Starting phenix.real_space_refine on Fri Jul 19 02:29:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgm_41241/07_2024/8tgm_41241_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgm_41241/07_2024/8tgm_41241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgm_41241/07_2024/8tgm_41241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgm_41241/07_2024/8tgm_41241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgm_41241/07_2024/8tgm_41241_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgm_41241/07_2024/8tgm_41241_trim.cif" } resolution = 3.5 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= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 3878 2.51 5 N 900 2.21 5 O 990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 224": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 5826 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2869 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 21, 'TRANS': 362} Chain breaks: 2 Chain: "B" Number of atoms: 2869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2869 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 21, 'TRANS': 362} Chain breaks: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.52, per 1000 atoms: 1.12 Number of scatterers: 5826 At special positions: 0 Unit cell: (73.04, 65.736, 114.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 990 8.00 N 900 7.00 C 3878 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: 2.59 Conformation dependent library (CDL) restraints added in 1.6 seconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1368 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 90.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 21 through 40 removed outlier: 3.738A pdb=" N VAL A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 54 Processing helix chain 'A' and resid 131 through 144 removed outlier: 4.004A pdb=" N GLU A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N THR A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ARG A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 165 Proline residue: A 155 - end of helix removed outlier: 4.369A pdb=" N GLY A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Proline residue: A 159 - end of helix Processing helix chain 'A' and resid 166 through 187 Processing helix chain 'A' and resid 189 through 219 removed outlier: 3.683A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 254 removed outlier: 4.082A pdb=" N ARG A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Proline residue: A 245 - end of helix removed outlier: 4.051A pdb=" N SER A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.533A pdb=" N LEU A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N CYS A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 299 through 318 removed outlier: 3.895A pdb=" N ALA A 305 " --> pdb=" O TYR A 301 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 330 Processing helix chain 'A' and resid 334 through 341 removed outlier: 3.877A pdb=" N LEU A 338 " --> pdb=" O LYS A 335 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLY A 339 " --> pdb=" O TRP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 364 removed outlier: 3.664A pdb=" N TYR A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASN A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYS A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N MET A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 383 removed outlier: 3.542A pdb=" N LEU A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 376 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY A 377 " --> pdb=" O MET A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 388 through 391 Processing helix chain 'A' and resid 392 through 422 removed outlier: 4.155A pdb=" N MET A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 427 through 455 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 456 through 472 removed outlier: 3.692A pdb=" N LEU A 460 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET A 461 " --> pdb=" O PHE A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.535A pdb=" N ARG A 479 " --> pdb=" O TYR A 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 54 removed outlier: 3.971A pdb=" N VAL B 23 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Proline residue: B 43 - end of helix Proline residue: B 46 - end of helix removed outlier: 3.720A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 165 removed outlier: 4.098A pdb=" N GLU B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N THR B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA B 144 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER B 145 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) Proline residue: B 155 - end of helix removed outlier: 4.338A pdb=" N GLY B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 166 through 187 removed outlier: 3.523A pdb=" N MET B 170 " --> pdb=" O TYR B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 219 removed outlier: 3.861A pdb=" N LEU B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 244 removed outlier: 3.765A pdb=" N GLY B 226 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG B 227 " --> pdb=" O HIS B 223 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 254 removed outlier: 3.782A pdb=" N GLU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE B 253 " --> pdb=" O VAL B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.593A pdb=" N LEU B 261 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS B 276 " --> pdb=" O ALA B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 299 through 318 removed outlier: 3.511A pdb=" N ALA B 305 " --> pdb=" O TYR B 301 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 330 Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.505A pdb=" N ALA B 341 " --> pdb=" O LEU B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 342 through 360 removed outlier: 3.835A pdb=" N TYR B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 383 removed outlier: 3.522A pdb=" N CYS B 368 " --> pdb=" O GLY B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 388 through 391 Processing helix chain 'B' and resid 392 through 422 removed outlier: 4.115A pdb=" N MET B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) Proline residue: B 412 - end of helix Processing helix chain 'B' and resid 427 through 455 removed outlier: 3.681A pdb=" N ILE B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Proline residue: B 445 - end of helix removed outlier: 3.875A pdb=" N ALA B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 472 removed outlier: 3.700A pdb=" N LEU B 460 " --> pdb=" O GLY B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 479 removed outlier: 3.634A pdb=" N TYR B 477 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 479 " --> pdb=" O TYR B 476 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 868 1.29 - 1.42: 1554 1.42 - 1.55: 3447 1.55 - 1.68: 3 1.68 - 1.81: 102 Bond restraints: 5974 Sorted by residual: bond pdb=" C PRO A 481 " pdb=" O PRO A 481 " ideal model delta sigma weight residual 1.240 1.161 0.080 1.12e-02 7.97e+03 5.06e+01 bond pdb=" C31 YHR A 601 " pdb=" O30 YHR A 601 " ideal model delta sigma weight residual 1.326 1.406 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C31 YHR B 601 " pdb=" O30 YHR B 601 " ideal model delta sigma weight residual 1.326 1.403 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C17 YHR B 601 " pdb=" O19 YHR B 601 " ideal model delta sigma weight residual 1.325 1.399 -0.074 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C PRO B 481 " pdb=" O PRO B 481 " ideal model delta sigma weight residual 1.240 1.200 0.041 1.12e-02 7.97e+03 1.33e+01 ... (remaining 5969 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.74: 228 106.74 - 114.20: 3430 114.20 - 121.67: 3420 121.67 - 129.13: 1023 129.13 - 136.60: 39 Bond angle restraints: 8140 Sorted by residual: angle pdb=" C PRO B 482 " pdb=" CA PRO B 482 " pdb=" CB PRO B 482 " ideal model delta sigma weight residual 111.46 102.41 9.05 1.29e+00 6.01e-01 4.92e+01 angle pdb=" N ARG B 225 " pdb=" CA ARG B 225 " pdb=" C ARG B 225 " ideal model delta sigma weight residual 111.28 104.37 6.91 1.09e+00 8.42e-01 4.02e+01 angle pdb=" C7 YHR A 601 " pdb=" N8 YHR A 601 " pdb=" C9 YHR A 601 " ideal model delta sigma weight residual 111.89 130.73 -18.84 3.00e+00 1.11e-01 3.95e+01 angle pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C9 YHR B 601 " ideal model delta sigma weight residual 111.89 130.67 -18.78 3.00e+00 1.11e-01 3.92e+01 angle pdb=" C PRO A 481 " pdb=" N PRO A 482 " pdb=" CA PRO A 482 " ideal model delta sigma weight residual 120.98 115.56 5.42 1.07e+00 8.73e-01 2.56e+01 ... (remaining 8135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.89: 3150 22.89 - 45.78: 333 45.78 - 68.66: 35 68.66 - 91.55: 14 91.55 - 114.44: 2 Dihedral angle restraints: 3534 sinusoidal: 1380 harmonic: 2154 Sorted by residual: dihedral pdb=" C PRO B 482 " pdb=" N PRO B 482 " pdb=" CA PRO B 482 " pdb=" CB PRO B 482 " ideal model delta harmonic sigma weight residual -120.70 -110.63 -10.07 0 2.50e+00 1.60e-01 1.62e+01 dihedral pdb=" C13 YHR A 601 " pdb=" C7 YHR A 601 " pdb=" N8 YHR A 601 " pdb=" C6 YHR A 601 " ideal model delta sinusoidal sigma weight residual 57.66 -56.78 114.44 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" C13 YHR B 601 " pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C6 YHR B 601 " ideal model delta sinusoidal sigma weight residual 57.66 -56.10 113.76 1 3.00e+01 1.11e-03 1.50e+01 ... (remaining 3531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 874 0.082 - 0.165: 93 0.165 - 0.247: 4 0.247 - 0.329: 1 0.329 - 0.411: 2 Chirality restraints: 974 Sorted by residual: chirality pdb=" C13 YHR A 601 " pdb=" C12 YHR A 601 " pdb=" C14 YHR A 601 " pdb=" N8 YHR A 601 " both_signs ideal model delta sigma weight residual False -2.29 -2.70 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" C13 YHR B 601 " pdb=" C12 YHR B 601 " pdb=" C14 YHR B 601 " pdb=" N8 YHR B 601 " both_signs ideal model delta sigma weight residual False -2.29 -2.69 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA PHE A 131 " pdb=" N PHE A 131 " pdb=" C PHE A 131 " pdb=" CB PHE A 131 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 971 not shown) Planarity restraints: 988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 472 " 0.062 5.00e-02 4.00e+02 9.41e-02 1.42e+01 pdb=" N PRO B 473 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO B 473 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 473 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 426 " 0.015 2.00e-02 2.50e+03 2.16e-02 9.33e+00 pdb=" CG TYR A 426 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 426 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 426 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR A 426 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 426 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 426 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 426 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 42 " 0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO B 43 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 43 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 43 " 0.041 5.00e-02 4.00e+02 ... (remaining 985 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1653 2.80 - 3.33: 5569 3.33 - 3.85: 9526 3.85 - 4.38: 10285 4.38 - 4.90: 18577 Nonbonded interactions: 45610 Sorted by model distance: nonbonded pdb=" O THR B 291 " pdb=" OG1 THR B 291 " model vdw 2.279 2.440 nonbonded pdb=" OE1 GLU A 135 " pdb=" NH1 ARG A 138 " model vdw 2.283 2.520 nonbonded pdb=" O ARG A 365 " pdb=" OG SER A 409 " model vdw 2.309 2.440 nonbonded pdb=" O GLY A 158 " pdb=" OG1 THR A 161 " model vdw 2.325 2.440 nonbonded pdb=" OG1 THR A 291 " pdb=" O THR A 423 " model vdw 2.347 2.440 ... (remaining 45605 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' } 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: 5.170 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.600 Find NCS groups from input model: 0.220 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 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 0.080 5974 Z= 0.426 Angle : 0.973 18.843 8140 Z= 0.523 Chirality : 0.052 0.411 974 Planarity : 0.009 0.094 988 Dihedral : 17.986 114.441 2166 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.04 % Favored : 96.83 % Rotamer: Outliers : 0.65 % Allowed : 32.41 % Favored : 66.94 % Cbeta Deviations : 0.15 % 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: 0.63 (0.30), residues: 756 helix: 1.09 (0.21), residues: 578 sheet: None (None), residues: 0 loop : -1.73 (0.41), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.005 0.001 HIS A 387 PHE 0.019 0.002 PHE B 265 TYR 0.052 0.002 TYR A 426 ARG 0.010 0.001 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 137 time to evaluate : 0.617 Fit side-chains REVERT: A 439 MET cc_start: 0.8235 (tpp) cc_final: 0.7662 (mpp) REVERT: B 163 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7453 (mtp180) REVERT: B 229 MET cc_start: 0.7887 (mmm) cc_final: 0.7625 (mmm) REVERT: B 373 MET cc_start: 0.7738 (mtp) cc_final: 0.7413 (mtp) REVERT: B 482 PRO cc_start: 0.8860 (Cg_exo) cc_final: 0.8607 (Cg_endo) outliers start: 4 outliers final: 3 residues processed: 138 average time/residue: 0.1232 time to fit residues: 24.5249 Evaluate side-chains 130 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 163 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 31 optimal weight: 0.0270 chunk 19 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 23 optimal weight: 0.0040 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.0370 chunk 69 optimal weight: 0.7980 overall best weight: 0.2128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 329 GLN B 35 ASN B 329 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5974 Z= 0.170 Angle : 0.665 7.632 8140 Z= 0.315 Chirality : 0.042 0.143 974 Planarity : 0.006 0.057 988 Dihedral : 7.071 53.202 944 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.07 % Allowed : 28.66 % Favored : 67.26 % 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: 1.75 (0.31), residues: 756 helix: 1.85 (0.22), residues: 590 sheet: None (None), residues: 0 loop : -1.39 (0.45), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 459 HIS 0.001 0.000 HIS B 223 PHE 0.015 0.001 PHE A 356 TYR 0.008 0.001 TYR B 219 ARG 0.006 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 0.593 Fit side-chains REVERT: A 168 ILE cc_start: 0.8098 (mp) cc_final: 0.7879 (mm) REVERT: A 174 PHE cc_start: 0.8035 (t80) cc_final: 0.7746 (t80) REVERT: A 381 LEU cc_start: 0.8308 (mp) cc_final: 0.7900 (mp) REVERT: B 229 MET cc_start: 0.7891 (mmm) cc_final: 0.7374 (mmm) REVERT: B 245 PRO cc_start: 0.8358 (Cg_endo) cc_final: 0.8048 (Cg_exo) REVERT: B 261 LEU cc_start: 0.7924 (mm) cc_final: 0.7673 (mm) REVERT: B 274 GLN cc_start: 0.7719 (pt0) cc_final: 0.7096 (pt0) REVERT: B 373 MET cc_start: 0.7742 (mtp) cc_final: 0.7380 (mtp) outliers start: 25 outliers final: 8 residues processed: 152 average time/residue: 0.1266 time to fit residues: 27.2040 Evaluate side-chains 143 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 240 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 ASN B 313 ASN B 361 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5974 Z= 0.297 Angle : 0.681 7.101 8140 Z= 0.327 Chirality : 0.045 0.189 974 Planarity : 0.006 0.047 988 Dihedral : 6.230 51.432 938 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.05 % Allowed : 27.20 % Favored : 67.75 % 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: 1.60 (0.32), residues: 756 helix: 1.82 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -2.19 (0.42), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 366 HIS 0.001 0.000 HIS A 416 PHE 0.017 0.001 PHE B 356 TYR 0.013 0.001 TYR A 190 ARG 0.003 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 0.608 Fit side-chains REVERT: A 174 PHE cc_start: 0.8133 (t80) cc_final: 0.7871 (t80) REVERT: A 296 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8262 (mp) REVERT: A 340 LEU cc_start: 0.7857 (mt) cc_final: 0.7477 (mp) REVERT: A 381 LEU cc_start: 0.8336 (mp) cc_final: 0.7927 (mp) REVERT: B 229 MET cc_start: 0.7863 (mmm) cc_final: 0.7591 (mmm) REVERT: B 261 LEU cc_start: 0.8004 (mm) cc_final: 0.7751 (mm) REVERT: B 274 GLN cc_start: 0.7834 (pt0) cc_final: 0.7282 (pt0) REVERT: B 295 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7045 (mpp) REVERT: B 331 MET cc_start: 0.7921 (mtt) cc_final: 0.7582 (mtt) REVERT: B 373 MET cc_start: 0.7815 (mtp) cc_final: 0.7520 (mtp) outliers start: 31 outliers final: 13 residues processed: 151 average time/residue: 0.1222 time to fit residues: 26.3866 Evaluate side-chains 149 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 447 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 46 optimal weight: 0.3980 chunk 69 optimal weight: 0.0870 chunk 73 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN A 200 GLN B 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5974 Z= 0.202 Angle : 0.649 8.143 8140 Z= 0.305 Chirality : 0.043 0.155 974 Planarity : 0.005 0.042 988 Dihedral : 5.903 53.334 938 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.54 % Allowed : 27.69 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.32), residues: 756 helix: 1.91 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -2.03 (0.43), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 366 HIS 0.001 0.000 HIS A 387 PHE 0.016 0.001 PHE B 356 TYR 0.010 0.001 TYR B 476 ARG 0.002 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 0.597 Fit side-chains REVERT: A 40 VAL cc_start: 0.8012 (OUTLIER) cc_final: 0.7802 (p) REVERT: A 149 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7408 (ttm) REVERT: A 174 PHE cc_start: 0.8104 (t80) cc_final: 0.7803 (t80) REVERT: A 245 PRO cc_start: 0.8621 (Cg_endo) cc_final: 0.8394 (Cg_exo) REVERT: A 340 LEU cc_start: 0.7822 (mt) cc_final: 0.7447 (mp) REVERT: A 381 LEU cc_start: 0.8354 (mp) cc_final: 0.8038 (mp) REVERT: B 261 LEU cc_start: 0.7986 (mm) cc_final: 0.7762 (mm) REVERT: B 295 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7149 (mpp) REVERT: B 331 MET cc_start: 0.7908 (mtt) cc_final: 0.7563 (mtt) REVERT: B 373 MET cc_start: 0.7823 (mtp) cc_final: 0.7502 (mtp) outliers start: 34 outliers final: 19 residues processed: 155 average time/residue: 0.1124 time to fit residues: 25.5222 Evaluate side-chains 151 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 447 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.0770 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5974 Z= 0.235 Angle : 0.646 7.271 8140 Z= 0.307 Chirality : 0.043 0.148 974 Planarity : 0.006 0.064 988 Dihedral : 5.778 54.099 938 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.70 % Allowed : 28.34 % Favored : 65.96 % 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: 1.77 (0.32), residues: 756 helix: 1.91 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -2.01 (0.43), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.001 0.000 HIS A 416 PHE 0.020 0.001 PHE B 356 TYR 0.012 0.001 TYR B 476 ARG 0.002 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 138 time to evaluate : 0.594 Fit side-chains REVERT: A 149 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7468 (ttm) REVERT: A 174 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7838 (t80) REVERT: A 245 PRO cc_start: 0.8614 (Cg_endo) cc_final: 0.8374 (Cg_exo) REVERT: A 340 LEU cc_start: 0.7843 (mt) cc_final: 0.7510 (mp) REVERT: A 381 LEU cc_start: 0.8365 (mp) cc_final: 0.8047 (mp) REVERT: B 245 PRO cc_start: 0.8314 (Cg_endo) cc_final: 0.8016 (Cg_exo) REVERT: B 261 LEU cc_start: 0.7975 (mm) cc_final: 0.7758 (mm) REVERT: B 295 MET cc_start: 0.7507 (OUTLIER) cc_final: 0.7079 (mpp) REVERT: B 331 MET cc_start: 0.7970 (mtt) cc_final: 0.7611 (mtt) REVERT: B 373 MET cc_start: 0.7825 (mtp) cc_final: 0.7511 (mtp) outliers start: 35 outliers final: 20 residues processed: 153 average time/residue: 0.1106 time to fit residues: 24.7478 Evaluate side-chains 158 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 135 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 447 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 73 optimal weight: 0.0970 chunk 61 optimal weight: 0.1980 chunk 34 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 70 optimal weight: 0.0470 overall best weight: 0.2676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5974 Z= 0.164 Angle : 0.616 7.662 8140 Z= 0.291 Chirality : 0.041 0.139 974 Planarity : 0.005 0.055 988 Dihedral : 5.597 54.391 936 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 5.05 % Allowed : 30.13 % Favored : 64.82 % 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: 1.93 (0.32), residues: 756 helix: 2.05 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -2.09 (0.42), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.001 0.000 HIS A 387 PHE 0.016 0.001 PHE B 356 TYR 0.007 0.001 TYR B 190 ARG 0.001 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 0.585 Fit side-chains REVERT: A 174 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7716 (t80) REVERT: A 340 LEU cc_start: 0.7783 (mt) cc_final: 0.7472 (mp) REVERT: A 381 LEU cc_start: 0.8393 (mp) cc_final: 0.8063 (mp) REVERT: A 479 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6798 (ptt-90) REVERT: B 245 PRO cc_start: 0.8226 (Cg_endo) cc_final: 0.7915 (Cg_exo) REVERT: B 261 LEU cc_start: 0.7970 (mm) cc_final: 0.7746 (mm) REVERT: B 295 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7161 (mpp) REVERT: B 331 MET cc_start: 0.7880 (mtt) cc_final: 0.7633 (mmt) REVERT: B 370 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7510 (tt) REVERT: B 373 MET cc_start: 0.7814 (mtp) cc_final: 0.7492 (mtp) outliers start: 31 outliers final: 17 residues processed: 150 average time/residue: 0.1180 time to fit residues: 25.5688 Evaluate side-chains 153 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 132 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 447 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 73 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 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 274 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5974 Z= 0.242 Angle : 0.662 8.207 8140 Z= 0.311 Chirality : 0.044 0.159 974 Planarity : 0.006 0.063 988 Dihedral : 5.800 55.870 936 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.21 % Allowed : 31.60 % Favored : 63.19 % 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: 1.84 (0.32), residues: 756 helix: 1.99 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -2.12 (0.42), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 366 HIS 0.001 0.000 HIS A 416 PHE 0.014 0.001 PHE B 246 TYR 0.012 0.001 TYR B 476 ARG 0.002 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 0.596 Fit side-chains REVERT: A 174 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7801 (t80) REVERT: A 340 LEU cc_start: 0.7849 (mt) cc_final: 0.7521 (mp) REVERT: A 371 ILE cc_start: 0.7986 (mm) cc_final: 0.7640 (mt) REVERT: A 381 LEU cc_start: 0.8402 (mp) cc_final: 0.8088 (mp) REVERT: A 410 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7225 (mmt) REVERT: A 479 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.6884 (ptt-90) REVERT: B 245 PRO cc_start: 0.8256 (Cg_endo) cc_final: 0.7941 (Cg_exo) REVERT: B 261 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7736 (mm) REVERT: B 295 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7157 (mpp) REVERT: B 370 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7626 (tt) REVERT: B 373 MET cc_start: 0.7830 (mtp) cc_final: 0.7549 (mtp) outliers start: 32 outliers final: 20 residues processed: 149 average time/residue: 0.1205 time to fit residues: 25.7982 Evaluate side-chains 157 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 447 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5974 Z= 0.247 Angle : 0.657 7.423 8140 Z= 0.313 Chirality : 0.044 0.223 974 Planarity : 0.006 0.056 988 Dihedral : 5.794 57.847 936 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.72 % Allowed : 31.76 % Favored : 63.52 % 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: 1.78 (0.32), residues: 756 helix: 1.95 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -2.09 (0.42), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 366 HIS 0.001 0.000 HIS A 416 PHE 0.016 0.001 PHE B 246 TYR 0.013 0.001 TYR B 476 ARG 0.002 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 0.595 Fit side-chains REVERT: A 174 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7869 (t80) REVERT: A 340 LEU cc_start: 0.7876 (mt) cc_final: 0.7545 (mp) REVERT: A 371 ILE cc_start: 0.8001 (mm) cc_final: 0.7641 (mt) REVERT: A 381 LEU cc_start: 0.8400 (mp) cc_final: 0.8092 (mp) REVERT: A 410 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7243 (mmt) REVERT: A 439 MET cc_start: 0.8190 (tpp) cc_final: 0.7833 (mpp) REVERT: A 479 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6928 (ptt-90) REVERT: B 245 PRO cc_start: 0.8275 (Cg_endo) cc_final: 0.7947 (Cg_exo) REVERT: B 257 SER cc_start: 0.8642 (m) cc_final: 0.8277 (p) REVERT: B 261 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7813 (mm) REVERT: B 295 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7074 (mpp) REVERT: B 373 MET cc_start: 0.7837 (mtp) cc_final: 0.7547 (mtp) outliers start: 29 outliers final: 19 residues processed: 145 average time/residue: 0.1196 time to fit residues: 25.0685 Evaluate side-chains 155 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 447 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.0670 chunk 68 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 34 optimal weight: 0.0970 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 0.0070 overall best weight: 0.2134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5974 Z= 0.162 Angle : 0.624 7.332 8140 Z= 0.295 Chirality : 0.041 0.142 974 Planarity : 0.006 0.054 988 Dihedral : 5.675 56.612 936 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.75 % Allowed : 33.22 % Favored : 63.03 % 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: 1.91 (0.32), residues: 756 helix: 2.03 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -2.12 (0.42), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.001 0.000 HIS A 387 PHE 0.014 0.001 PHE A 356 TYR 0.007 0.001 TYR B 190 ARG 0.002 0.000 ARG A 479 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 0.597 Fit side-chains REVERT: A 174 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7701 (t80) REVERT: A 340 LEU cc_start: 0.7779 (mt) cc_final: 0.7467 (mp) REVERT: A 371 ILE cc_start: 0.7972 (mm) cc_final: 0.7615 (mt) REVERT: A 381 LEU cc_start: 0.8425 (mp) cc_final: 0.8092 (mp) REVERT: A 410 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7254 (mmt) REVERT: B 245 PRO cc_start: 0.8102 (Cg_endo) cc_final: 0.7797 (Cg_exo) REVERT: B 261 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7739 (mm) REVERT: B 295 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.7161 (mpp) REVERT: B 373 MET cc_start: 0.7811 (mtp) cc_final: 0.7488 (mtp) outliers start: 23 outliers final: 14 residues processed: 140 average time/residue: 0.1177 time to fit residues: 24.1774 Evaluate side-chains 148 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 447 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.9990 chunk 60 optimal weight: 0.0030 chunk 6 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.1980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5974 Z= 0.196 Angle : 0.647 7.845 8140 Z= 0.301 Chirality : 0.042 0.159 974 Planarity : 0.006 0.071 988 Dihedral : 5.853 57.654 936 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.26 % Allowed : 33.39 % Favored : 63.36 % 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: 1.94 (0.32), residues: 756 helix: 2.03 (0.22), residues: 608 sheet: None (None), residues: 0 loop : -2.03 (0.42), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 366 HIS 0.001 0.000 HIS A 422 PHE 0.015 0.001 PHE A 356 TYR 0.010 0.001 TYR B 476 ARG 0.002 0.000 ARG A 479 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 0.634 Fit side-chains REVERT: A 174 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7783 (t80) REVERT: A 340 LEU cc_start: 0.7802 (mt) cc_final: 0.7482 (mp) REVERT: A 371 ILE cc_start: 0.7970 (mm) cc_final: 0.7609 (mt) REVERT: A 381 LEU cc_start: 0.8422 (mp) cc_final: 0.8095 (mp) REVERT: A 410 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7264 (mmt) REVERT: A 479 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6833 (ptt-90) REVERT: B 245 PRO cc_start: 0.8134 (Cg_endo) cc_final: 0.7814 (Cg_exo) REVERT: B 261 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7786 (mm) REVERT: B 295 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.7150 (mpp) REVERT: B 373 MET cc_start: 0.7814 (mtp) cc_final: 0.7489 (mtp) outliers start: 20 outliers final: 14 residues processed: 141 average time/residue: 0.1213 time to fit residues: 24.6579 Evaluate side-chains 152 residues out of total 614 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 410 MET Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 447 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 40 optimal weight: 0.0270 chunk 51 optimal weight: 0.7980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.117292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.106532 restraints weight = 7958.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.109471 restraints weight = 3862.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.111357 restraints weight = 2264.433| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5974 Z= 0.216 Angle : 0.652 8.026 8140 Z= 0.306 Chirality : 0.044 0.188 974 Planarity : 0.006 0.070 988 Dihedral : 5.897 58.806 936 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.58 % Allowed : 33.06 % Favored : 63.36 % 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: 1.84 (0.31), residues: 756 helix: 2.00 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -2.11 (0.41), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 366 HIS 0.001 0.000 HIS A 422 PHE 0.018 0.001 PHE B 246 TYR 0.011 0.001 TYR B 476 ARG 0.004 0.000 ARG A 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1626.16 seconds wall clock time: 29 minutes 57.18 seconds (1797.18 seconds total)