Starting phenix.real_space_refine on Fri Feb 14 00:40:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x17_21991/02_2025/6x17_21991.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x17_21991/02_2025/6x17_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/cci-nas-00/data/ceres_data/6x17_21991/02_2025/6x17_21991.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x17_21991/02_2025/6x17_21991.map" model { file = "/net/cci-nas-00/data/ceres_data/6x17_21991/02_2025/6x17_21991.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x17_21991/02_2025/6x17_21991.cif" } 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. Time to flip 51 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9390 Number of models: 1 Model: "" Number of chains: 5 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: "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: "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} Restraints were copied for chains: C, B Time building chain proxies: 5.74, per 1000 atoms: 0.61 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 - 3.00 Amino acid : True - 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: 2.45 Conformation dependent library (CDL) restraints added in 1.3 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... Secondary structure from input PDB file: 57 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 11 through 33 removed outlier: 3.533A pdb=" N LYS A 15 " --> pdb=" O PRO A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 removed outlier: 3.537A pdb=" N VAL A 39 " --> pdb=" O TYR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 57 removed outlier: 3.942A pdb=" N GLY A 47 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.639A pdb=" N ILE A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 107 removed outlier: 3.790A pdb=" N ARG A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 141 through 148 removed outlier: 4.169A pdb=" N ASN A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 169 Processing helix chain 'A' and resid 175 through 220 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 227 through 254 removed outlier: 3.978A pdb=" N VAL A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) 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 257 through 276 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) removed outlier: 3.574A pdb=" N ARG A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 295 through 307 removed outlier: 3.558A pdb=" N TYR A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) 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 311 through 329 Processing helix chain 'A' and resid 337 through 352 removed outlier: 3.558A pdb=" N ILE A 341 " --> pdb=" O GLN A 337 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 4.009A pdb=" N ILE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 387 Processing helix chain 'A' and resid 389 through 416 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 10 Processing helix chain 'B' and resid 11 through 33 removed outlier: 3.532A pdb=" N LYS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 43 removed outlier: 3.536A pdb=" N VAL B 39 " --> pdb=" O TYR B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 57 removed outlier: 3.942A pdb=" N GLY B 47 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 68 removed outlier: 3.639A pdb=" N ILE B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 107 removed outlier: 3.790A pdb=" N ARG B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 136 Processing helix chain 'B' and resid 141 through 148 removed outlier: 4.169A pdb=" N ASN B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 169 Processing helix chain 'B' and resid 175 through 220 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 227 through 254 removed outlier: 3.978A pdb=" N VAL B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) 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 257 through 276 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) removed outlier: 3.574A pdb=" N ARG B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 295 through 307 removed outlier: 3.559A pdb=" N TYR B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) 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 311 through 329 Processing helix chain 'B' and resid 337 through 352 removed outlier: 3.557A pdb=" N ILE B 341 " --> pdb=" O GLN B 337 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 371 removed outlier: 4.008A pdb=" N ILE B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 370 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 387 Processing helix chain 'B' and resid 389 through 416 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 10 Processing helix chain 'C' and resid 11 through 33 removed outlier: 3.532A pdb=" N LYS C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 43 removed outlier: 3.537A pdb=" N VAL C 39 " --> pdb=" O TYR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 57 removed outlier: 3.942A pdb=" N GLY C 47 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU C 57 " --> pdb=" O LEU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 68 removed outlier: 3.640A pdb=" N ILE C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU C 66 " --> pdb=" O VAL C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 107 removed outlier: 3.790A pdb=" N ARG C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'C' and resid 141 through 148 removed outlier: 4.169A pdb=" N ASN C 148 " --> pdb=" O GLY C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 169 Processing helix chain 'C' and resid 175 through 220 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 227 through 254 removed outlier: 3.978A pdb=" N VAL C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) 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 257 through 276 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) removed outlier: 3.573A pdb=" N ARG C 276 " --> pdb=" O ALA C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 295 through 307 removed outlier: 3.558A pdb=" N TYR C 299 " --> pdb=" O SER C 295 " (cutoff:3.500A) 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 311 through 329 Processing helix chain 'C' and resid 337 through 352 removed outlier: 3.558A pdb=" N ILE C 341 " --> pdb=" O GLN C 337 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 371 removed outlier: 4.009A pdb=" N ILE C 361 " --> pdb=" O GLY C 357 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 370 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 387 Processing helix chain 'C' and resid 389 through 416 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) 706 hydrogen bonds defined for protein. 2118 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: 2.58 Time building geometry restraints manager: 2.84 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: 0.00 - 3.13: 12738 3.13 - 6.26: 222 6.26 - 9.39: 45 9.39 - 12.51: 6 12.51 - 15.64: 3 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: 8925 3.33 - 3.85: 15445 3.85 - 4.38: 16959 4.38 - 4.90: 30388 Nonbonded interactions: 74337 Sorted by model distance: nonbonded pdb=" O SER C 65 " pdb=" OG SER C 300 " model vdw 2.284 3.040 nonbonded pdb=" O SER A 65 " pdb=" OG SER A 300 " model vdw 2.284 3.040 nonbonded pdb=" O SER B 65 " pdb=" OG SER B 300 " model vdw 2.284 3.040 nonbonded pdb=" O GLN A 337 " pdb=" OG1 THR A 340 " model vdw 2.295 3.040 nonbonded pdb=" O GLN C 337 " pdb=" OG1 THR C 340 " model vdw 2.295 3.040 ... (remaining 74332 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 23.450 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.310 ------------------------------------------------------------------------------- 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= 0.482 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 to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.911 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: 0.1841 time to fit residues: 70.3960 Evaluate side-chains 204 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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: 1.9990 chunk 93 optimal weight: 8.9990 chunk 51 optimal weight: 0.0970 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 71 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 14 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.117005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.099174 restraints weight = 12612.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.101637 restraints weight = 7421.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.103451 restraints weight = 5174.963| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9567 Z= 0.169 Angle : 0.593 8.825 13014 Z= 0.293 Chirality : 0.038 0.136 1614 Planarity : 0.005 0.049 1593 Dihedral : 10.311 93.053 1440 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.16 % Allowed : 16.05 % Favored : 81.79 % 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 (0.22), residues: 1239 helix: 0.13 (0.15), residues: 984 sheet: None (None), residues: 0 loop : -2.81 (0.32), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 32 PHE 0.011 0.001 PHE B 323 TYR 0.013 0.001 TYR C 299 ARG 0.001 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 to be fit. rotamer outliers: 21 poor density : 234 time to evaluate : 0.847 Fit side-chains REVERT: A 33 TYR cc_start: 0.7790 (m-10) cc_final: 0.7560 (m-10) REVERT: A 269 MET cc_start: 0.8415 (mtp) cc_final: 0.8072 (mtm) REVERT: A 286 MET cc_start: 0.9062 (mtp) cc_final: 0.8830 (mtm) REVERT: A 362 MET cc_start: 0.8107 (mtp) cc_final: 0.7843 (mtp) REVERT: B 18 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8542 (mp) REVERT: B 128 PRO cc_start: 0.8340 (Cg_endo) cc_final: 0.8138 (Cg_exo) REVERT: B 362 MET cc_start: 0.7920 (mtp) cc_final: 0.7595 (ttm) REVERT: C 103 MET cc_start: 0.8791 (tpp) cc_final: 0.8568 (mmt) outliers start: 21 outliers final: 14 residues processed: 241 average time/residue: 0.1897 time to fit residues: 65.4547 Evaluate side-chains 232 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 217 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 18 ILE 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 332 HIS 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 115 optimal weight: 0.9990 chunk 37 optimal weight: 0.0670 chunk 84 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- 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 32 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS C 14 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.114589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.096644 restraints weight = 12900.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.099114 restraints weight = 7585.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.100895 restraints weight = 5278.424| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9567 Z= 0.208 Angle : 0.598 9.179 13014 Z= 0.293 Chirality : 0.039 0.133 1614 Planarity : 0.004 0.046 1593 Dihedral : 9.740 78.481 1440 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.37 % Allowed : 19.44 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.23), residues: 1239 helix: 0.99 (0.16), residues: 990 sheet: None (None), residues: 0 loop : -2.49 (0.34), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS B 32 PHE 0.009 0.001 PHE C 323 TYR 0.016 0.001 TYR C 299 ARG 0.004 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 244 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 221 time to evaluate : 0.958 Fit side-chains REVERT: A 269 MET cc_start: 0.8445 (mtp) cc_final: 0.8159 (mtm) REVERT: A 362 MET cc_start: 0.8094 (mtp) cc_final: 0.7873 (mtp) REVERT: B 340 THR cc_start: 0.9045 (p) cc_final: 0.8844 (p) REVERT: C 103 MET cc_start: 0.8827 (tpp) cc_final: 0.8567 (mmt) REVERT: C 136 ASP cc_start: 0.7555 (t0) cc_final: 0.7015 (t0) REVERT: C 286 MET cc_start: 0.8808 (mtm) cc_final: 0.8437 (mtp) outliers start: 23 outliers final: 17 residues processed: 231 average time/residue: 0.1953 time to fit residues: 64.3238 Evaluate side-chains 223 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL 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 133 ILE Chi-restraints excluded: chain C residue 332 HIS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 84 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 106 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 112 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 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 B 223 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN C 318 GLN C 337 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.116093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.098408 restraints weight = 12762.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.100931 restraints weight = 7605.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.102637 restraints weight = 5309.288| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9567 Z= 0.175 Angle : 0.581 12.733 13014 Z= 0.282 Chirality : 0.039 0.167 1614 Planarity : 0.004 0.043 1593 Dihedral : 9.280 67.851 1440 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.57 % Allowed : 21.09 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.24), residues: 1239 helix: 1.44 (0.16), residues: 987 sheet: None (None), residues: 0 loop : -2.41 (0.34), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 32 PHE 0.009 0.001 PHE B 323 TYR 0.014 0.001 TYR B 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 240 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 0.937 Fit side-chains REVERT: A 115 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7836 (pp) REVERT: A 194 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8853 (mmt) REVERT: A 269 MET cc_start: 0.8435 (mtp) cc_final: 0.8169 (mtm) REVERT: B 101 ILE cc_start: 0.9492 (mm) cc_final: 0.9221 (mm) REVERT: B 340 THR cc_start: 0.8997 (p) cc_final: 0.8743 (p) REVERT: B 362 MET cc_start: 0.8099 (mtp) cc_final: 0.7672 (ttm) REVERT: C 103 MET cc_start: 0.8775 (tpp) cc_final: 0.8526 (mmt) REVERT: C 134 LEU cc_start: 0.7856 (tt) cc_final: 0.7436 (mp) REVERT: C 136 ASP cc_start: 0.7429 (t0) cc_final: 0.6976 (t0) REVERT: C 286 MET cc_start: 0.8714 (mtm) cc_final: 0.8322 (mtp) outliers start: 25 outliers final: 19 residues processed: 226 average time/residue: 0.2058 time to fit residues: 65.7355 Evaluate side-chains 228 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 224 VAL 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 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 101 ILE Chi-restraints excluded: chain C residue 133 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 105 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 95 optimal weight: 0.0170 chunk 65 optimal weight: 1.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- 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 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.116216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.098542 restraints weight = 12789.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.100978 restraints weight = 7650.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.102668 restraints weight = 5372.605| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9567 Z= 0.179 Angle : 0.572 9.706 13014 Z= 0.279 Chirality : 0.039 0.131 1614 Planarity : 0.004 0.043 1593 Dihedral : 8.909 66.116 1440 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.50 % Allowed : 21.19 % Favored : 75.31 % 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: 1.33 (0.24), residues: 1239 helix: 1.67 (0.16), residues: 987 sheet: None (None), residues: 0 loop : -2.34 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 32 PHE 0.011 0.001 PHE B 323 TYR 0.013 0.001 TYR C 299 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 248 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 0.926 Fit side-chains REVERT: A 115 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7868 (pp) REVERT: A 194 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8870 (mmt) REVERT: A 269 MET cc_start: 0.8447 (mtp) cc_final: 0.8207 (mtm) REVERT: A 362 MET cc_start: 0.7837 (mtp) cc_final: 0.7419 (mtp) REVERT: B 136 ASP cc_start: 0.7375 (t0) cc_final: 0.6953 (t0) REVERT: B 169 MET cc_start: 0.8621 (mmm) cc_final: 0.7967 (mtp) REVERT: B 340 THR cc_start: 0.8973 (p) cc_final: 0.8692 (p) REVERT: C 123 GLN cc_start: 0.7808 (tm-30) cc_final: 0.7295 (tm-30) REVERT: C 136 ASP cc_start: 0.7343 (t0) cc_final: 0.6945 (t0) REVERT: C 227 GLU cc_start: 0.8165 (tp30) cc_final: 0.7948 (mm-30) REVERT: C 286 MET cc_start: 0.8743 (mtm) cc_final: 0.8348 (mtp) outliers start: 34 outliers final: 24 residues processed: 235 average time/residue: 0.1991 time to fit residues: 66.2137 Evaluate side-chains 236 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 332 HIS 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 133 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 198 VAL 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 332 HIS 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 91 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 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 223 HIS B 32 HIS B 223 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.114985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.097357 restraints weight = 12917.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.099772 restraints weight = 7605.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.101495 restraints weight = 5343.964| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2632 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= 0.200 Angle : 0.601 15.037 13014 Z= 0.290 Chirality : 0.039 0.144 1614 Planarity : 0.004 0.042 1593 Dihedral : 8.808 67.750 1440 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.91 % Allowed : 21.71 % 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: 1.44 (0.24), residues: 1239 helix: 1.71 (0.16), residues: 993 sheet: None (None), residues: 0 loop : -2.27 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 32 PHE 0.009 0.001 PHE B 323 TYR 0.019 0.001 TYR A 88 ARG 0.006 0.000 ARG A 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 256 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 218 time to evaluate : 0.959 Fit side-chains REVERT: A 269 MET cc_start: 0.8463 (mtp) cc_final: 0.8204 (mtm) REVERT: A 362 MET cc_start: 0.7900 (mtp) cc_final: 0.7372 (mtp) REVERT: B 136 ASP cc_start: 0.7464 (t0) cc_final: 0.7058 (t0) REVERT: B 169 MET cc_start: 0.8588 (mmm) cc_final: 0.8107 (mtp) REVERT: B 340 THR cc_start: 0.8952 (p) cc_final: 0.8672 (p) REVERT: B 362 MET cc_start: 0.8130 (mtp) cc_final: 0.7713 (ttm) REVERT: C 136 ASP cc_start: 0.7277 (t0) cc_final: 0.6892 (t0) REVERT: C 286 MET cc_start: 0.8725 (mtm) cc_final: 0.8311 (mtp) outliers start: 38 outliers final: 25 residues processed: 242 average time/residue: 0.1928 time to fit residues: 66.6449 Evaluate side-chains 234 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 224 VAL 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 138 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 335 VAL 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 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 9 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.114823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.097122 restraints weight = 12992.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.099574 restraints weight = 7628.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.101398 restraints weight = 5353.019| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2752 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= 0.200 Angle : 0.599 13.767 13014 Z= 0.291 Chirality : 0.039 0.142 1614 Planarity : 0.004 0.042 1593 Dihedral : 8.528 71.307 1440 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.81 % Allowed : 22.74 % Favored : 73.46 % 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: 1.58 (0.24), residues: 1239 helix: 1.83 (0.16), residues: 990 sheet: None (None), residues: 0 loop : -2.22 (0.36), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.000 HIS B 32 PHE 0.010 0.001 PHE C 323 TYR 0.016 0.001 TYR A 88 ARG 0.005 0.000 ARG A 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 253 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 1.032 Fit side-chains REVERT: A 269 MET cc_start: 0.8430 (mtp) cc_final: 0.8178 (mtm) REVERT: A 362 MET cc_start: 0.7878 (mtp) cc_final: 0.7372 (mtp) REVERT: B 136 ASP cc_start: 0.7365 (t0) cc_final: 0.6999 (t0) REVERT: B 169 MET cc_start: 0.8567 (mmm) cc_final: 0.7986 (mtm) REVERT: B 242 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.6980 (tp40) REVERT: B 340 THR cc_start: 0.8929 (p) cc_final: 0.8654 (p) REVERT: B 362 MET cc_start: 0.8180 (mtp) cc_final: 0.7715 (ttm) REVERT: C 123 GLN cc_start: 0.7744 (tm-30) cc_final: 0.7233 (tm-30) REVERT: C 136 ASP cc_start: 0.7306 (t0) cc_final: 0.6961 (t0) REVERT: C 241 LEU cc_start: 0.8693 (mp) cc_final: 0.8491 (mp) REVERT: C 286 MET cc_start: 0.8707 (mtm) cc_final: 0.8368 (mtp) outliers start: 37 outliers final: 30 residues processed: 240 average time/residue: 0.1931 time to fit residues: 66.3050 Evaluate side-chains 241 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 210 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 332 HIS 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 133 ILE 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 242 GLN Chi-restraints excluded: chain B residue 323 PHE Chi-restraints excluded: chain B residue 335 VAL 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 332 HIS 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 62 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 93 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 70 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS B 223 HIS ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS C 337 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.115571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.097962 restraints weight = 13044.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.100435 restraints weight = 7637.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.102259 restraints weight = 5320.366| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9567 Z= 0.187 Angle : 0.602 12.599 13014 Z= 0.291 Chirality : 0.039 0.135 1614 Planarity : 0.004 0.042 1593 Dihedral : 8.283 74.278 1440 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.60 % Allowed : 22.74 % Favored : 73.66 % 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: 1.71 (0.24), residues: 1239 helix: 1.88 (0.16), residues: 993 sheet: None (None), residues: 0 loop : -2.09 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 32 PHE 0.009 0.001 PHE A 323 TYR 0.022 0.001 TYR A 88 ARG 0.005 0.000 ARG A 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 248 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 213 time to evaluate : 1.130 Fit side-chains REVERT: A 269 MET cc_start: 0.8458 (mtp) cc_final: 0.8224 (mtm) REVERT: A 362 MET cc_start: 0.7832 (mtp) cc_final: 0.7347 (mtp) REVERT: B 136 ASP cc_start: 0.7407 (t0) cc_final: 0.7036 (t0) REVERT: B 169 MET cc_start: 0.8562 (mmm) cc_final: 0.7968 (mtm) REVERT: B 242 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.6951 (tp40) REVERT: B 362 MET cc_start: 0.8152 (mtp) cc_final: 0.7677 (ttm) REVERT: C 123 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7229 (tm-30) REVERT: C 136 ASP cc_start: 0.7294 (t0) cc_final: 0.6962 (t0) REVERT: C 286 MET cc_start: 0.8668 (mtm) cc_final: 0.8364 (mtp) outliers start: 35 outliers final: 30 residues processed: 233 average time/residue: 0.2025 time to fit residues: 66.9526 Evaluate side-chains 240 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 332 HIS 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 133 ILE 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 242 GLN Chi-restraints excluded: chain B residue 335 VAL 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 28 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 332 HIS 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 116 optimal weight: 4.9990 chunk 111 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 48 optimal weight: 0.0670 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.0870 chunk 4 optimal weight: 0.0270 overall best weight: 0.2554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS B 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.119288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.101800 restraints weight = 12822.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.104358 restraints weight = 7593.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.106138 restraints weight = 5282.922| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9567 Z= 0.154 Angle : 0.587 11.458 13014 Z= 0.284 Chirality : 0.039 0.168 1614 Planarity : 0.003 0.041 1593 Dihedral : 8.014 76.418 1440 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.19 % Allowed : 23.05 % Favored : 73.77 % 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: 1.89 (0.24), residues: 1239 helix: 2.04 (0.16), residues: 993 sheet: None (None), residues: 0 loop : -2.14 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.000 HIS B 32 PHE 0.007 0.001 PHE C 210 TYR 0.018 0.001 TYR A 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 256 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 225 time to evaluate : 0.892 Fit side-chains REVERT: A 18 ILE cc_start: 0.8698 (mt) cc_final: 0.8481 (mp) REVERT: A 30 LEU cc_start: 0.8982 (mt) cc_final: 0.8756 (mt) REVERT: A 194 MET cc_start: 0.8852 (mmt) cc_final: 0.8598 (mmp) REVERT: A 269 MET cc_start: 0.8408 (mtp) cc_final: 0.8177 (mtm) REVERT: A 362 MET cc_start: 0.7677 (mtp) cc_final: 0.7317 (mtp) REVERT: B 136 ASP cc_start: 0.7492 (t0) cc_final: 0.7092 (t0) REVERT: B 169 MET cc_start: 0.8457 (mmm) cc_final: 0.7830 (mtm) REVERT: B 242 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.6423 (tp40) REVERT: B 362 MET cc_start: 0.8012 (mtp) cc_final: 0.7646 (ttm) REVERT: C 13 LEU cc_start: 0.8259 (mt) cc_final: 0.8016 (mt) REVERT: C 136 ASP cc_start: 0.7277 (t0) cc_final: 0.6942 (t0) REVERT: C 215 TYR cc_start: 0.7987 (t80) cc_final: 0.7776 (t80) REVERT: C 286 MET cc_start: 0.8627 (mtm) cc_final: 0.8327 (mtp) outliers start: 31 outliers final: 25 residues processed: 246 average time/residue: 0.1801 time to fit residues: 63.9599 Evaluate side-chains 238 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 369 SER 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 133 ILE 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 242 GLN Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 VAL 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 332 HIS 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 89 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 78 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.117817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.100438 restraints weight = 12957.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.102876 restraints weight = 7674.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.104688 restraints weight = 5369.176| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9567 Z= 0.174 Angle : 0.616 16.052 13014 Z= 0.292 Chirality : 0.039 0.132 1614 Planarity : 0.003 0.041 1593 Dihedral : 7.943 76.326 1440 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.78 % Allowed : 24.59 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.24), residues: 1239 helix: 2.04 (0.16), residues: 999 sheet: None (None), residues: 0 loop : -1.77 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS B 32 PHE 0.007 0.001 PHE C 323 TYR 0.016 0.001 TYR A 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 239 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 0.954 Fit side-chains REVERT: A 18 ILE cc_start: 0.8696 (mt) cc_final: 0.8493 (mp) REVERT: A 30 LEU cc_start: 0.8941 (mt) cc_final: 0.8704 (mt) REVERT: A 362 MET cc_start: 0.7757 (mtp) cc_final: 0.7312 (mtp) REVERT: B 136 ASP cc_start: 0.7546 (t0) cc_final: 0.7166 (t0) REVERT: B 169 MET cc_start: 0.8472 (mmm) cc_final: 0.7889 (mtm) REVERT: B 217 MET cc_start: 0.9180 (tpp) cc_final: 0.8950 (tpp) REVERT: B 242 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.6396 (tp40) REVERT: B 261 PHE cc_start: 0.8995 (t80) cc_final: 0.8737 (t80) REVERT: B 362 MET cc_start: 0.8088 (mtp) cc_final: 0.7619 (ttm) REVERT: C 13 LEU cc_start: 0.8293 (mt) cc_final: 0.8028 (mt) REVERT: C 136 ASP cc_start: 0.7245 (t0) cc_final: 0.6924 (t0) REVERT: C 215 TYR cc_start: 0.8001 (t80) cc_final: 0.7768 (t80) REVERT: C 286 MET cc_start: 0.8736 (mtm) cc_final: 0.8409 (mtp) outliers start: 27 outliers final: 26 residues processed: 231 average time/residue: 0.1988 time to fit residues: 65.9578 Evaluate side-chains 238 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 369 SER 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 133 ILE 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 242 GLN Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 402 VAL 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 332 HIS Chi-restraints excluded: chain C residue 340 THR 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 112 optimal weight: 0.5980 chunk 9 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 0.0770 chunk 61 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.118300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.100855 restraints weight = 12932.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.103262 restraints weight = 7681.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.105066 restraints weight = 5398.095| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9567 Z= 0.172 Angle : 0.613 16.408 13014 Z= 0.292 Chirality : 0.039 0.131 1614 Planarity : 0.003 0.041 1593 Dihedral : 7.900 76.966 1440 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.09 % Allowed : 24.38 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.24), residues: 1239 helix: 2.07 (0.16), residues: 999 sheet: None (None), residues: 0 loop : -1.69 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.000 HIS B 32 PHE 0.007 0.001 PHE C 323 TYR 0.016 0.001 TYR A 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: 2731.90 seconds wall clock time: 50 minutes 2.31 seconds (3002.31 seconds total)