611 Dihedral : 7.292 53.217 1803 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.43 % Allowed : 16.76 % Favored : 81.81 % 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: 3.16 (0.25), residues: 1257 helix: 2.61 (0.16), residues: 1035 sheet: 0.51 (0.74), residues: 60 loop : -0.88 (0.56), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 286 HIS 0.002 0.001 HIS C 143 PHE 0.012 0.001 PHE C 388 TYR 0.026 0.002 TYR C 287 ARG 0.001 0.000 ARG C 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2043.99 seconds wall clock time: 37 minutes 34.08 seconds (2254.08 seconds total)