Starting phenix.real_space_refine on Wed Feb 14 13:32:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x17_21991/02_2024/6x17_21991_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x17_21991/02_2024/6x17_21991.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x17_21991/02_2024/6x17_21991.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x17_21991/02_2024/6x17_21991.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x17_21991/02_2024/6x17_21991_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x17_21991/02_2024/6x17_21991_updated.pdb" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 51 5.16 5 C 6195 2.51 5 N 1500 2.21 5 O 1641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 5": "NH1" <-> "NH2" Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 257": "OD1" <-> "OD2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 136": "OD1" <-> "OD2" Residue "B PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 257": "OD1" <-> "OD2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 390": "OD1" <-> "OD2" Residue "B ASP 405": "OD1" <-> "OD2" Residue "C ARG 5": "NH1" <-> "NH2" Residue "C TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 136": "OD1" <-> "OD2" Residue "C PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 257": "OD1" <-> "OD2" Residue "C GLU 291": "OE1" <-> "OE2" Residue "C TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 390": "OD1" <-> "OD2" Residue "C ASP 405": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9390 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3086 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 18, 'TRANS': 396} Chain: "B" Number of atoms: 3086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3086 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 18, 'TRANS': 396} Chain: "C" Number of atoms: 3086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3086 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 18, 'TRANS': 396} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'6OU': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'6OU': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'6OU': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.31, per 1000 atoms: 0.57 Number of scatterers: 9390 At special positions: 0 Unit cell: (109.472, 106.252, 82.6403, 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 51 16.00 P 3 15.00 O 1641 8.00 N 1500 7.00 C 6195 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: 3.56 Conformation dependent library (CDL) restraints added in 2.0 seconds 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2238 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 0 sheets defined 74.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 Processing helix chain 'A' and resid 12 through 32 Processing helix chain 'A' and resid 36 through 42 Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 58 through 67 removed outlier: 3.787A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 106 Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 151 through 170 removed outlier: 4.166A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 219 removed outlier: 3.573A pdb=" N ASP A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 228 through 253 removed outlier: 4.724A pdb=" N PHE A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 275 removed outlier: 5.806A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 Processing helix chain 'A' and resid 296 through 306 removed outlier: 4.793A pdb=" N PHE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 312 through 328 Processing helix chain 'A' and resid 338 through 351 removed outlier: 3.533A pdb=" N SER A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 370 removed outlier: 3.690A pdb=" N VAL A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 415 removed outlier: 3.875A pdb=" N GLY A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE A 389 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP A 390 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 9 Processing helix chain 'B' and resid 12 through 32 Processing helix chain 'B' and resid 36 through 42 Processing helix chain 'B' and resid 44 through 56 Processing helix chain 'B' and resid 58 through 67 removed outlier: 3.787A pdb=" N LEU B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 106 Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 151 through 170 removed outlier: 4.166A pdb=" N ASN B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 219 removed outlier: 3.573A pdb=" N ASP B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) Proline residue: B 206 - end of helix Processing helix chain 'B' and resid 228 through 253 removed outlier: 4.724A pdb=" N PHE B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 removed outlier: 5.807A pdb=" N ASP B 267 " --> pdb=" O LYS B 263 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ALA B 268 " --> pdb=" O HIS B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 296 through 306 removed outlier: 4.793A pdb=" N PHE B 301 " --> pdb=" O GLY B 297 " (cutoff:3.500A) Proline residue: B 304 - end of helix Processing helix chain 'B' and resid 312 through 328 Processing helix chain 'B' and resid 338 through 351 removed outlier: 3.533A pdb=" N SER B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 370 removed outlier: 3.690A pdb=" N VAL B 370 " --> pdb=" O VAL B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 415 removed outlier: 3.876A pdb=" N GLY B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE B 389 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP B 390 " --> pdb=" O ILE B 386 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY B 396 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 9 Processing helix chain 'C' and resid 12 through 32 Processing helix chain 'C' and resid 36 through 42 Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 58 through 67 removed outlier: 3.787A pdb=" N LEU C 66 " --> pdb=" O VAL C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 106 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'C' and resid 151 through 170 removed outlier: 4.166A pdb=" N ASN C 170 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 219 removed outlier: 3.572A pdb=" N ASP C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY C 200 " --> pdb=" O LYS C 196 " (cutoff:3.500A) Proline residue: C 206 - end of helix Processing helix chain 'C' and resid 228 through 253 removed outlier: 4.724A pdb=" N PHE C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 275 removed outlier: 5.807A pdb=" N ASP C 267 " --> pdb=" O LYS C 263 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ALA C 268 " --> pdb=" O HIS C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 290 Processing helix chain 'C' and resid 296 through 306 removed outlier: 4.793A pdb=" N PHE C 301 " --> pdb=" O GLY C 297 " (cutoff:3.500A) Proline residue: C 304 - end of helix Processing helix chain 'C' and resid 312 through 328 Processing helix chain 'C' and resid 338 through 351 removed outlier: 3.533A pdb=" N SER C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 removed outlier: 3.691A pdb=" N VAL C 370 " --> pdb=" O VAL C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 415 removed outlier: 3.875A pdb=" N GLY C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE C 389 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP C 390 " --> pdb=" O ILE C 386 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 393 " --> pdb=" O ILE C 389 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY C 396 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1920 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1440 1.31 - 1.43: 2305 1.43 - 1.56: 5672 1.56 - 1.68: 51 1.68 - 1.80: 99 Bond restraints: 9567 Sorted by residual: bond pdb=" C16 6OU C 501 " pdb=" O18 6OU C 501 " ideal model delta sigma weight residual 1.327 1.416 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C16 6OU A 501 " pdb=" O18 6OU A 501 " ideal model delta sigma weight residual 1.327 1.416 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C16 6OU B 501 " pdb=" O18 6OU B 501 " ideal model delta sigma weight residual 1.327 1.416 -0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" C31 6OU C 501 " pdb=" O30 6OU C 501 " ideal model delta sigma weight residual 1.331 1.407 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C31 6OU A 501 " pdb=" O30 6OU A 501 " ideal model delta sigma weight residual 1.331 1.406 -0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 9562 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.43: 289 106.43 - 113.22: 5472 113.22 - 120.01: 3263 120.01 - 126.80: 3906 126.80 - 133.59: 84 Bond angle restraints: 13014 Sorted by residual: angle pdb=" O22 6OU C 501 " pdb=" P23 6OU C 501 " pdb=" O26 6OU C 501 " ideal model delta sigma weight residual 93.95 109.59 -15.64 3.00e+00 1.11e-01 2.72e+01 angle pdb=" O22 6OU A 501 " pdb=" P23 6OU A 501 " pdb=" O26 6OU A 501 " ideal model delta sigma weight residual 93.95 109.57 -15.62 3.00e+00 1.11e-01 2.71e+01 angle pdb=" O22 6OU B 501 " pdb=" P23 6OU B 501 " pdb=" O26 6OU B 501 " ideal model delta sigma weight residual 93.95 109.56 -15.61 3.00e+00 1.11e-01 2.71e+01 angle pdb=" N ALA B 205 " pdb=" CA ALA B 205 " pdb=" C ALA B 205 " ideal model delta sigma weight residual 109.81 119.47 -9.66 2.21e+00 2.05e-01 1.91e+01 angle pdb=" N ALA A 205 " pdb=" CA ALA A 205 " pdb=" C ALA A 205 " ideal model delta sigma weight residual 109.81 119.45 -9.64 2.21e+00 2.05e-01 1.90e+01 ... (remaining 13009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.60: 5297 25.60 - 51.21: 331 51.21 - 76.81: 30 76.81 - 102.42: 0 102.42 - 128.02: 6 Dihedral angle restraints: 5664 sinusoidal: 2130 harmonic: 3534 Sorted by residual: dihedral pdb=" CA LEU C 333 " pdb=" C LEU C 333 " pdb=" N THR C 334 " pdb=" CA THR C 334 " ideal model delta harmonic sigma weight residual 180.00 141.62 38.38 0 5.00e+00 4.00e-02 5.89e+01 dihedral pdb=" CA LEU B 333 " pdb=" C LEU B 333 " pdb=" N THR B 334 " pdb=" CA THR B 334 " ideal model delta harmonic sigma weight residual 180.00 141.63 38.37 0 5.00e+00 4.00e-02 5.89e+01 dihedral pdb=" CA LEU A 333 " pdb=" C LEU A 333 " pdb=" N THR A 334 " pdb=" CA THR A 334 " ideal model delta harmonic sigma weight residual 180.00 141.67 38.33 0 5.00e+00 4.00e-02 5.88e+01 ... (remaining 5661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1028 0.040 - 0.080: 412 0.080 - 0.119: 111 0.119 - 0.159: 39 0.159 - 0.199: 24 Chirality restraints: 1614 Sorted by residual: chirality pdb=" CA SER C 74 " pdb=" N SER C 74 " pdb=" C SER C 74 " pdb=" CB SER C 74 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.88e-01 chirality pdb=" CA SER A 74 " pdb=" N SER A 74 " pdb=" C SER A 74 " pdb=" CB SER A 74 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.57e-01 chirality pdb=" CA SER B 74 " pdb=" N SER B 74 " pdb=" C SER B 74 " pdb=" CB SER B 74 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.41e-01 ... (remaining 1611 not shown) Planarity restraints: 1593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 405 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" CG ASP A 405 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP A 405 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP A 405 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 405 " -0.014 2.00e-02 2.50e+03 2.94e-02 8.65e+00 pdb=" CG ASP C 405 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP C 405 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP C 405 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 405 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.64e+00 pdb=" CG ASP B 405 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP B 405 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP B 405 " 0.018 2.00e-02 2.50e+03 ... (remaining 1590 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2620 2.81 - 3.33: 8973 3.33 - 3.85: 15517 3.85 - 4.38: 17091 4.38 - 4.90: 30400 Nonbonded interactions: 74601 Sorted by model distance: nonbonded pdb=" O SER C 65 " pdb=" OG SER C 300 " model vdw 2.284 2.440 nonbonded pdb=" O SER A 65 " pdb=" OG SER A 300 " model vdw 2.284 2.440 nonbonded pdb=" O SER B 65 " pdb=" OG SER B 300 " model vdw 2.284 2.440 nonbonded pdb=" O GLN A 337 " pdb=" OG1 THR A 340 " model vdw 2.295 2.440 nonbonded pdb=" O GLN C 337 " pdb=" OG1 THR C 340 " model vdw 2.295 2.440 ... (remaining 74596 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.330 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 28.100 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 9567 Z= 0.476 Angle : 1.053 15.642 13014 Z= 0.533 Chirality : 0.051 0.199 1614 Planarity : 0.008 0.063 1593 Dihedral : 16.083 128.021 3426 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.74 (0.18), residues: 1239 helix: -2.09 (0.12), residues: 984 sheet: None (None), residues: 0 loop : -3.16 (0.30), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 264 PHE 0.009 0.001 PHE A 301 TYR 0.018 0.002 TYR A 299 ARG 0.002 0.000 ARG C 397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 1.018 Fit side-chains REVERT: A 105 ARG cc_start: 0.8383 (mtp-110) cc_final: 0.8178 (mtm180) REVERT: A 115 LEU cc_start: 0.7992 (pp) cc_final: 0.7682 (pp) REVERT: A 203 GLN cc_start: 0.8481 (tp-100) cc_final: 0.8159 (tp-100) REVERT: A 362 MET cc_start: 0.8084 (mtp) cc_final: 0.7740 (mtp) REVERT: B 105 ARG cc_start: 0.8195 (mtp-110) cc_final: 0.7915 (mtm180) REVERT: B 120 GLN cc_start: 0.6800 (pp30) cc_final: 0.6566 (pp30) REVERT: B 401 ASN cc_start: 0.8127 (m-40) cc_final: 0.7725 (m-40) REVERT: C 312 ASP cc_start: 0.8933 (m-30) cc_final: 0.8468 (m-30) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.1912 time to fit residues: 72.8603 Evaluate side-chains 204 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 318 GLN A 327 ASN B 32 HIS B 223 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS C 318 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9567 Z= 0.198 Angle : 0.596 8.435 13014 Z= 0.291 Chirality : 0.038 0.148 1614 Planarity : 0.004 0.045 1593 Dihedral : 10.279 91.473 1440 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.88 % Allowed : 16.46 % Favored : 80.66 % 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: -1.07 (0.22), residues: 1239 helix: -0.14 (0.15), residues: 987 sheet: None (None), residues: 0 loop : -2.59 (0.34), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 32 PHE 0.012 0.001 PHE B 323 TYR 0.013 0.001 TYR C 299 ARG 0.002 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 227 time to evaluate : 0.964 Fit side-chains REVERT: A 212 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8807 (mp) REVERT: A 269 MET cc_start: 0.8466 (mtp) cc_final: 0.8167 (mtm) REVERT: A 362 MET cc_start: 0.8093 (mtp) cc_final: 0.7770 (mtp) REVERT: B 312 ASP cc_start: 0.8993 (m-30) cc_final: 0.8739 (m-30) REVERT: B 401 ASN cc_start: 0.8009 (m-40) cc_final: 0.7612 (m-40) REVERT: C 312 ASP cc_start: 0.9003 (m-30) cc_final: 0.8429 (m-30) outliers start: 28 outliers final: 20 residues processed: 239 average time/residue: 0.1894 time to fit residues: 64.7993 Evaluate side-chains 232 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 211 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 332 HIS Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 337 GLN Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 0.0770 chunk 76 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 223 HIS B 14 GLN B 32 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS C 14 GLN C 32 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9567 Z= 0.180 Angle : 0.569 8.113 13014 Z= 0.276 Chirality : 0.038 0.139 1614 Planarity : 0.004 0.040 1593 Dihedral : 9.651 77.662 1440 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.29 % Allowed : 20.16 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.23), residues: 1239 helix: 0.87 (0.16), residues: 966 sheet: None (None), residues: 0 loop : -2.44 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS C 32 PHE 0.008 0.001 PHE C 323 TYR 0.013 0.001 TYR C 299 ARG 0.003 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 227 time to evaluate : 0.909 Fit side-chains REVERT: A 194 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8822 (mmt) REVERT: A 212 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8789 (mp) REVERT: A 269 MET cc_start: 0.8458 (mtp) cc_final: 0.8209 (mtm) REVERT: B 312 ASP cc_start: 0.9048 (m-30) cc_final: 0.8847 (m-30) REVERT: C 312 ASP cc_start: 0.9061 (m-30) cc_final: 0.8497 (m-30) outliers start: 32 outliers final: 26 residues processed: 241 average time/residue: 0.1902 time to fit residues: 65.2823 Evaluate side-chains 240 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 212 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 332 HIS Chi-restraints excluded: chain C residue 337 GLN Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 0.0010 chunk 12 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 32 HIS B 337 GLN C 32 HIS C 318 GLN C 337 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9567 Z= 0.172 Angle : 0.558 8.981 13014 Z= 0.269 Chirality : 0.038 0.126 1614 Planarity : 0.003 0.039 1593 Dihedral : 9.148 65.980 1440 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.70 % Allowed : 20.68 % Favored : 75.62 % 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: 0.78 (0.24), residues: 1239 helix: 1.32 (0.17), residues: 966 sheet: None (None), residues: 0 loop : -2.43 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS C 32 PHE 0.010 0.001 PHE A 323 TYR 0.012 0.001 TYR C 299 ARG 0.004 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 221 time to evaluate : 0.932 Fit side-chains REVERT: A 115 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7857 (pp) REVERT: A 194 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8927 (mmt) REVERT: A 212 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8802 (mp) REVERT: A 269 MET cc_start: 0.8478 (mtp) cc_final: 0.8228 (mtm) REVERT: B 101 ILE cc_start: 0.9505 (mm) cc_final: 0.9254 (mm) REVERT: B 416 GLU cc_start: 0.7269 (mm-30) cc_final: 0.7050 (tp30) REVERT: C 228 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8857 (mt) REVERT: C 312 ASP cc_start: 0.9047 (m-30) cc_final: 0.8538 (m-30) outliers start: 36 outliers final: 27 residues processed: 239 average time/residue: 0.1965 time to fit residues: 66.2324 Evaluate side-chains 245 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 214 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 32 HIS B 223 HIS B 337 GLN C 32 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9567 Z= 0.219 Angle : 0.571 9.352 13014 Z= 0.278 Chirality : 0.039 0.128 1614 Planarity : 0.003 0.040 1593 Dihedral : 8.911 66.778 1440 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.94 % Allowed : 20.68 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.24), residues: 1239 helix: 1.48 (0.17), residues: 969 sheet: None (None), residues: 0 loop : -2.38 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS C 32 PHE 0.014 0.001 PHE C 323 TYR 0.016 0.001 TYR C 88 ARG 0.004 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 221 time to evaluate : 0.960 Fit side-chains REVERT: A 115 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7907 (pp) REVERT: A 136 ASP cc_start: 0.7299 (t0) cc_final: 0.7024 (t0) REVERT: A 212 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8832 (mp) REVERT: A 269 MET cc_start: 0.8469 (mtp) cc_final: 0.8226 (mtm) REVERT: B 212 LEU cc_start: 0.9103 (mt) cc_final: 0.8780 (mp) REVERT: B 416 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6996 (tp30) REVERT: C 242 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.7610 (tp40) outliers start: 48 outliers final: 36 residues processed: 250 average time/residue: 0.1912 time to fit residues: 68.1777 Evaluate side-chains 255 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 216 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 332 HIS Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 119 optimal weight: 0.1980 chunk 98 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 32 HIS C 32 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9567 Z= 0.171 Angle : 0.574 13.381 13014 Z= 0.275 Chirality : 0.039 0.142 1614 Planarity : 0.003 0.038 1593 Dihedral : 8.727 68.775 1440 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.32 % Allowed : 22.43 % Favored : 73.25 % 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: 1.24 (0.24), residues: 1239 helix: 1.65 (0.17), residues: 969 sheet: None (None), residues: 0 loop : -2.33 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS C 32 PHE 0.010 0.001 PHE C 323 TYR 0.022 0.001 TYR A 88 ARG 0.007 0.000 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 218 time to evaluate : 1.047 Fit side-chains REVERT: A 136 ASP cc_start: 0.7246 (t0) cc_final: 0.6955 (t0) REVERT: A 194 MET cc_start: 0.8902 (mmt) cc_final: 0.8607 (mmt) REVERT: A 212 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8818 (mp) REVERT: B 212 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8717 (mp) REVERT: C 242 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.7530 (tp40) REVERT: C 286 MET cc_start: 0.8774 (mtm) cc_final: 0.8320 (mtp) outliers start: 42 outliers final: 30 residues processed: 244 average time/residue: 0.2075 time to fit residues: 72.4767 Evaluate side-chains 244 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 211 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 332 HIS Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 86 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 32 HIS B 223 HIS C 32 HIS C 40 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9567 Z= 0.192 Angle : 0.564 8.048 13014 Z= 0.275 Chirality : 0.039 0.189 1614 Planarity : 0.003 0.039 1593 Dihedral : 8.379 72.264 1440 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.25 % Allowed : 22.33 % Favored : 72.43 % 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: 1.40 (0.24), residues: 1239 helix: 1.77 (0.17), residues: 969 sheet: None (None), residues: 0 loop : -2.27 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS C 32 PHE 0.011 0.001 PHE C 323 TYR 0.017 0.001 TYR C 88 ARG 0.005 0.000 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 214 time to evaluate : 1.055 Fit side-chains REVERT: A 136 ASP cc_start: 0.7304 (t0) cc_final: 0.6935 (t0) REVERT: A 194 MET cc_start: 0.8931 (mmt) cc_final: 0.8530 (mmt) REVERT: A 212 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8826 (mp) REVERT: A 242 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.7511 (tp40) REVERT: A 269 MET cc_start: 0.8511 (mtp) cc_final: 0.8151 (mtm) REVERT: A 385 MET cc_start: 0.8404 (tmm) cc_final: 0.8162 (ttp) REVERT: B 169 MET cc_start: 0.8633 (mmm) cc_final: 0.7970 (mtp) REVERT: B 212 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8711 (mp) REVERT: B 242 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.6888 (tp40) REVERT: C 242 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.7517 (tp40) REVERT: C 286 MET cc_start: 0.8786 (mtm) cc_final: 0.8334 (mtp) REVERT: C 312 ASP cc_start: 0.9029 (m-30) cc_final: 0.8560 (m-30) outliers start: 51 outliers final: 37 residues processed: 247 average time/residue: 0.1859 time to fit residues: 65.6805 Evaluate side-chains 250 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 208 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 11 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 107 optimal weight: 0.4980 chunk 113 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS C 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9567 Z= 0.175 Angle : 0.569 9.392 13014 Z= 0.273 Chirality : 0.039 0.170 1614 Planarity : 0.003 0.038 1593 Dihedral : 8.140 75.286 1440 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.53 % Allowed : 23.66 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.24), residues: 1239 helix: 1.86 (0.16), residues: 966 sheet: None (None), residues: 0 loop : -2.21 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS C 32 PHE 0.009 0.001 PHE C 323 TYR 0.015 0.001 TYR C 88 ARG 0.005 0.000 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 214 time to evaluate : 0.827 Fit side-chains REVERT: A 136 ASP cc_start: 0.7346 (t0) cc_final: 0.6943 (t0) REVERT: A 212 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8796 (mp) REVERT: A 242 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.7477 (tp40) REVERT: A 269 MET cc_start: 0.8501 (mtp) cc_final: 0.8153 (mtm) REVERT: A 276 ARG cc_start: 0.8665 (mtm-85) cc_final: 0.8463 (mtm-85) REVERT: A 385 MET cc_start: 0.8369 (tmm) cc_final: 0.8157 (ttp) REVERT: B 136 ASP cc_start: 0.7509 (t0) cc_final: 0.7091 (t0) REVERT: B 169 MET cc_start: 0.8614 (mmm) cc_final: 0.8190 (mtm) REVERT: B 212 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8701 (mp) REVERT: B 242 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.6800 (tp40) REVERT: C 242 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.7484 (tp40) REVERT: C 286 MET cc_start: 0.8736 (mtm) cc_final: 0.8296 (mtp) outliers start: 44 outliers final: 39 residues processed: 245 average time/residue: 0.1878 time to fit residues: 65.1998 Evaluate side-chains 255 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 211 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.2980 chunk 110 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 0.0970 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS B 32 HIS C 32 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9567 Z= 0.165 Angle : 0.568 8.839 13014 Z= 0.272 Chirality : 0.039 0.154 1614 Planarity : 0.003 0.038 1593 Dihedral : 7.983 76.433 1440 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.73 % Allowed : 23.77 % Favored : 71.50 % 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: 1.66 (0.24), residues: 1239 helix: 1.94 (0.16), residues: 966 sheet: None (None), residues: 0 loop : -2.11 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS A 32 PHE 0.009 0.001 PHE C 323 TYR 0.014 0.001 TYR C 88 ARG 0.004 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 213 time to evaluate : 1.041 Fit side-chains REVERT: A 136 ASP cc_start: 0.7404 (t0) cc_final: 0.6984 (t0) REVERT: A 212 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8784 (mp) REVERT: A 242 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7383 (tp40) REVERT: A 269 MET cc_start: 0.8475 (mtp) cc_final: 0.8142 (mtm) REVERT: A 276 ARG cc_start: 0.8676 (mtm-85) cc_final: 0.8457 (mtm-85) REVERT: A 385 MET cc_start: 0.8352 (tmm) cc_final: 0.8146 (ttp) REVERT: B 136 ASP cc_start: 0.7527 (t0) cc_final: 0.7121 (t0) REVERT: B 169 MET cc_start: 0.8536 (mmm) cc_final: 0.8154 (mtm) REVERT: B 212 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8694 (mp) REVERT: B 242 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.6686 (tp40) REVERT: C 13 LEU cc_start: 0.8347 (mt) cc_final: 0.8105 (mt) REVERT: C 53 LEU cc_start: 0.9076 (mt) cc_final: 0.8865 (mt) REVERT: C 242 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.7427 (tp40) outliers start: 46 outliers final: 37 residues processed: 244 average time/residue: 0.2004 time to fit residues: 69.4920 Evaluate side-chains 253 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 211 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 103 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 40 HIS B 32 HIS C 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9567 Z= 0.174 Angle : 0.575 8.838 13014 Z= 0.276 Chirality : 0.039 0.148 1614 Planarity : 0.003 0.038 1593 Dihedral : 7.921 76.102 1440 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.63 % Allowed : 23.97 % Favored : 71.40 % 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: 1.67 (0.24), residues: 1239 helix: 1.97 (0.16), residues: 963 sheet: None (None), residues: 0 loop : -2.12 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS A 32 PHE 0.009 0.001 PHE C 323 TYR 0.037 0.001 TYR B 88 ARG 0.004 0.000 ARG A 276 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 207 time to evaluate : 1.068 Fit side-chains REVERT: A 136 ASP cc_start: 0.7425 (t0) cc_final: 0.6992 (t0) REVERT: A 212 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8773 (mp) REVERT: A 242 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.7390 (tp40) REVERT: A 269 MET cc_start: 0.8481 (mtp) cc_final: 0.8145 (mtm) REVERT: B 136 ASP cc_start: 0.7560 (t0) cc_final: 0.7157 (t0) REVERT: B 169 MET cc_start: 0.8528 (mmm) cc_final: 0.8166 (mtm) REVERT: B 212 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8728 (mp) REVERT: B 242 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.6671 (tp40) REVERT: B 362 MET cc_start: 0.7486 (ttm) cc_final: 0.7095 (ttm) REVERT: C 13 LEU cc_start: 0.8353 (mt) cc_final: 0.8121 (mt) REVERT: C 53 LEU cc_start: 0.9070 (mt) cc_final: 0.8865 (mt) REVERT: C 242 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.7315 (tp40) outliers start: 45 outliers final: 38 residues processed: 238 average time/residue: 0.1857 time to fit residues: 63.6211 Evaluate side-chains 250 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 207 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 411 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 402 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.6980 chunk 89 optimal weight: 0.0670 chunk 14 optimal weight: 0.0060 chunk 27 optimal weight: 0.0170 chunk 97 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.2572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS C 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.119573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.102130 restraints weight = 12722.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.104734 restraints weight = 7449.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.106387 restraints weight = 5148.038| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9567 Z= 0.144 Angle : 0.564 8.984 13014 Z= 0.271 Chirality : 0.039 0.146 1614 Planarity : 0.003 0.037 1593 Dihedral : 7.743 76.188 1440 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.70 % Allowed : 25.00 % Favored : 71.30 % 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: 1.85 (0.24), residues: 1239 helix: 2.09 (0.17), residues: 960 sheet: None (None), residues: 0 loop : -2.00 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 32 PHE 0.008 0.001 PHE C 323 TYR 0.032 0.001 TYR B 88 ARG 0.004 0.000 ARG A 276 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2043.30 seconds wall clock time: 37 minutes 53.21 seconds (2273.21 seconds total)