Starting phenix.real_space_refine on Fri Jul 19 02:10:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgg_41235/07_2024/8tgg_41235_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgg_41235/07_2024/8tgg_41235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgg_41235/07_2024/8tgg_41235.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgg_41235/07_2024/8tgg_41235.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgg_41235/07_2024/8tgg_41235_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgg_41235/07_2024/8tgg_41235_trim.cif" } resolution = 3.6 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= 0.019 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 57 5.16 5 C 3802 2.51 5 N 888 2.21 5 O 970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 5717 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2856 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 359} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2804 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 21, 'TRANS': 353} Chain breaks: 2 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'WRF': 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: 4.54, per 1000 atoms: 0.79 Number of scatterers: 5717 At special positions: 0 Unit cell: (76.1387, 64.6293, 115.093, 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 57 16.00 O 970 8.00 N 888 7.00 C 3802 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: 2.50 Conformation dependent library (CDL) restraints added in 1.0 seconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 89.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 19 through 41 removed outlier: 4.023A pdb=" N LEU A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 39 " --> pdb=" O ASN A 35 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 51 removed outlier: 3.614A pdb=" N TYR A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 144 Processing helix chain 'A' and resid 144 through 154 Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 166 through 187 removed outlier: 3.707A pdb=" N MET A 170 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 219 removed outlier: 3.906A pdb=" N VAL A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 254 removed outlier: 4.013A pdb=" N ARG A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Proline residue: A 245 - end of helix Processing helix chain 'A' and resid 256 through 278 removed outlier: 4.550A pdb=" N PHE A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 removed outlier: 3.634A pdb=" N LEU A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 297' Processing helix chain 'A' and resid 299 through 320 removed outlier: 3.681A pdb=" N GLY A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 317 " --> pdb=" O ASN A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 331 removed outlier: 3.582A pdb=" N TRP A 326 " --> pdb=" O THR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.158A pdb=" N PHE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 364 removed outlier: 5.050A pdb=" N ASN A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LYS A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 383 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 421 Proline residue: A 412 - end of helix removed outlier: 4.159A pdb=" N GLY A 415 " --> pdb=" O MET A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 455 removed outlier: 3.517A pdb=" N TYR A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) Proline residue: A 445 - end of helix removed outlier: 4.803A pdb=" N GLY A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ALA A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 470 Processing helix chain 'A' and resid 471 through 480 removed outlier: 3.828A pdb=" N TYR A 476 " --> pdb=" O PRO A 473 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG A 479 " --> pdb=" O TYR A 476 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER A 480 " --> pdb=" O TYR A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 42 removed outlier: 3.602A pdb=" N PHE B 38 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 removed outlier: 3.628A pdb=" N MET B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 154 removed outlier: 4.289A pdb=" N GLU B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N THR B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ARG B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 165 removed outlier: 3.644A pdb=" N LEU B 160 " --> pdb=" O PHE B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 187 removed outlier: 3.567A pdb=" N MET B 170 " --> pdb=" O TYR B 166 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 219 removed outlier: 3.840A pdb=" N LEU B 193 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 194 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 195 " --> pdb=" O THR B 191 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 250 removed outlier: 4.006A pdb=" N ARG B 227 " --> pdb=" O HIS B 223 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Proline residue: B 245 - end of helix removed outlier: 4.197A pdb=" N SER B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 276 removed outlier: 3.538A pdb=" N ALA B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 331 removed outlier: 4.215A pdb=" N GLY B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU B 320 " --> pdb=" O VAL B 316 " (cutoff:3.500A) Proline residue: B 321 - end of helix Proline residue: B 324 - end of helix Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 342 through 360 removed outlier: 3.698A pdb=" N TYR B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 383 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 Proline residue: B 412 - end of helix removed outlier: 3.568A pdb=" N ARG B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 455 removed outlier: 3.648A pdb=" N ALA B 431 " --> pdb=" O GLY B 427 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) Proline residue: B 445 - end of helix removed outlier: 3.745A pdb=" N ALA B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 472 Processing helix chain 'B' and resid 473 through 479 removed outlier: 3.844A pdb=" N TYR B 476 " --> pdb=" O PRO B 473 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR B 477 " --> pdb=" O LEU B 474 " (cutoff:3.500A) 440 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: 1.68 Time building geometry restraints manager: 2.70 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: 855 1.29 - 1.42: 1510 1.42 - 1.55: 3393 1.55 - 1.69: 2 1.69 - 1.82: 100 Bond restraints: 5860 Sorted by residual: bond pdb=" C VAL A 466 " pdb=" O VAL A 466 " ideal model delta sigma weight residual 1.237 1.161 0.076 1.17e-02 7.31e+03 4.25e+01 bond pdb=" C PRO A 473 " pdb=" O PRO A 473 " ideal model delta sigma weight residual 1.238 1.156 0.082 1.42e-02 4.96e+03 3.30e+01 bond pdb=" C ILE A 469 " pdb=" O ILE A 469 " ideal model delta sigma weight residual 1.237 1.166 0.071 1.29e-02 6.01e+03 3.03e+01 bond pdb=" C ALA A 472 " pdb=" O ALA A 472 " ideal model delta sigma weight residual 1.244 1.197 0.046 1.00e-02 1.00e+04 2.12e+01 bond pdb=" C TYR A 476 " pdb=" O TYR A 476 " ideal model delta sigma weight residual 1.235 1.180 0.055 1.26e-02 6.30e+03 1.90e+01 ... (remaining 5855 not shown) Histogram of bond angle deviations from ideal: 98.40 - 105.92: 195 105.92 - 113.44: 3218 113.44 - 120.96: 3225 120.96 - 128.49: 1301 128.49 - 136.01: 43 Bond angle restraints: 7982 Sorted by residual: angle pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C9 YHR B 601 " ideal model delta sigma weight residual 111.89 129.90 -18.01 3.00e+00 1.11e-01 3.60e+01 angle pdb=" CA VAL A 466 " pdb=" C VAL A 466 " pdb=" O VAL A 466 " ideal model delta sigma weight residual 120.95 115.35 5.60 1.04e+00 9.25e-01 2.90e+01 angle pdb=" N TYR A 50 " pdb=" CA TYR A 50 " pdb=" C TYR A 50 " ideal model delta sigma weight residual 111.28 105.59 5.69 1.09e+00 8.42e-01 2.72e+01 angle pdb=" N LEU A 49 " pdb=" CA LEU A 49 " pdb=" C LEU A 49 " ideal model delta sigma weight residual 111.28 105.61 5.67 1.09e+00 8.42e-01 2.71e+01 angle pdb=" O THR A 464 " pdb=" C THR A 464 " pdb=" N GLY A 465 " ideal model delta sigma weight residual 122.07 126.97 -4.90 1.03e+00 9.43e-01 2.27e+01 ... (remaining 7977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.26: 3068 24.26 - 48.51: 324 48.51 - 72.76: 33 72.76 - 97.02: 8 97.02 - 121.27: 2 Dihedral angle restraints: 3435 sinusoidal: 1303 harmonic: 2132 Sorted by residual: 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 -63.61 121.27 1 3.00e+01 1.11e-03 1.62e+01 dihedral pdb=" CA PHE A 356 " pdb=" C PHE A 356 " pdb=" N GLY A 357 " pdb=" CA GLY A 357 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" C TYR A 476 " pdb=" N TYR A 476 " pdb=" CA TYR A 476 " pdb=" CB TYR A 476 " ideal model delta harmonic sigma weight residual -122.60 -113.42 -9.18 0 2.50e+00 1.60e-01 1.35e+01 ... (remaining 3432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 830 0.066 - 0.131: 113 0.131 - 0.196: 8 0.196 - 0.262: 3 0.262 - 0.327: 3 Chirality restraints: 957 Sorted by residual: 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 -2.62 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA TYR A 476 " pdb=" N TYR A 476 " pdb=" C TYR A 476 " pdb=" CB TYR A 476 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CB VAL A 470 " pdb=" CA VAL A 470 " pdb=" CG1 VAL A 470 " pdb=" CG2 VAL A 470 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 954 not shown) Planarity restraints: 973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 471 " -0.021 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C TYR A 471 " 0.075 2.00e-02 2.50e+03 pdb=" O TYR A 471 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA A 472 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 472 " -0.022 2.00e-02 2.50e+03 4.26e-02 1.82e+01 pdb=" C ALA A 472 " 0.074 2.00e-02 2.50e+03 pdb=" O ALA A 472 " -0.026 2.00e-02 2.50e+03 pdb=" N PRO A 473 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 468 " -0.014 2.00e-02 2.50e+03 2.90e-02 8.39e+00 pdb=" C ASN A 468 " 0.050 2.00e-02 2.50e+03 pdb=" O ASN A 468 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE A 469 " -0.017 2.00e-02 2.50e+03 ... (remaining 970 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 733 2.75 - 3.29: 5869 3.29 - 3.82: 9636 3.82 - 4.36: 10362 4.36 - 4.90: 18960 Nonbonded interactions: 45560 Sorted by model distance: nonbonded pdb=" O MET B 405 " pdb=" OG SER B 409 " model vdw 2.212 2.440 nonbonded pdb=" O LEU A 142 " pdb=" OG SER A 145 " model vdw 2.215 2.440 nonbonded pdb=" O GLY A 158 " pdb=" OG1 THR A 161 " model vdw 2.259 2.440 nonbonded pdb=" O GLN A 150 " pdb=" ND2 ASN A 154 " model vdw 2.304 2.520 nonbonded pdb=" O VAL A 375 " pdb=" OG SER A 379 " model vdw 2.363 2.440 ... (remaining 45555 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' and (resid 19 through 276 or resid 291 through 483)) selection = (chain 'B' and (resid 19 through 51 or resid 134 through 483)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.160 Find NCS groups from input model: 0.290 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 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 : 0.006 0.082 5860 Z= 0.371 Angle : 0.858 18.007 7982 Z= 0.476 Chirality : 0.048 0.327 957 Planarity : 0.007 0.052 973 Dihedral : 18.104 121.271 2079 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.01 % Favored : 97.86 % Rotamer: Outliers : 0.49 % Allowed : 33.88 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.29), residues: 746 helix: 0.94 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.69 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 336 HIS 0.004 0.001 HIS B 223 PHE 0.048 0.002 PHE B 178 TYR 0.035 0.002 TYR A 476 ARG 0.001 0.000 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 0.639 Fit side-chains REVERT: B 183 MET cc_start: 0.6919 (ptp) cc_final: 0.6620 (ptp) outliers start: 3 outliers final: 1 residues processed: 125 average time/residue: 0.1354 time to fit residues: 23.5285 Evaluate side-chains 122 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 470 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.9990 chunk 56 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 0.1980 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN B 35 ASN B 274 GLN B 468 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5860 Z= 0.249 Angle : 0.665 7.078 7982 Z= 0.322 Chirality : 0.043 0.160 957 Planarity : 0.005 0.040 973 Dihedral : 7.119 79.627 860 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 5.10 % Allowed : 30.92 % Favored : 63.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.31), residues: 746 helix: 1.43 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -1.44 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 336 HIS 0.003 0.001 HIS A 422 PHE 0.014 0.001 PHE A 356 TYR 0.011 0.001 TYR A 430 ARG 0.002 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 0.543 Fit side-chains REVERT: A 38 PHE cc_start: 0.7492 (t80) cc_final: 0.7214 (t80) REVERT: A 149 MET cc_start: 0.7853 (tpp) cc_final: 0.7359 (tpp) REVERT: A 177 MET cc_start: 0.6728 (tmm) cc_final: 0.5912 (tmm) REVERT: B 183 MET cc_start: 0.7109 (ptp) cc_final: 0.6737 (ptp) outliers start: 31 outliers final: 18 residues processed: 145 average time/residue: 0.1123 time to fit residues: 23.5446 Evaluate side-chains 144 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 464 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.2980 chunk 21 optimal weight: 0.9990 chunk 56 optimal weight: 0.0010 chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 73 optimal weight: 0.4980 chunk 60 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 23 optimal weight: 0.0370 chunk 54 optimal weight: 0.5980 overall best weight: 0.2864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5860 Z= 0.192 Angle : 0.607 6.680 7982 Z= 0.293 Chirality : 0.041 0.153 957 Planarity : 0.005 0.040 973 Dihedral : 6.264 69.280 859 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 6.91 % Allowed : 29.61 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.31), residues: 746 helix: 1.60 (0.21), residues: 601 sheet: None (None), residues: 0 loop : -1.51 (0.51), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 366 HIS 0.002 0.000 HIS A 422 PHE 0.013 0.001 PHE A 356 TYR 0.007 0.001 TYR A 430 ARG 0.001 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 123 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.7917 (tpp) cc_final: 0.7511 (tpp) REVERT: A 154 ASN cc_start: 0.8084 (m-40) cc_final: 0.7812 (m-40) REVERT: A 177 MET cc_start: 0.6729 (tmm) cc_final: 0.5940 (tmm) REVERT: A 231 THR cc_start: 0.7075 (OUTLIER) cc_final: 0.6730 (p) REVERT: A 434 ASP cc_start: 0.7205 (t0) cc_final: 0.6903 (t0) REVERT: B 183 MET cc_start: 0.7036 (ptp) cc_final: 0.6497 (ptp) outliers start: 42 outliers final: 28 residues processed: 147 average time/residue: 0.1194 time to fit residues: 24.9909 Evaluate side-chains 153 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 124 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 464 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 35 optimal weight: 0.3980 chunk 7 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 60 optimal weight: 0.0670 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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: 0.7016 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5860 Z= 0.236 Angle : 0.622 6.615 7982 Z= 0.302 Chirality : 0.042 0.157 957 Planarity : 0.005 0.041 973 Dihedral : 5.988 64.290 859 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 6.91 % Allowed : 30.59 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.31), residues: 746 helix: 1.69 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -1.58 (0.51), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.002 0.001 HIS A 422 PHE 0.018 0.001 PHE B 178 TYR 0.011 0.001 TYR A 430 ARG 0.002 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 133 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.7973 (tpp) cc_final: 0.7606 (tpp) REVERT: A 154 ASN cc_start: 0.8096 (m-40) cc_final: 0.7694 (m-40) REVERT: A 177 MET cc_start: 0.6731 (tmm) cc_final: 0.5836 (tmm) REVERT: A 434 ASP cc_start: 0.7174 (t0) cc_final: 0.6817 (t0) REVERT: B 183 MET cc_start: 0.7015 (ptp) cc_final: 0.6408 (ptp) outliers start: 42 outliers final: 28 residues processed: 154 average time/residue: 0.1256 time to fit residues: 27.2958 Evaluate side-chains 159 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 464 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7054 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5860 Z= 0.317 Angle : 0.660 7.088 7982 Z= 0.323 Chirality : 0.044 0.158 957 Planarity : 0.005 0.043 973 Dihedral : 6.151 63.488 859 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 7.24 % Allowed : 30.92 % Favored : 61.84 % 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: 1.51 (0.31), residues: 746 helix: 1.60 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -1.49 (0.50), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 366 HIS 0.003 0.001 HIS B 422 PHE 0.016 0.001 PHE B 246 TYR 0.013 0.002 TYR A 349 ARG 0.002 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 133 time to evaluate : 0.651 Fit side-chains REVERT: A 149 MET cc_start: 0.8027 (tpp) cc_final: 0.7483 (tpp) REVERT: A 154 ASN cc_start: 0.8111 (m-40) cc_final: 0.7749 (m-40) REVERT: A 434 ASP cc_start: 0.7218 (t0) cc_final: 0.6901 (t0) outliers start: 44 outliers final: 35 residues processed: 153 average time/residue: 0.1245 time to fit residues: 26.9028 Evaluate side-chains 166 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 131 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 464 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.0040 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 60 optimal weight: 0.0070 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.3010 ------------------------------------------------------------------------------- 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: 0.7000 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5860 Z= 0.193 Angle : 0.611 7.112 7982 Z= 0.296 Chirality : 0.041 0.152 957 Planarity : 0.005 0.042 973 Dihedral : 5.662 52.580 859 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 6.09 % Allowed : 32.73 % Favored : 61.18 % 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 (0.31), residues: 746 helix: 1.83 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -1.43 (0.49), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 366 HIS 0.002 0.000 HIS A 422 PHE 0.014 0.001 PHE A 356 TYR 0.008 0.001 TYR A 430 ARG 0.001 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 131 time to evaluate : 0.573 Fit side-chains REVERT: A 149 MET cc_start: 0.7979 (tpp) cc_final: 0.7457 (tpp) REVERT: A 152 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8113 (mm) REVERT: A 154 ASN cc_start: 0.8114 (m-40) cc_final: 0.7635 (m-40) REVERT: A 434 ASP cc_start: 0.7184 (t0) cc_final: 0.6803 (t0) REVERT: B 439 MET cc_start: 0.6119 (mmt) cc_final: 0.5856 (mmt) outliers start: 37 outliers final: 26 residues processed: 151 average time/residue: 0.1195 time to fit residues: 25.7396 Evaluate side-chains 157 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 413 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.7074 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5860 Z= 0.353 Angle : 0.672 7.065 7982 Z= 0.331 Chirality : 0.045 0.160 957 Planarity : 0.005 0.042 973 Dihedral : 5.907 51.367 859 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 6.09 % Allowed : 32.40 % Favored : 61.51 % 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: 1.56 (0.31), residues: 746 helix: 1.66 (0.21), residues: 593 sheet: None (None), residues: 0 loop : -1.46 (0.49), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.003 0.001 HIS B 422 PHE 0.016 0.001 PHE A 28 TYR 0.015 0.002 TYR A 349 ARG 0.002 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 134 time to evaluate : 0.588 Fit side-chains revert: symmetry clash REVERT: A 38 PHE cc_start: 0.7427 (t80) cc_final: 0.7199 (t80) REVERT: A 149 MET cc_start: 0.8030 (tpp) cc_final: 0.7584 (tpp) REVERT: A 154 ASN cc_start: 0.8128 (m-40) cc_final: 0.7790 (m-40) REVERT: A 328 MET cc_start: 0.7970 (mtp) cc_final: 0.7613 (mtp) REVERT: A 337 GLN cc_start: 0.7103 (pm20) cc_final: 0.6844 (pm20) REVERT: A 434 ASP cc_start: 0.7214 (t0) cc_final: 0.6926 (t0) REVERT: B 36 MET cc_start: 0.6605 (mmm) cc_final: 0.6387 (mmm) outliers start: 37 outliers final: 29 residues processed: 151 average time/residue: 0.1293 time to fit residues: 27.1940 Evaluate side-chains 162 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 432 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 56 optimal weight: 0.0970 chunk 65 optimal weight: 0.0870 chunk 69 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 overall best weight: 0.3956 ------------------------------------------------------------------------------- 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: 0.7024 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5860 Z= 0.219 Angle : 0.620 8.037 7982 Z= 0.303 Chirality : 0.042 0.152 957 Planarity : 0.005 0.042 973 Dihedral : 5.414 48.519 859 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 5.43 % Allowed : 33.22 % Favored : 61.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.31), residues: 746 helix: 1.89 (0.21), residues: 591 sheet: None (None), residues: 0 loop : -1.35 (0.49), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.001 0.000 HIS A 422 PHE 0.014 0.001 PHE A 356 TYR 0.009 0.001 TYR A 430 ARG 0.001 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.8001 (tpp) cc_final: 0.7599 (tpp) REVERT: A 154 ASN cc_start: 0.8138 (m-40) cc_final: 0.7668 (m-40) REVERT: A 434 ASP cc_start: 0.7150 (t0) cc_final: 0.6793 (t0) REVERT: B 439 MET cc_start: 0.6265 (mmt) cc_final: 0.6002 (mmt) outliers start: 33 outliers final: 28 residues processed: 145 average time/residue: 0.1289 time to fit residues: 26.5430 Evaluate side-chains 156 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 464 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7068 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5860 Z= 0.314 Angle : 0.662 8.622 7982 Z= 0.325 Chirality : 0.044 0.158 957 Planarity : 0.005 0.042 973 Dihedral : 5.431 49.145 859 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 5.26 % Allowed : 32.73 % Favored : 62.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.31), residues: 746 helix: 1.70 (0.21), residues: 596 sheet: None (None), residues: 0 loop : -1.28 (0.50), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.003 0.001 HIS B 422 PHE 0.015 0.001 PHE A 28 TYR 0.012 0.002 TYR A 349 ARG 0.002 0.000 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 132 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8157 (m-40) cc_final: 0.7762 (m-40) REVERT: A 328 MET cc_start: 0.7980 (mtp) cc_final: 0.7613 (mtp) REVERT: A 434 ASP cc_start: 0.7213 (t0) cc_final: 0.6891 (t0) REVERT: B 439 MET cc_start: 0.6389 (mmt) cc_final: 0.6101 (mmt) outliers start: 32 outliers final: 29 residues processed: 146 average time/residue: 0.1348 time to fit residues: 27.4841 Evaluate side-chains 161 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 464 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.2980 chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 68 optimal weight: 0.4980 chunk 59 optimal weight: 0.6980 chunk 6 optimal weight: 0.0050 chunk 45 optimal weight: 0.0050 chunk 36 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 63 optimal weight: 0.3980 chunk 18 optimal weight: 0.0770 overall best weight: 0.1566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5860 Z= 0.174 Angle : 0.626 12.797 7982 Z= 0.304 Chirality : 0.041 0.153 957 Planarity : 0.005 0.041 973 Dihedral : 5.012 47.534 859 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.61 % Allowed : 33.88 % Favored : 61.51 % 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: 1.97 (0.31), residues: 746 helix: 1.95 (0.21), residues: 594 sheet: None (None), residues: 0 loop : -1.30 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 336 HIS 0.012 0.001 HIS B 223 PHE 0.026 0.001 PHE B 178 TYR 0.009 0.001 TYR A 430 ARG 0.003 0.000 ARG A 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.7955 (tpp) cc_final: 0.7508 (tpp) REVERT: A 152 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8142 (mm) REVERT: A 382 CYS cc_start: 0.6944 (m) cc_final: 0.6576 (m) REVERT: B 439 MET cc_start: 0.6235 (mmt) cc_final: 0.5962 (mmt) outliers start: 28 outliers final: 23 residues processed: 141 average time/residue: 0.1340 time to fit residues: 26.5973 Evaluate side-chains 150 residues out of total 609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 294 PHE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 464 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN B 223 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.140995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117326 restraints weight = 8399.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.120738 restraints weight = 4665.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.123086 restraints weight = 3056.791| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5860 Z= 0.319 Angle : 0.674 11.327 7982 Z= 0.330 Chirality : 0.044 0.158 957 Planarity : 0.005 0.042 973 Dihedral : 5.196 47.209 859 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.61 % Allowed : 34.05 % Favored : 61.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.31), residues: 746 helix: 1.83 (0.21), residues: 593 sheet: None (None), residues: 0 loop : -1.24 (0.49), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 336 HIS 0.017 0.002 HIS B 223 PHE 0.016 0.001 PHE A 441 TYR 0.012 0.002 TYR A 476 ARG 0.005 0.000 ARG B 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1490.00 seconds wall clock time: 27 minutes 17.84 seconds (1637.84 seconds total)