Starting phenix.real_space_refine on Fri Aug 2 18:02:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fof_50621/08_2024/9fof_50621.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fof_50621/08_2024/9fof_50621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fof_50621/08_2024/9fof_50621.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fof_50621/08_2024/9fof_50621.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fof_50621/08_2024/9fof_50621.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9fof_50621/08_2024/9fof_50621.cif" } resolution = 2.9 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= 0.004 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 60 5.16 5 C 2538 2.51 5 N 750 2.21 5 O 828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "q ARG 293": "NH1" <-> "NH2" Residue "q PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 293": "NH1" <-> "NH2" Residue "C PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 293": "NH1" <-> "NH2" Residue "E PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 293": "NH1" <-> "NH2" Residue "G PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 293": "NH1" <-> "NH2" Residue "I PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4176 Number of models: 1 Model: "" Number of chains: 12 Chain: "q" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 431 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "r" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 265 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "A" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 431 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "B" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 265 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "C" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 431 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "D" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 265 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "E" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 431 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "F" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 265 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 431 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "H" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 265 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "I" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 431 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "J" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 265 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Time building chain proxies: 3.07, per 1000 atoms: 0.74 Number of scatterers: 4176 At special positions: 0 Unit cell: (68.8, 90.3, 54.18, 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 60 16.00 O 828 8.00 N 750 7.00 C 2538 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: 1.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 936 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 301 through 302 removed outlier: 3.515A pdb=" N ASN A 302 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASN q 301 " --> pdb=" O ASN C 302 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN q 302 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN E 302 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN G 302 " --> pdb=" O ASN I 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 305 through 307 removed outlier: 6.033A pdb=" N SER q 305 " --> pdb=" O ASN C 306 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 311 through 312 removed outlier: 6.291A pdb=" N MET q 311 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 317 through 318 removed outlier: 7.297A pdb=" N SER q 317 " --> pdb=" O ILE C 318 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 323 through 324 removed outlier: 7.379A pdb=" N MET q 323 " --> pdb=" O ALA C 324 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 328 through 337 removed outlier: 3.500A pdb=" N TRP C 334 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N MET C 336 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N MET A 337 " --> pdb=" O MET C 336 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ALA q 328 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N GLN C 331 " --> pdb=" O ALA q 328 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU q 330 " --> pdb=" O GLN C 331 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N SER C 333 " --> pdb=" O LEU q 330 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N SER q 332 " --> pdb=" O SER C 333 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLY C 335 " --> pdb=" O SER q 332 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N TRP q 334 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N MET C 337 " --> pdb=" O TRP q 334 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N MET q 336 " --> pdb=" O MET C 337 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP E 334 " --> pdb=" O SER q 333 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N MET E 336 " --> pdb=" O GLY q 335 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N MET q 337 " --> pdb=" O MET E 336 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP G 334 " --> pdb=" O SER E 333 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N MET G 336 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N MET E 337 " --> pdb=" O MET G 336 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP I 334 " --> pdb=" O SER G 333 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET I 336 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N MET G 337 " --> pdb=" O MET I 336 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 342 through 343 removed outlier: 7.316A pdb=" N SER A 342 " --> pdb=" O GLN C 343 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N SER q 342 " --> pdb=" O GLN E 343 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N SER E 342 " --> pdb=" O GLN G 343 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N SER G 342 " --> pdb=" O GLN I 343 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 40 through 50 removed outlier: 3.564A pdb=" N GLY D 47 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE D 49 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASN B 50 " --> pdb=" O PHE D 49 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ASN r 41 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N THR D 44 " --> pdb=" O ASN r 41 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ALA r 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ALA D 46 " --> pdb=" O ALA r 43 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N TYR r 45 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLN D 48 " --> pdb=" O TYR r 45 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLY r 47 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ASN D 50 " --> pdb=" O GLY r 47 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N PHE r 49 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY F 47 " --> pdb=" O ALA r 46 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE F 49 " --> pdb=" O GLN r 48 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASN r 50 " --> pdb=" O PHE F 49 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY H 47 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE H 49 " --> pdb=" O GLN F 48 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASN F 50 " --> pdb=" O PHE H 49 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY J 47 " --> pdb=" O ALA H 46 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE J 49 " --> pdb=" O GLN H 48 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ASN H 50 " --> pdb=" O PHE J 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 65 removed outlier: 6.402A pdb=" N ALA B 58 " --> pdb=" O ALA D 59 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N MET D 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASN B 60 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLY D 63 " --> pdb=" O ASN B 60 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N SER B 62 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N PHE D 65 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N THR B 64 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA r 58 " --> pdb=" O ALA F 59 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N MET F 61 " --> pdb=" O ALA r 58 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASN r 60 " --> pdb=" O MET F 61 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLY F 63 " --> pdb=" O ASN r 60 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N SER r 62 " --> pdb=" O GLY F 63 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N PHE F 65 " --> pdb=" O SER r 62 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N THR r 64 " --> pdb=" O PHE F 65 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA F 58 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N MET H 61 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASN F 60 " --> pdb=" O MET H 61 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N GLY H 63 " --> pdb=" O ASN F 60 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N SER F 62 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE H 65 " --> pdb=" O SER F 62 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N THR F 64 " --> pdb=" O PHE H 65 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA H 58 " --> pdb=" O ALA J 59 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N MET J 61 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ASN H 60 " --> pdb=" O MET J 61 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N GLY J 63 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER H 62 " --> pdb=" O GLY J 63 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE J 65 " --> pdb=" O SER H 62 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N THR H 64 " --> pdb=" O PHE J 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 72 through 73 removed outlier: 5.926A pdb=" N ASN B 72 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASN r 72 " --> pdb=" O LEU F 73 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASN F 72 " --> pdb=" O LEU H 73 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASN H 72 " --> pdb=" O LEU J 73 " (cutoff:3.500A) 82 hydrogen bonds defined for protein. 246 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 891 1.34 - 1.45: 1053 1.45 - 1.57: 2178 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 4242 Sorted by residual: bond pdb=" C MET H 70 " pdb=" N PRO H 71 " ideal model delta sigma weight residual 1.333 1.363 -0.030 1.17e-02 7.31e+03 6.58e+00 bond pdb=" C MET J 70 " pdb=" N PRO J 71 " ideal model delta sigma weight residual 1.333 1.363 -0.030 1.17e-02 7.31e+03 6.50e+00 bond pdb=" C MET B 70 " pdb=" N PRO B 71 " ideal model delta sigma weight residual 1.333 1.362 -0.030 1.17e-02 7.31e+03 6.47e+00 bond pdb=" C MET F 70 " pdb=" N PRO F 71 " ideal model delta sigma weight residual 1.333 1.362 -0.030 1.17e-02 7.31e+03 6.47e+00 bond pdb=" C ASN J 69 " pdb=" N MET J 70 " ideal model delta sigma weight residual 1.332 1.354 -0.022 8.60e-03 1.35e+04 6.40e+00 ... (remaining 4237 not shown) Histogram of bond angle deviations from ideal: 100.59 - 107.48: 146 107.48 - 114.37: 1875 114.37 - 121.25: 2220 121.25 - 128.14: 1411 128.14 - 135.03: 18 Bond angle restraints: 5670 Sorted by residual: angle pdb=" CA ASP J 52 " pdb=" CB ASP J 52 " pdb=" CG ASP J 52 " ideal model delta sigma weight residual 112.60 117.50 -4.90 1.00e+00 1.00e+00 2.40e+01 angle pdb=" CA ASP F 52 " pdb=" CB ASP F 52 " pdb=" CG ASP F 52 " ideal model delta sigma weight residual 112.60 117.49 -4.89 1.00e+00 1.00e+00 2.39e+01 angle pdb=" CA ASP B 52 " pdb=" CB ASP B 52 " pdb=" CG ASP B 52 " ideal model delta sigma weight residual 112.60 117.48 -4.88 1.00e+00 1.00e+00 2.38e+01 angle pdb=" CA ASP r 52 " pdb=" CB ASP r 52 " pdb=" CG ASP r 52 " ideal model delta sigma weight residual 112.60 117.47 -4.87 1.00e+00 1.00e+00 2.37e+01 angle pdb=" CA ASP D 52 " pdb=" CB ASP D 52 " pdb=" CG ASP D 52 " ideal model delta sigma weight residual 112.60 117.45 -4.85 1.00e+00 1.00e+00 2.35e+01 ... (remaining 5665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.35: 2124 14.35 - 28.71: 192 28.71 - 43.06: 36 43.06 - 57.41: 12 57.41 - 71.76: 18 Dihedral angle restraints: 2382 sinusoidal: 840 harmonic: 1542 Sorted by residual: dihedral pdb=" N GLN J 48 " pdb=" C GLN J 48 " pdb=" CA GLN J 48 " pdb=" CB GLN J 48 " ideal model delta harmonic sigma weight residual 122.80 133.22 -10.42 0 2.50e+00 1.60e-01 1.74e+01 dihedral pdb=" N GLN D 48 " pdb=" C GLN D 48 " pdb=" CA GLN D 48 " pdb=" CB GLN D 48 " ideal model delta harmonic sigma weight residual 122.80 133.22 -10.42 0 2.50e+00 1.60e-01 1.74e+01 dihedral pdb=" N GLN F 48 " pdb=" C GLN F 48 " pdb=" CA GLN F 48 " pdb=" CB GLN F 48 " ideal model delta harmonic sigma weight residual 122.80 133.22 -10.42 0 2.50e+00 1.60e-01 1.74e+01 ... (remaining 2379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 378 0.073 - 0.147: 114 0.147 - 0.220: 24 0.220 - 0.293: 6 0.293 - 0.366: 6 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA GLN B 48 " pdb=" N GLN B 48 " pdb=" C GLN B 48 " pdb=" CB GLN B 48 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CA GLN r 48 " pdb=" N GLN r 48 " pdb=" C GLN r 48 " pdb=" CB GLN r 48 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA GLN F 48 " pdb=" N GLN F 48 " pdb=" C GLN F 48 " pdb=" CB GLN F 48 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.37 2.00e-01 2.50e+01 3.33e+00 ... (remaining 525 not shown) Planarity restraints: 804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 334 " 0.024 2.00e-02 2.50e+03 1.26e-02 3.95e+00 pdb=" CG TRP G 334 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP G 334 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP G 334 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP G 334 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP G 334 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP G 334 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 334 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 334 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP G 334 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 334 " 0.024 2.00e-02 2.50e+03 1.25e-02 3.88e+00 pdb=" CG TRP A 334 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP A 334 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 334 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 334 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 334 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 334 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 334 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 334 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 334 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 334 " 0.024 2.00e-02 2.50e+03 1.24e-02 3.87e+00 pdb=" CG TRP E 334 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP E 334 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP E 334 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 334 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP E 334 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP E 334 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 334 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 334 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP E 334 " 0.004 2.00e-02 2.50e+03 ... (remaining 801 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 936 2.85 - 3.36: 3471 3.36 - 3.87: 6871 3.87 - 4.39: 7620 4.39 - 4.90: 13174 Nonbonded interactions: 32072 Sorted by model distance: nonbonded pdb=" NE2 GLN q 286 " pdb=" O SER E 292 " model vdw 2.332 3.120 nonbonded pdb=" NE2 GLN A 286 " pdb=" O SER C 292 " model vdw 2.332 3.120 nonbonded pdb=" NE2 GLN G 286 " pdb=" O SER I 292 " model vdw 2.332 3.120 nonbonded pdb=" O SER q 292 " pdb=" NE2 GLN C 286 " model vdw 2.332 3.120 nonbonded pdb=" NE2 GLN E 286 " pdb=" O SER G 292 " model vdw 2.333 3.120 ... (remaining 32067 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'q' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'r' } 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: 0.830 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.900 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5473 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 : 0.011 0.033 4242 Z= 0.755 Angle : 1.531 5.741 5670 Z= 1.029 Chirality : 0.084 0.366 528 Planarity : 0.008 0.064 804 Dihedral : 13.929 71.764 1446 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 1.04 % Allowed : 4.17 % Favored : 94.79 % Rotamer: Outliers : 1.56 % Allowed : 1.56 % Favored : 96.88 % Cbeta Deviations : 1.28 % 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: -4.04 (0.20), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.15), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.009 TRP G 334 PHE 0.015 0.004 PHE I 313 TYR 0.004 0.001 TYR J 53 ARG 0.011 0.005 ARG E 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: q 303 GLN cc_start: 0.8263 (mt0) cc_final: 0.7852 (mt0) REVERT: q 323 MET cc_start: 0.8369 (ttm) cc_final: 0.8073 (ttm) REVERT: r 70 MET cc_start: 0.7813 (mtp) cc_final: 0.6951 (ttp) REVERT: B 70 MET cc_start: 0.6459 (mtp) cc_final: 0.5856 (mmt) REVERT: C 307 MET cc_start: 0.6424 (tpt) cc_final: 0.6135 (tmt) REVERT: D 53 TYR cc_start: 0.6512 (m-80) cc_final: 0.6227 (m-80) REVERT: D 70 MET cc_start: 0.7314 (mtp) cc_final: 0.6443 (mmm) outliers start: 6 outliers final: 1 residues processed: 110 average time/residue: 1.0775 time to fit residues: 122.8742 Evaluate side-chains 92 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 319 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: q 345 ASN A 285 ASN A 319 ASN C 286 GLN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 ASN G 285 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6156 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4242 Z= 0.212 Angle : 0.730 7.350 5670 Z= 0.390 Chirality : 0.040 0.163 528 Planarity : 0.004 0.040 804 Dihedral : 6.274 24.305 614 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.65 % Allowed : 12.50 % Favored : 83.85 % 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: -3.99 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP I 334 PHE 0.013 0.002 PHE r 49 TYR 0.009 0.001 TYR J 45 ARG 0.005 0.001 ARG E 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 0.488 Fit side-chains REVERT: q 303 GLN cc_start: 0.7933 (mt0) cc_final: 0.7548 (mt0) REVERT: r 70 MET cc_start: 0.7707 (mtp) cc_final: 0.7078 (ttm) REVERT: B 70 MET cc_start: 0.6516 (mtp) cc_final: 0.6024 (mmt) REVERT: D 70 MET cc_start: 0.7464 (mtp) cc_final: 0.6611 (mmm) REVERT: E 299 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7828 (mm) REVERT: F 74 TYR cc_start: 0.6241 (m-80) cc_final: 0.6023 (m-80) REVERT: G 307 MET cc_start: 0.5868 (mpm) cc_final: 0.5308 (mtm) REVERT: G 322 MET cc_start: 0.6478 (ttt) cc_final: 0.5529 (ttt) REVERT: H 70 MET cc_start: 0.5776 (tmm) cc_final: 0.5545 (ttt) outliers start: 14 outliers final: 1 residues processed: 113 average time/residue: 1.0677 time to fit residues: 125.1481 Evaluate side-chains 98 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain E residue 299 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: q 286 GLN ** q 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 50 ASN A 286 GLN C 285 ASN C 291 ASN C 302 ASN ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 ASN F 60 ASN ** G 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN I 285 ASN I 312 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 1.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 4242 Z= 0.314 Angle : 0.942 7.759 5670 Z= 0.511 Chirality : 0.044 0.203 528 Planarity : 0.005 0.060 804 Dihedral : 7.136 25.267 612 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 4.43 % Allowed : 16.67 % Favored : 78.91 % 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: -4.32 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP E 334 PHE 0.021 0.003 PHE J 65 TYR 0.015 0.002 TYR B 45 ARG 0.003 0.001 ARG I 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 0.472 Fit side-chains REVERT: q 303 GLN cc_start: 0.8176 (mt0) cc_final: 0.7757 (mt0) REVERT: r 70 MET cc_start: 0.7540 (mtp) cc_final: 0.6881 (ttm) REVERT: C 337 MET cc_start: 0.8707 (ttm) cc_final: 0.8421 (mtp) REVERT: D 70 MET cc_start: 0.7068 (mtp) cc_final: 0.6723 (ttm) REVERT: G 307 MET cc_start: 0.6956 (mpm) cc_final: 0.6502 (tpt) REVERT: G 323 MET cc_start: 0.7709 (ttt) cc_final: 0.7396 (ttt) REVERT: H 53 TYR cc_start: 0.6910 (m-80) cc_final: 0.6698 (m-80) REVERT: J 57 MET cc_start: 0.5436 (tmt) cc_final: 0.4863 (ttm) REVERT: J 70 MET cc_start: 0.4996 (tmt) cc_final: 0.4787 (tmm) outliers start: 17 outliers final: 5 residues processed: 132 average time/residue: 0.9374 time to fit residues: 128.7517 Evaluate side-chains 113 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 319 ASN Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain J residue 44 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 GLN C 303 GLN ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 ASN F 60 ASN G 286 GLN I 312 ASN I 319 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 1.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4242 Z= 0.312 Angle : 0.928 9.210 5670 Z= 0.503 Chirality : 0.047 0.169 528 Planarity : 0.005 0.043 804 Dihedral : 6.365 21.276 612 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.65 % Allowed : 19.01 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.13), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP G 334 PHE 0.025 0.003 PHE E 289 TYR 0.016 0.002 TYR F 45 ARG 0.002 0.000 ARG I 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 0.431 Fit side-chains REVERT: q 303 GLN cc_start: 0.8314 (mt0) cc_final: 0.7909 (mt0) REVERT: r 70 MET cc_start: 0.7747 (mtp) cc_final: 0.6954 (ttp) REVERT: A 292 SER cc_start: 0.8446 (t) cc_final: 0.8146 (t) REVERT: A 332 SER cc_start: 0.8628 (t) cc_final: 0.8372 (p) REVERT: C 292 SER cc_start: 0.8548 (p) cc_final: 0.8235 (p) REVERT: E 289 PHE cc_start: 0.7161 (t80) cc_final: 0.6915 (t80) REVERT: I 339 MET cc_start: 0.7685 (OUTLIER) cc_final: 0.5211 (tpt) outliers start: 14 outliers final: 1 residues processed: 133 average time/residue: 0.9293 time to fit residues: 127.9423 Evaluate side-chains 118 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain I residue 339 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN A 319 ASN B 72 ASN C 303 GLN ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 319 ASN J 51 GLN J 60 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 1.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 4242 Z= 0.463 Angle : 1.031 10.111 5670 Z= 0.564 Chirality : 0.051 0.206 528 Planarity : 0.005 0.049 804 Dihedral : 6.552 19.395 612 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 5.21 % Allowed : 19.01 % Favored : 75.78 % 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: -4.58 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP G 334 PHE 0.033 0.004 PHE E 289 TYR 0.021 0.003 TYR F 45 ARG 0.001 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 0.399 Fit side-chains REVERT: A 299 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8063 (tt) REVERT: E 289 PHE cc_start: 0.7141 (t80) cc_final: 0.6773 (t80) REVERT: E 299 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8070 (tm) REVERT: F 41 ASN cc_start: 0.7596 (t0) cc_final: 0.7325 (t0) outliers start: 20 outliers final: 7 residues processed: 125 average time/residue: 1.0670 time to fit residues: 138.1176 Evaluate side-chains 123 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 114 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 292 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 319 ASN Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain G residue 292 SER Chi-restraints excluded: chain I residue 319 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: q 303 GLN r 48 GLN A 319 ASN B 60 ASN ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 1.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4242 Z= 0.251 Angle : 0.801 7.181 5670 Z= 0.438 Chirality : 0.043 0.162 528 Planarity : 0.004 0.049 804 Dihedral : 6.048 16.766 612 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.17 % Allowed : 21.35 % Favored : 74.48 % 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: -4.62 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP G 334 PHE 0.023 0.003 PHE E 289 TYR 0.013 0.001 TYR F 45 ARG 0.000 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 0.445 Fit side-chains REVERT: q 303 GLN cc_start: 0.8249 (mt0) cc_final: 0.7828 (mt0) REVERT: r 61 MET cc_start: 0.8389 (mtm) cc_final: 0.8163 (mtm) REVERT: A 292 SER cc_start: 0.8438 (t) cc_final: 0.8125 (t) REVERT: A 299 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8021 (tt) REVERT: C 292 SER cc_start: 0.8441 (p) cc_final: 0.8102 (p) REVERT: H 64 THR cc_start: 0.8786 (t) cc_final: 0.8469 (p) REVERT: I 289 PHE cc_start: 0.7406 (t80) cc_final: 0.7017 (t80) outliers start: 16 outliers final: 4 residues processed: 123 average time/residue: 1.0527 time to fit residues: 134.3169 Evaluate side-chains 119 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 114 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 319 ASN Chi-restraints excluded: chain E residue 319 ASN Chi-restraints excluded: chain G residue 292 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 52 optimal weight: 0.2980 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 overall best weight: 6.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN J 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 1.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4242 Z= 0.339 Angle : 0.889 11.134 5670 Z= 0.483 Chirality : 0.046 0.210 528 Planarity : 0.005 0.048 804 Dihedral : 6.170 16.788 612 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 4.17 % Allowed : 22.14 % Favored : 73.70 % 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: -4.71 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP G 334 PHE 0.017 0.003 PHE H 49 TYR 0.017 0.002 TYR F 45 ARG 0.001 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 0.419 Fit side-chains REVERT: A 299 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8007 (tt) REVERT: C 292 SER cc_start: 0.8445 (p) cc_final: 0.8071 (p) REVERT: I 337 MET cc_start: 0.8537 (mtt) cc_final: 0.8336 (mtp) outliers start: 16 outliers final: 7 residues processed: 119 average time/residue: 1.0478 time to fit residues: 129.3880 Evaluate side-chains 120 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 292 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain D residue 61 MET Chi-restraints excluded: chain E residue 319 ASN Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain G residue 292 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: q 303 GLN ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 1.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4242 Z= 0.202 Angle : 0.743 10.639 5670 Z= 0.401 Chirality : 0.041 0.172 528 Planarity : 0.004 0.048 804 Dihedral : 5.737 16.227 612 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.34 % Allowed : 24.22 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.70 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP G 334 PHE 0.015 0.002 PHE C 289 TYR 0.010 0.001 TYR F 45 ARG 0.001 0.000 ARG A 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 0.502 Fit side-chains REVERT: q 303 GLN cc_start: 0.8195 (mt0) cc_final: 0.7833 (mt0) REVERT: A 292 SER cc_start: 0.8404 (t) cc_final: 0.8088 (t) REVERT: A 299 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7994 (tt) REVERT: C 292 SER cc_start: 0.8418 (p) cc_final: 0.8144 (p) REVERT: F 61 MET cc_start: 0.8669 (mtp) cc_final: 0.8441 (mtm) REVERT: H 57 MET cc_start: 0.8763 (mtm) cc_final: 0.8480 (mtp) REVERT: H 64 THR cc_start: 0.8779 (t) cc_final: 0.8505 (p) outliers start: 9 outliers final: 2 residues processed: 118 average time/residue: 1.0122 time to fit residues: 124.0910 Evaluate side-chains 114 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 111 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain E residue 340 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 1.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 4242 Z= 0.366 Angle : 0.898 6.935 5670 Z= 0.493 Chirality : 0.045 0.181 528 Planarity : 0.005 0.046 804 Dihedral : 6.121 16.548 612 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 1.30 % Allowed : 24.22 % Favored : 74.48 % 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: -4.74 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP G 334 PHE 0.018 0.003 PHE H 49 TYR 0.017 0.002 TYR F 45 ARG 0.001 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 110 time to evaluate : 0.442 Fit side-chains REVERT: A 299 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8054 (tt) REVERT: C 292 SER cc_start: 0.8457 (p) cc_final: 0.8096 (p) REVERT: F 61 MET cc_start: 0.8613 (mtp) cc_final: 0.8350 (mtm) REVERT: G 289 PHE cc_start: 0.6758 (t80) cc_final: 0.6277 (m-80) outliers start: 5 outliers final: 3 residues processed: 113 average time/residue: 1.0633 time to fit residues: 124.5497 Evaluate side-chains 114 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 110 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain G residue 292 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 0.0010 chunk 42 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 overall best weight: 4.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: q 303 GLN ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 ASN H 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 1.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4242 Z= 0.270 Angle : 0.806 5.893 5670 Z= 0.442 Chirality : 0.043 0.169 528 Planarity : 0.004 0.046 804 Dihedral : 5.895 16.461 612 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.60 % Allowed : 22.92 % Favored : 74.48 % 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: -4.72 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP G 334 PHE 0.019 0.003 PHE C 289 TYR 0.014 0.002 TYR F 45 ARG 0.001 0.000 ARG A 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1152 Ramachandran restraints generated. 576 Oldfield, 0 Emsley, 576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.495 Fit side-chains REVERT: r 61 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8123 (mtm) REVERT: A 292 SER cc_start: 0.8395 (t) cc_final: 0.8091 (t) REVERT: A 299 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8028 (tt) REVERT: C 292 SER cc_start: 0.8447 (p) cc_final: 0.8138 (p) REVERT: F 61 MET cc_start: 0.8636 (mtp) cc_final: 0.8365 (mtm) REVERT: G 289 PHE cc_start: 0.6709 (t80) cc_final: 0.6321 (m-80) REVERT: H 64 THR cc_start: 0.8799 (t) cc_final: 0.8487 (p) outliers start: 10 outliers final: 5 residues processed: 113 average time/residue: 1.0279 time to fit residues: 120.6279 Evaluate side-chains 116 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain r residue 61 MET Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain E residue 319 ASN Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain G residue 292 SER Chi-restraints excluded: chain J residue 57 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: q 303 GLN ** A 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.098473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.088861 restraints weight = 5601.476| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.44 r_work: 0.3165 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 1.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4242 Z= 0.346 Angle : 0.882 6.742 5670 Z= 0.485 Chirality : 0.045 0.181 528 Planarity : 0.005 0.048 804 Dihedral : 6.058 16.531 612 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 2.08 % Allowed : 23.70 % Favored : 74.22 % 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: -4.75 (0.18), residues: 576 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.14), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP q 334 PHE 0.019 0.003 PHE C 289 TYR 0.017 0.002 TYR F 45 ARG 0.001 0.000 ARG C 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2275.19 seconds wall clock time: 42 minutes 4.67 seconds (2524.67 seconds total)