Starting phenix.real_space_refine on Sat Jan 20 05:23:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu3_21904/01_2024/6wu3_21904_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu3_21904/01_2024/6wu3_21904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu3_21904/01_2024/6wu3_21904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu3_21904/01_2024/6wu3_21904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu3_21904/01_2024/6wu3_21904_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu3_21904/01_2024/6wu3_21904_neut.pdb" } resolution = 3.16 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= 1.000 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: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 4450 2.51 5 N 1044 2.21 5 O 1128 1.98 5 H 6936 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 28": "OD1" <-> "OD2" Residue "A PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 121": "OD1" <-> "OD2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 172": "OD1" <-> "OD2" Residue "A PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 28": "OD1" <-> "OD2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 172": "OD1" <-> "OD2" Residue "C PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 251": "OD1" <-> "OD2" Residue "C PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 313": "OE1" <-> "OE2" Residue "C PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 394": "OE1" <-> "OE2" Residue "C TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13610 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 6805 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 6805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 6805 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.40, per 1000 atoms: 0.47 Number of scatterers: 13610 At special positions: 0 Unit cell: (90.789, 97.641, 76.514, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 1128 8.00 N 1044 7.00 C 4450 6.00 H 6936 1.00 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: 11.74 Conformation dependent library (CDL) restraints added in 1.6 seconds 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1656 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 19 through 38 removed outlier: 3.596A pdb=" N LEU A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 62 Processing helix chain 'A' and resid 65 through 79 Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 113 removed outlier: 3.795A pdb=" N PHE A 98 " --> pdb=" O ASN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 127 removed outlier: 3.521A pdb=" N ALA A 127 " --> pdb=" O VAL A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 147 Processing helix chain 'A' and resid 151 through 167 removed outlier: 3.796A pdb=" N ALA A 155 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Proline residue: A 160 - end of helix Processing helix chain 'A' and resid 174 through 193 removed outlier: 4.021A pdb=" N TYR A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 removed outlier: 3.907A pdb=" N ALA A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 240 removed outlier: 4.372A pdb=" N PHE A 220 " --> pdb=" O ASP A 216 " (cutoff:3.500A) Proline residue: A 223 - end of helix Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 260 through 277 Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 290 through 306 Processing helix chain 'A' and resid 310 through 318 Processing helix chain 'A' and resid 319 through 339 removed outlier: 3.680A pdb=" N LEU A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 356 removed outlier: 5.003A pdb=" N ASP A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N MET A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET A 356 " --> pdb=" O MET A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 373 Processing helix chain 'A' and resid 377 through 392 Proline residue: A 387 - end of helix Processing helix chain 'A' and resid 401 through 413 removed outlier: 3.754A pdb=" N SER A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 421 through 429 Processing helix chain 'A' and resid 434 through 460 Processing helix chain 'C' and resid 19 through 38 removed outlier: 3.596A pdb=" N LEU C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 62 Processing helix chain 'C' and resid 65 through 79 Proline residue: C 74 - end of helix Processing helix chain 'C' and resid 84 through 90 Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 94 through 113 removed outlier: 3.795A pdb=" N PHE C 98 " --> pdb=" O ASN C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 127 removed outlier: 3.522A pdb=" N ALA C 127 " --> pdb=" O VAL C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 147 Processing helix chain 'C' and resid 151 through 167 removed outlier: 3.797A pdb=" N ALA C 155 " --> pdb=" O ASN C 151 " (cutoff:3.500A) Proline residue: C 160 - end of helix Processing helix chain 'C' and resid 174 through 193 removed outlier: 4.022A pdb=" N TYR C 178 " --> pdb=" O GLN C 174 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 211 removed outlier: 3.906A pdb=" N ALA C 204 " --> pdb=" O SER C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 240 removed outlier: 4.372A pdb=" N PHE C 220 " --> pdb=" O ASP C 216 " (cutoff:3.500A) Proline residue: C 223 - end of helix Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 260 through 277 Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 290 through 306 Processing helix chain 'C' and resid 310 through 318 Processing helix chain 'C' and resid 319 through 339 removed outlier: 3.679A pdb=" N LEU C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 356 removed outlier: 5.003A pdb=" N ASP C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N MET C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET C 356 " --> pdb=" O MET C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 373 Processing helix chain 'C' and resid 377 through 392 Proline residue: C 387 - end of helix Processing helix chain 'C' and resid 401 through 413 removed outlier: 3.754A pdb=" N SER C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 420 Processing helix chain 'C' and resid 421 through 429 Processing helix chain 'C' and resid 434 through 460 490 hydrogen bonds defined for protein. 1464 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: 5.05 Time building geometry restraints manager: 12.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6930 1.03 - 1.22: 6 1.22 - 1.42: 2757 1.42 - 1.61: 3977 1.61 - 1.80: 98 Bond restraints: 13768 Sorted by residual: bond pdb=" CG LEU A 197 " pdb=" CD1 LEU A 197 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.33e+00 bond pdb=" CG LEU C 197 " pdb=" CD1 LEU C 197 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.33e+00 bond pdb=" CG LEU A 301 " pdb=" CD2 LEU A 301 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 bond pdb=" CG LEU C 301 " pdb=" CD2 LEU C 301 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.19e+00 bond pdb=" CG1 ILE A 71 " pdb=" CD1 ILE A 71 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.14e+00 ... (remaining 13763 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.31: 175 106.31 - 113.23: 16706 113.23 - 120.15: 4090 120.15 - 127.07: 3972 127.07 - 133.99: 81 Bond angle restraints: 25024 Sorted by residual: angle pdb=" N VAL A 401 " pdb=" CA VAL A 401 " pdb=" C VAL A 401 " ideal model delta sigma weight residual 112.96 109.12 3.84 1.00e+00 1.00e+00 1.47e+01 angle pdb=" N VAL C 401 " pdb=" CA VAL C 401 " pdb=" C VAL C 401 " ideal model delta sigma weight residual 112.96 109.14 3.82 1.00e+00 1.00e+00 1.46e+01 angle pdb=" CA VAL A 401 " pdb=" C VAL A 401 " pdb=" N LEU A 402 " ideal model delta sigma weight residual 118.65 115.98 2.67 1.07e+00 8.73e-01 6.23e+00 angle pdb=" CA VAL C 401 " pdb=" C VAL C 401 " pdb=" N LEU C 402 " ideal model delta sigma weight residual 118.65 116.02 2.63 1.07e+00 8.73e-01 6.04e+00 angle pdb=" CG LYS A 259 " pdb=" CD LYS A 259 " pdb=" CE LYS A 259 " ideal model delta sigma weight residual 111.30 116.30 -5.00 2.30e+00 1.89e-01 4.72e+00 ... (remaining 25019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 5549 17.32 - 34.63: 551 34.63 - 51.95: 173 51.95 - 69.26: 40 69.26 - 86.58: 23 Dihedral angle restraints: 6336 sinusoidal: 3260 harmonic: 3076 Sorted by residual: dihedral pdb=" CA PHE C 83 " pdb=" C PHE C 83 " pdb=" N GLU C 84 " pdb=" CA GLU C 84 " ideal model delta harmonic sigma weight residual 180.00 162.03 17.97 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA PHE A 83 " pdb=" C PHE A 83 " pdb=" N GLU A 84 " pdb=" CA GLU A 84 " ideal model delta harmonic sigma weight residual 180.00 162.06 17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA PHE C 80 " pdb=" C PHE C 80 " pdb=" N GLY C 81 " pdb=" CA GLY C 81 " ideal model delta harmonic sigma weight residual 180.00 164.11 15.89 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 6333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 575 0.024 - 0.048: 302 0.048 - 0.072: 209 0.072 - 0.097: 59 0.097 - 0.121: 13 Chirality restraints: 1158 Sorted by residual: chirality pdb=" CA PRO C 418 " pdb=" N PRO C 418 " pdb=" C PRO C 418 " pdb=" CB PRO C 418 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.64e-01 chirality pdb=" CA PRO A 418 " pdb=" N PRO A 418 " pdb=" C PRO A 418 " pdb=" CB PRO A 418 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.60e-01 chirality pdb=" CA ILE C 433 " pdb=" N ILE C 433 " pdb=" C ILE C 433 " pdb=" CB ILE C 433 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.21e-01 ... (remaining 1155 not shown) Planarity restraints: 1986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 421 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO A 422 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 422 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 422 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 421 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.22e+00 pdb=" N PRO C 422 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 422 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 422 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 159 " -0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO C 160 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 160 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 160 " -0.017 5.00e-02 4.00e+02 ... (remaining 1983 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 729 2.16 - 2.77: 27577 2.77 - 3.38: 39437 3.38 - 3.99: 50104 3.99 - 4.60: 80706 Nonbonded interactions: 198553 Sorted by model distance: nonbonded pdb=" O GLY A 184 " pdb=" HG SER A 188 " model vdw 1.555 1.850 nonbonded pdb=" O GLY C 184 " pdb=" HG SER C 188 " model vdw 1.575 1.850 nonbonded pdb=" O VAL C 57 " pdb=" HG1 THR C 61 " model vdw 1.607 1.850 nonbonded pdb=" O PRO C 387 " pdb=" HG1 THR C 391 " model vdw 1.611 1.850 nonbonded pdb=" O ILE C 267 " pdb=" HG1 THR C 271 " model vdw 1.614 1.850 ... (remaining 198548 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 '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: 2.430 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: 0.210 Extract box with map and model: 12.200 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 46.750 Find NCS groups from input model: 0.520 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 : 0.008 0.042 6832 Z= 0.496 Angle : 0.603 4.997 9318 Z= 0.341 Chirality : 0.039 0.121 1158 Planarity : 0.004 0.037 1128 Dihedral : 15.887 84.129 2292 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 6.27 % Allowed : 14.96 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.23), residues: 886 helix: -1.65 (0.16), residues: 696 sheet: None (None), residues: 0 loop : -4.72 (0.31), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 311 HIS 0.003 0.001 HIS C 432 PHE 0.014 0.001 PHE C 98 TYR 0.008 0.001 TYR C 36 ARG 0.001 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 150 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.6681 (ptpp) REVERT: A 216 ASP cc_start: 0.7898 (t0) cc_final: 0.7648 (t0) REVERT: C 173 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6628 (ptpp) REVERT: C 216 ASP cc_start: 0.7867 (t0) cc_final: 0.7650 (t0) outliers start: 44 outliers final: 34 residues processed: 183 average time/residue: 0.3910 time to fit residues: 95.3553 Evaluate side-chains 164 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 454 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN C 245 ASN C 334 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6832 Z= 0.203 Angle : 0.561 4.770 9318 Z= 0.295 Chirality : 0.035 0.131 1158 Planarity : 0.004 0.036 1128 Dihedral : 9.159 59.691 960 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.99 % Allowed : 17.52 % Favored : 78.49 % 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: -1.31 (0.27), residues: 886 helix: 0.04 (0.19), residues: 706 sheet: None (None), residues: 0 loop : -4.38 (0.36), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 311 HIS 0.004 0.001 HIS C 310 PHE 0.017 0.001 PHE A 277 TYR 0.007 0.001 TYR C 36 ARG 0.002 0.000 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 133 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.6783 (ptpp) REVERT: A 439 MET cc_start: 0.7663 (mtm) cc_final: 0.7397 (mtt) REVERT: C 173 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.6812 (ptpp) REVERT: C 216 ASP cc_start: 0.8031 (t0) cc_final: 0.7788 (t0) outliers start: 28 outliers final: 23 residues processed: 155 average time/residue: 0.3273 time to fit residues: 72.7402 Evaluate side-chains 149 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 378 ASN Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 454 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6832 Z= 0.223 Angle : 0.533 7.533 9318 Z= 0.277 Chirality : 0.034 0.126 1158 Planarity : 0.004 0.033 1128 Dihedral : 8.566 59.641 940 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.27 % Allowed : 18.38 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.29), residues: 886 helix: 0.71 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -4.14 (0.38), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 311 HIS 0.002 0.001 HIS C 19 PHE 0.019 0.001 PHE C 54 TYR 0.006 0.001 TYR C 36 ARG 0.001 0.000 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 168 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 VAL cc_start: 0.9196 (m) cc_final: 0.8970 (p) REVERT: A 439 MET cc_start: 0.7666 (mtm) cc_final: 0.7403 (mtt) REVERT: C 173 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.6791 (ptpp) outliers start: 30 outliers final: 26 residues processed: 159 average time/residue: 0.3602 time to fit residues: 79.0593 Evaluate side-chains 157 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 454 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6832 Z= 0.323 Angle : 0.580 5.064 9318 Z= 0.307 Chirality : 0.036 0.150 1158 Planarity : 0.004 0.036 1128 Dihedral : 8.277 59.265 936 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.13 % Allowed : 16.81 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.29), residues: 886 helix: 0.87 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -4.12 (0.36), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 311 HIS 0.004 0.001 HIS C 355 PHE 0.038 0.002 PHE C 139 TYR 0.007 0.001 TYR C 36 ARG 0.001 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 136 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.6946 (ptpp) outliers start: 36 outliers final: 30 residues processed: 162 average time/residue: 0.3327 time to fit residues: 75.9462 Evaluate side-chains 163 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 132 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 378 ASN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 454 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6832 Z= 0.251 Angle : 0.541 6.225 9318 Z= 0.282 Chirality : 0.034 0.122 1158 Planarity : 0.003 0.035 1128 Dihedral : 7.767 59.242 930 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 4.84 % Allowed : 17.95 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.29), residues: 886 helix: 1.15 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -3.91 (0.38), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 311 HIS 0.005 0.001 HIS A 355 PHE 0.031 0.001 PHE A 139 TYR 0.004 0.001 TYR C 36 ARG 0.002 0.000 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 169 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.6893 (ptpp) REVERT: A 210 VAL cc_start: 0.9141 (m) cc_final: 0.8937 (p) outliers start: 34 outliers final: 29 residues processed: 155 average time/residue: 0.3319 time to fit residues: 72.7234 Evaluate side-chains 164 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 134 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 454 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6832 Z= 0.202 Angle : 0.519 4.870 9318 Z= 0.269 Chirality : 0.034 0.165 1158 Planarity : 0.003 0.035 1128 Dihedral : 7.330 59.040 929 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.27 % Allowed : 18.66 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.29), residues: 886 helix: 1.43 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -3.80 (0.38), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 311 HIS 0.006 0.001 HIS A 355 PHE 0.015 0.001 PHE A 139 TYR 0.004 0.001 TYR A 187 ARG 0.004 0.000 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 169 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.6891 (ptpp) REVERT: C 173 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.6766 (ptpp) outliers start: 30 outliers final: 27 residues processed: 155 average time/residue: 0.3458 time to fit residues: 75.1854 Evaluate side-chains 161 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 459 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6832 Z= 0.246 Angle : 0.534 4.990 9318 Z= 0.277 Chirality : 0.035 0.189 1158 Planarity : 0.003 0.035 1128 Dihedral : 7.151 58.485 929 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 4.27 % Allowed : 19.09 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.30), residues: 886 helix: 1.50 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -3.79 (0.39), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 311 HIS 0.004 0.001 HIS A 355 PHE 0.015 0.001 PHE A 54 TYR 0.003 0.001 TYR C 36 ARG 0.003 0.000 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.6804 (ptpp) REVERT: C 173 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.6841 (ptpp) outliers start: 30 outliers final: 28 residues processed: 146 average time/residue: 0.3607 time to fit residues: 73.7522 Evaluate side-chains 159 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 129 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 59 TRP Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 459 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6832 Z= 0.226 Angle : 0.521 4.857 9318 Z= 0.271 Chirality : 0.035 0.170 1158 Planarity : 0.003 0.037 1128 Dihedral : 6.890 58.100 928 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.70 % Allowed : 18.52 % Favored : 76.78 % 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: 0.87 (0.30), residues: 886 helix: 1.59 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -3.74 (0.39), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 311 HIS 0.004 0.001 HIS C 355 PHE 0.013 0.001 PHE A 54 TYR 0.003 0.001 TYR A 36 ARG 0.003 0.000 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.6932 (ptpp) outliers start: 33 outliers final: 27 residues processed: 151 average time/residue: 0.3486 time to fit residues: 74.8324 Evaluate side-chains 154 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 59 TRP Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 459 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6832 Z= 0.219 Angle : 0.521 5.127 9318 Z= 0.270 Chirality : 0.035 0.171 1158 Planarity : 0.003 0.037 1128 Dihedral : 6.021 57.552 922 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.99 % Allowed : 19.09 % Favored : 76.92 % 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: 1.03 (0.30), residues: 886 helix: 1.69 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -3.54 (0.41), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 311 HIS 0.004 0.001 HIS C 355 PHE 0.013 0.001 PHE A 54 TYR 0.003 0.001 TYR A 36 ARG 0.003 0.000 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.6978 (ptpp) REVERT: C 173 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.6883 (ptpp) outliers start: 28 outliers final: 23 residues processed: 148 average time/residue: 0.3618 time to fit residues: 75.5317 Evaluate side-chains 156 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 131 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 59 TRP Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 459 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6832 Z= 0.214 Angle : 0.518 4.927 9318 Z= 0.268 Chirality : 0.034 0.176 1158 Planarity : 0.003 0.037 1128 Dihedral : 5.824 57.098 921 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.85 % Allowed : 19.09 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.30), residues: 886 helix: 1.73 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -3.53 (0.40), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 311 HIS 0.004 0.001 HIS C 355 PHE 0.013 0.001 PHE A 54 TYR 0.004 0.001 TYR A 178 ARG 0.003 0.000 ARG C 307 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Residue LYS 219 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 136 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7027 (ptpp) REVERT: C 173 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7015 (ptpp) outliers start: 27 outliers final: 22 residues processed: 152 average time/residue: 0.3500 time to fit residues: 74.4327 Evaluate side-chains 158 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 59 TRP Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 200 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 343 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 432 HIS Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 459 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 0.1980 chunk 71 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.118368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.092789 restraints weight = 28257.152| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.29 r_work: 0.2945 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6832 Z= 0.158 Angle : 0.503 5.049 9318 Z= 0.258 Chirality : 0.034 0.164 1158 Planarity : 0.003 0.037 1128 Dihedral : 5.614 56.673 920 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.13 % Allowed : 19.66 % Favored : 77.21 % 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: 1.28 (0.30), residues: 886 helix: 1.85 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -3.38 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 311 HIS 0.004 0.001 HIS A 355 PHE 0.012 0.001 PHE A 54 TYR 0.005 0.001 TYR A 187 ARG 0.002 0.000 ARG A 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3697.63 seconds wall clock time: 65 minutes 44.88 seconds (3944.88 seconds total)