Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 14:54:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xr4_33407/04_2023/7xr4_33407.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xr4_33407/04_2023/7xr4_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_33407/04_2023/7xr4_33407.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xr4_33407/04_2023/7xr4_33407.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xr4_33407/04_2023/7xr4_33407.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xr4_33407/04_2023/7xr4_33407.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 224 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: 224 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: 224 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: 5.79, per 1000 atoms: 0.58 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: 4.32 Conformation dependent library (CDL) restraints added in 1.5 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: 0.58 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: 3.08 Time building geometry restraints manager: 4.61 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: 5793 25.07 - 50.14: 267 50.14 - 75.21: 36 75.21 - 100.28: 0 100.28 - 125.35: 3 Dihedral angle restraints: 6099 sinusoidal: 2496 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 6096 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: 0.960 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: 4.370 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 29.900 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.050 ------------------------------------------------------------------------------- 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 : 14.226 125.349 3783 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 % 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 *********************** 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 : 1.267 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 176 average time/residue: 0.1985 time to fit residues: 51.2111 Evaluate side-chains 150 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1282 time to fit residues: 1.8037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 114 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN B 397 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 10155 Z= 0.176 Angle : 0.512 5.731 13653 Z= 0.264 Chirality : 0.039 0.118 1701 Planarity : 0.004 0.041 1611 Dihedral : 10.390 118.257 1629 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer Outliers : 0.10 % 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: 2.56 (0.25), residues: 1257 helix: 2.21 (0.16), residues: 1044 sheet: -0.46 (0.66), residues: 60 loop : -1.09 (0.59), residues: 153 *********************** 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 168 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 1.211 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 167 average time/residue: 0.1744 time to fit residues: 44.8411 Evaluate side-chains 153 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 152 time to evaluate : 1.223 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0934 time to fit residues: 1.7893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 114 optimal weight: 0.2980 chunk 123 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8112 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 10155 Z= 0.186 Angle : 0.498 5.649 13653 Z= 0.256 Chirality : 0.039 0.118 1701 Planarity : 0.004 0.035 1611 Dihedral : 9.789 117.474 1629 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer Outliers : 0.86 % 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: 2.85 (0.25), residues: 1257 helix: 2.38 (0.16), residues: 1047 sheet: -0.20 (0.67), residues: 60 loop : -0.90 (0.61), residues: 150 *********************** 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 167 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 158 time to evaluate : 1.184 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 163 average time/residue: 0.1846 time to fit residues: 45.2506 Evaluate side-chains 154 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 1.145 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0992 time to fit residues: 2.5119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 2.9990 chunk 86 optimal weight: 0.0980 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 0.1980 chunk 60 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.8088 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 10155 Z= 0.170 Angle : 0.492 5.578 13653 Z= 0.252 Chirality : 0.039 0.122 1701 Planarity : 0.004 0.039 1611 Dihedral : 9.315 117.471 1629 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer Outliers : 0.67 % 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: 3.03 (0.25), residues: 1257 helix: 2.48 (0.16), residues: 1050 sheet: 0.12 (0.69), residues: 60 loop : -0.83 (0.62), residues: 147 *********************** 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 157 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 150 time to evaluate : 1.244 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 155 average time/residue: 0.1900 time to fit residues: 44.1371 Evaluate side-chains 148 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 144 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1099 time to fit residues: 2.3271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 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: 8.9990 chunk 62 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1773 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= 0.206 Angle : 0.509 6.827 13653 Z= 0.259 Chirality : 0.039 0.150 1701 Planarity : 0.004 0.042 1611 Dihedral : 9.206 117.035 1629 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer Outliers : 1.05 % 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: 3.01 (0.25), residues: 1257 helix: 2.48 (0.16), residues: 1041 sheet: 0.24 (0.70), residues: 60 loop : -0.82 (0.58), residues: 156 *********************** 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 168 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 157 time to evaluate : 1.235 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 161 average time/residue: 0.1846 time to fit residues: 45.3682 Evaluate side-chains 156 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 150 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1166 time to fit residues: 2.8676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 30 optimal weight: 0.0980 chunk 121 optimal weight: 0.2980 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.0980 chunk 10 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 10155 Z= 0.155 Angle : 0.483 6.837 13653 Z= 0.247 Chirality : 0.039 0.138 1701 Planarity : 0.004 0.043 1611 Dihedral : 8.702 117.340 1629 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer Outliers : 0.19 % 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: 2.64 (0.16), residues: 1047 sheet: 0.33 (0.72), residues: 60 loop : -0.84 (0.60), residues: 150 *********************** 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 163 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 161 time to evaluate : 1.148 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 161 average time/residue: 0.1897 time to fit residues: 45.9898 Evaluate side-chains 154 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1256 time to fit residues: 1.8193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 121 optimal weight: 0.0870 chunk 76 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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: 0.2054 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= 0.182 Angle : 0.493 5.629 13653 Z= 0.252 Chirality : 0.039 0.149 1701 Planarity : 0.004 0.044 1611 Dihedral : 8.659 116.857 1629 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer Outliers : 0.29 % 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: 3.23 (0.25), residues: 1257 helix: 2.68 (0.16), residues: 1032 sheet: 0.35 (0.73), residues: 60 loop : -0.88 (0.55), residues: 165 *********************** 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 160 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 157 time to evaluate : 1.154 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 157 average time/residue: 0.1841 time to fit residues: 43.2404 Evaluate side-chains 155 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 153 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1052 time to fit residues: 1.8863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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: 0.8115 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 10155 Z= 0.233 Angle : 0.537 8.346 13653 Z= 0.270 Chirality : 0.040 0.157 1701 Planarity : 0.004 0.043 1611 Dihedral : 8.823 116.287 1629 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.05 (0.25), residues: 1257 helix: 2.55 (0.16), residues: 1029 sheet: 0.36 (0.73), residues: 60 loop : -0.91 (0.54), residues: 168 *********************** 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 157 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 153 time to evaluate : 1.174 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 154 average time/residue: 0.1856 time to fit residues: 43.0405 Evaluate side-chains 156 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 153 time to evaluate : 1.100 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1036 time to fit residues: 2.1590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 0.0020 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 119 optimal weight: 0.2980 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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: 0.8066 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 10155 Z= 0.170 Angle : 0.503 8.403 13653 Z= 0.254 Chirality : 0.039 0.165 1701 Planarity : 0.004 0.042 1611 Dihedral : 8.502 116.683 1629 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer Outliers : 0.19 % 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: 3.23 (0.25), residues: 1257 helix: 2.67 (0.16), residues: 1035 sheet: 0.42 (0.74), residues: 60 loop : -0.94 (0.55), residues: 162 *********************** 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 162 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 160 time to evaluate : 1.055 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 162 average time/residue: 0.1869 time to fit residues: 45.6334 Evaluate side-chains 155 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 99 optimal weight: 0.4980 chunk 10 optimal weight: 0.0980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 0.3980 chunk 106 optimal weight: 0.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- 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: 0.8077 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 10155 Z= 0.185 Angle : 0.518 8.197 13653 Z= 0.261 Chirality : 0.039 0.184 1701 Planarity : 0.004 0.043 1611 Dihedral : 8.510 116.371 1629 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer Outliers : 0.19 % 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: 3.21 (0.25), residues: 1257 helix: 2.65 (0.16), residues: 1035 sheet: 0.49 (0.75), residues: 60 loop : -0.96 (0.55), residues: 162 ********************** 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 160 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 158 time to evaluate : 1.093 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 158 average time/residue: 0.1861 time to fit residues: 44.5938 Evaluate side-chains 157 residues out of total 1050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 1.222 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0880 time to fit residues: 1.7344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.0980 chunk 92 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 0.4980 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.125119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.102707 restraints weight = 12211.433| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.38 r_work: 0.2928 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 10155 Z= 0.189 Angle : 0.516 8.038 13653 Z= 0.261 Chirality : 0.039 0.176 1701 Planarity : 0.004 0.042 1611 Dihedral : 8.439 116.213 1629 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer Outliers : 0.10 % 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: 3.19 (0.25), residues: 1257 helix: 2.64 (0.16), residues: 1035 sheet: 0.53 (0.75), residues: 60 loop : -0.97 (0.55), residues: 162 =============================================================================== Job complete usr+sys time: 2026.33 seconds wall clock time: 37 minutes 43.09 seconds (2263.09 seconds total)