Starting phenix.real_space_refine on Tue Feb 11 13:12:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tgg_41235/02_2025/8tgg_41235_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tgg_41235/02_2025/8tgg_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/cci-nas-00/data/ceres_data/8tgg_41235/02_2025/8tgg_41235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tgg_41235/02_2025/8tgg_41235.map" model { file = "/net/cci-nas-00/data/ceres_data/8tgg_41235/02_2025/8tgg_41235_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tgg_41235/02_2025/8tgg_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. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.45, per 1000 atoms: 0.78 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 824.8 milliseconds 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: 0.51 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: 1.55 Time building geometry restraints manager: 1.69 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: 0.00 - 3.60: 7882 3.60 - 7.20: 94 7.20 - 10.80: 5 10.80 - 14.41: 0 14.41 - 18.01: 1 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 3.040 nonbonded pdb=" O LEU A 142 " pdb=" OG SER A 145 " model vdw 2.215 3.040 nonbonded pdb=" O GLY A 158 " pdb=" OG1 THR A 161 " model vdw 2.259 3.040 nonbonded pdb=" O GLN A 150 " pdb=" ND2 ASN A 154 " model vdw 2.304 3.120 nonbonded pdb=" O VAL A 375 " pdb=" OG SER A 379 " model vdw 2.363 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 2.160 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.250 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.760 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 3 poor density : 122 time to evaluate : 0.599 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: 0.1352 time to fit residues: 23.6726 Evaluate side-chains 122 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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: 0.9980 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.142571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.119279 restraints weight = 8415.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.122703 restraints weight = 4683.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.125008 restraints weight = 3083.501| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5860 Z= 0.326 Angle : 0.708 7.201 7982 Z= 0.346 Chirality : 0.045 0.163 957 Planarity : 0.006 0.041 973 Dihedral : 7.383 82.416 860 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 5.26 % Allowed : 31.09 % Favored : 63.65 % 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: 1.14 (0.31), residues: 746 helix: 1.29 (0.21), residues: 604 sheet: None (None), residues: 0 loop : -1.41 (0.52), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 336 HIS 0.003 0.001 HIS A 422 PHE 0.015 0.002 PHE A 356 TYR 0.012 0.002 TYR A 349 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 165 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.560 Fit side-chains REVERT: A 177 MET cc_start: 0.6770 (tmm) cc_final: 0.5947 (tmm) REVERT: A 434 ASP cc_start: 0.7154 (t0) cc_final: 0.6870 (t0) REVERT: B 183 MET cc_start: 0.7090 (ptp) cc_final: 0.6742 (ptp) REVERT: B 291 THR cc_start: 0.8248 (p) cc_final: 0.8018 (t) outliers start: 32 outliers final: 20 residues processed: 148 average time/residue: 0.1149 time to fit residues: 24.7565 Evaluate side-chains 147 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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 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 393 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 423 THR 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 137 THR Chi-restraints excluded: chain B residue 174 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 423 THR Chi-restraints excluded: chain B residue 432 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 30 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 chunk 6 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 74 optimal weight: 0.1980 chunk 22 optimal weight: 0.0050 chunk 53 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 overall best weight: 0.2592 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.144706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.121357 restraints weight = 8445.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124890 restraints weight = 4654.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.127278 restraints weight = 3030.656| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5860 Z= 0.188 Angle : 0.606 6.527 7982 Z= 0.295 Chirality : 0.041 0.157 957 Planarity : 0.005 0.039 973 Dihedral : 6.266 71.172 859 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 5.10 % Allowed : 32.24 % Favored : 62.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.31), residues: 746 helix: 1.59 (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 0.007 0.001 TRP B 326 HIS 0.002 0.000 HIS A 422 PHE 0.014 0.001 PHE A 294 TYR 0.007 0.001 TYR B 476 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 159 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.599 Fit side-chains REVERT: A 177 MET cc_start: 0.6753 (tmm) cc_final: 0.5988 (tmm) REVERT: B 183 MET cc_start: 0.7072 (ptp) cc_final: 0.6599 (ptp) outliers start: 31 outliers final: 21 residues processed: 144 average time/residue: 0.1291 time to fit residues: 26.1746 Evaluate side-chains 145 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 303 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 392 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 316 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 38 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 47 optimal weight: 0.2980 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 73 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.140472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.118155 restraints weight = 8830.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.120929 restraints weight = 4719.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124307 restraints weight = 2974.181| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5860 Z= 0.295 Angle : 0.652 6.679 7982 Z= 0.318 Chirality : 0.044 0.159 957 Planarity : 0.005 0.040 973 Dihedral : 6.337 71.443 859 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 7.07 % Allowed : 31.74 % 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: 1.52 (0.31), residues: 746 helix: 1.58 (0.21), residues: 603 sheet: None (None), residues: 0 loop : -1.42 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 366 HIS 0.003 0.001 HIS B 422 PHE 0.017 0.001 PHE B 178 TYR 0.012 0.002 TYR A 349 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 174 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8163 (m110) cc_final: 0.7941 (m-40) REVERT: A 177 MET cc_start: 0.6804 (tmm) cc_final: 0.5905 (tmm) REVERT: A 434 ASP cc_start: 0.7096 (t0) cc_final: 0.6850 (t0) REVERT: B 183 MET cc_start: 0.6964 (ptp) cc_final: 0.6370 (ptp) outliers start: 43 outliers final: 29 residues processed: 152 average time/residue: 0.1283 time to fit residues: 27.9472 Evaluate side-chains 156 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 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 325 ILE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 423 THR 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 137 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 383 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 35 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 38 optimal weight: 4.9990 chunk 64 optimal weight: 0.3980 chunk 62 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.142131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.119064 restraints weight = 8572.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.122380 restraints weight = 4782.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.124587 restraints weight = 3143.460| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5860 Z= 0.235 Angle : 0.624 6.309 7982 Z= 0.306 Chirality : 0.042 0.154 957 Planarity : 0.005 0.045 973 Dihedral : 6.132 67.494 859 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 6.74 % Allowed : 32.24 % Favored : 61.02 % 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: 1.70 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -1.53 (0.50), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 366 HIS 0.002 0.000 HIS A 422 PHE 0.014 0.001 PHE A 356 TYR 0.009 0.001 TYR A 166 ARG 0.001 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 173 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 38 PHE cc_start: 0.7454 (t80) cc_final: 0.7096 (t80) REVERT: A 154 ASN cc_start: 0.8142 (m110) cc_final: 0.7896 (m-40) REVERT: A 434 ASP cc_start: 0.7046 (t0) cc_final: 0.6796 (t0) REVERT: B 36 MET cc_start: 0.6629 (mmm) cc_final: 0.6329 (tpp) REVERT: B 183 MET cc_start: 0.6919 (ptp) cc_final: 0.6280 (ptp) outliers start: 41 outliers final: 32 residues processed: 152 average time/residue: 0.1216 time to fit residues: 26.3004 Evaluate side-chains 163 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 152 LEU Chi-restraints excluded: chain A residue 182 VAL 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 325 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 452 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 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 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 Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 432 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 7 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 44 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.141269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.118202 restraints weight = 8557.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.121468 restraints weight = 4794.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.123557 restraints weight = 3158.337| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5860 Z= 0.288 Angle : 0.647 6.781 7982 Z= 0.317 Chirality : 0.043 0.155 957 Planarity : 0.005 0.042 973 Dihedral : 6.185 65.728 859 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 6.74 % Allowed : 32.57 % Favored : 60.69 % 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: 1.57 (0.31), residues: 746 helix: 1.64 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -1.41 (0.49), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 366 HIS 0.002 0.001 HIS B 422 PHE 0.014 0.001 PHE A 28 TYR 0.012 0.001 TYR A 349 ARG 0.002 0.000 ARG A 197 *********************** 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 173 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 0.619 Fit side-chains REVERT: A 38 PHE cc_start: 0.7448 (t80) cc_final: 0.7148 (t80) REVERT: A 154 ASN cc_start: 0.8133 (m110) cc_final: 0.7929 (m-40) REVERT: A 434 ASP cc_start: 0.7054 (t0) cc_final: 0.6837 (t0) REVERT: B 183 MET cc_start: 0.7027 (ptp) cc_final: 0.6620 (ptm) REVERT: B 439 MET cc_start: 0.6192 (mmt) cc_final: 0.5937 (mmt) outliers start: 41 outliers final: 30 residues processed: 151 average time/residue: 0.1256 time to fit residues: 27.0769 Evaluate side-chains 161 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 182 VAL 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 325 ILE Chi-restraints excluded: chain A residue 392 LEU 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 47 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 174 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 423 THR Chi-restraints excluded: chain B residue 432 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 6 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 60 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 396 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.143193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.120870 restraints weight = 8504.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.124122 restraints weight = 4719.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.126212 restraints weight = 3083.915| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5860 Z= 0.241 Angle : 0.632 7.394 7982 Z= 0.310 Chirality : 0.042 0.156 957 Planarity : 0.005 0.042 973 Dihedral : 6.014 61.851 859 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 6.09 % Allowed : 33.55 % Favored : 60.36 % 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: 1.64 (0.31), residues: 746 helix: 1.70 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -1.43 (0.50), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 336 HIS 0.002 0.001 HIS A 422 PHE 0.030 0.001 PHE B 246 TYR 0.009 0.001 TYR A 166 ARG 0.001 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 170 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.559 Fit side-chains REVERT: A 38 PHE cc_start: 0.7451 (t80) cc_final: 0.7145 (t80) REVERT: A 154 ASN cc_start: 0.8124 (m110) cc_final: 0.7816 (m-40) REVERT: A 296 LEU cc_start: 0.8266 (mt) cc_final: 0.7907 (mp) REVERT: A 434 ASP cc_start: 0.7031 (t0) cc_final: 0.6767 (t0) REVERT: B 36 MET cc_start: 0.6659 (mmm) cc_final: 0.6332 (tpp) REVERT: B 183 MET cc_start: 0.7029 (ptp) cc_final: 0.6638 (ptm) REVERT: B 439 MET cc_start: 0.6268 (mmt) cc_final: 0.6015 (mmt) outliers start: 37 outliers final: 27 residues processed: 149 average time/residue: 0.1217 time to fit residues: 25.8250 Evaluate side-chains 158 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 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 392 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 47 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 174 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 383 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 6 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 28 optimal weight: 0.0670 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.144838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.122255 restraints weight = 8251.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125537 restraints weight = 4579.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127740 restraints weight = 2988.445| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2322 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= 0.238 Angle : 0.629 8.059 7982 Z= 0.307 Chirality : 0.042 0.158 957 Planarity : 0.005 0.042 973 Dihedral : 5.783 53.058 859 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 5.92 % Allowed : 33.55 % Favored : 60.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.31), residues: 746 helix: 1.73 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -1.39 (0.50), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.011 0.001 HIS B 223 PHE 0.025 0.001 PHE B 246 TYR 0.010 0.001 TYR A 430 ARG 0.002 0.000 ARG A 225 *********************** 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 166 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 130 time to evaluate : 0.588 Fit side-chains REVERT: A 154 ASN cc_start: 0.8173 (m110) cc_final: 0.7907 (m-40) REVERT: A 231 THR cc_start: 0.7213 (OUTLIER) cc_final: 0.6946 (p) REVERT: A 434 ASP cc_start: 0.7017 (t0) cc_final: 0.6801 (t0) REVERT: B 36 MET cc_start: 0.6559 (mmm) cc_final: 0.6258 (tpp) REVERT: B 183 MET cc_start: 0.6988 (ptp) cc_final: 0.6563 (ptm) REVERT: B 331 MET cc_start: 0.7897 (mtt) cc_final: 0.7678 (mtp) REVERT: B 439 MET cc_start: 0.6229 (mmt) cc_final: 0.6002 (mmt) outliers start: 36 outliers final: 31 residues processed: 144 average time/residue: 0.1412 time to fit residues: 28.9586 Evaluate side-chains 162 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 152 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 263 LEU 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 392 LEU Chi-restraints excluded: chain A residue 420 LEU 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 137 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 223 HIS 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 383 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 6 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 21 optimal weight: 0.0970 chunk 71 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 223 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.141360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.117783 restraints weight = 8497.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.121209 restraints weight = 4727.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.123548 restraints weight = 3091.363| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5860 Z= 0.258 Angle : 0.638 8.779 7982 Z= 0.313 Chirality : 0.043 0.162 957 Planarity : 0.005 0.042 973 Dihedral : 5.300 47.875 859 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 5.59 % Allowed : 33.55 % Favored : 60.86 % 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: 1.69 (0.31), residues: 746 helix: 1.72 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -1.36 (0.50), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.012 0.001 HIS B 223 PHE 0.026 0.001 PHE B 246 TYR 0.010 0.001 TYR A 166 ARG 0.002 0.000 ARG A 225 *********************** 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 160 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.567 Fit side-chains REVERT: A 154 ASN cc_start: 0.8152 (m110) cc_final: 0.7871 (m-40) REVERT: A 231 THR cc_start: 0.7202 (OUTLIER) cc_final: 0.6918 (p) REVERT: A 434 ASP cc_start: 0.7029 (t0) cc_final: 0.6789 (t0) REVERT: B 36 MET cc_start: 0.6641 (mmm) cc_final: 0.6313 (tpp) REVERT: B 183 MET cc_start: 0.6971 (ptp) cc_final: 0.6567 (ptm) REVERT: B 331 MET cc_start: 0.7928 (mtt) cc_final: 0.7705 (mtp) REVERT: B 439 MET cc_start: 0.6309 (mmt) cc_final: 0.6063 (mmt) outliers start: 34 outliers final: 31 residues processed: 142 average time/residue: 0.1279 time to fit residues: 25.8783 Evaluate side-chains 157 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 152 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 420 LEU 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 137 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 223 HIS 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 383 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 17 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 0.2980 chunk 64 optimal weight: 0.2980 chunk 59 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 54 optimal weight: 0.0570 chunk 19 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 74 optimal weight: 0.3980 overall best weight: 0.2298 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.144358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.120817 restraints weight = 8472.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.124165 restraints weight = 4698.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126439 restraints weight = 3077.378| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.2375 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= 0.186 Angle : 0.612 7.767 7982 Z= 0.299 Chirality : 0.041 0.161 957 Planarity : 0.005 0.042 973 Dihedral : 5.108 47.745 859 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.61 % Allowed : 34.38 % Favored : 61.02 % 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: 1.82 (0.31), residues: 746 helix: 1.81 (0.21), residues: 598 sheet: None (None), residues: 0 loop : -1.31 (0.50), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.023 0.002 HIS B 223 PHE 0.023 0.001 PHE B 246 TYR 0.009 0.001 TYR A 430 ARG 0.001 0.000 ARG B 225 ********************** 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 155 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.589 Fit side-chains REVERT: A 154 ASN cc_start: 0.8163 (m110) cc_final: 0.7834 (m-40) REVERT: A 434 ASP cc_start: 0.6999 (t0) cc_final: 0.6751 (t0) REVERT: B 36 MET cc_start: 0.6574 (mmm) cc_final: 0.6284 (tpp) REVERT: B 183 MET cc_start: 0.6926 (ptp) cc_final: 0.6514 (ptm) REVERT: B 331 MET cc_start: 0.7898 (mtt) cc_final: 0.7671 (mtp) REVERT: B 439 MET cc_start: 0.6213 (mmt) cc_final: 0.5971 (mmt) outliers start: 28 outliers final: 24 residues processed: 141 average time/residue: 0.1282 time to fit residues: 25.8552 Evaluate side-chains 149 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 189 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 392 LEU 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 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 223 HIS Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 383 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 0.0470 chunk 71 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.141236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.117513 restraints weight = 8543.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.120950 restraints weight = 4740.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.123284 restraints weight = 3093.351| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2445 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= 0.283 Angle : 0.640 7.848 7982 Z= 0.315 Chirality : 0.043 0.161 957 Planarity : 0.005 0.042 973 Dihedral : 5.194 47.100 859 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.77 % Allowed : 33.88 % 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: 1.88 (0.31), residues: 746 helix: 1.85 (0.21), residues: 591 sheet: None (None), residues: 0 loop : -1.08 (0.51), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.022 0.002 HIS B 223 PHE 0.025 0.001 PHE B 246 TYR 0.013 0.001 TYR A 476 ARG 0.002 0.000 ARG A 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1895.61 seconds wall clock time: 34 minutes 45.34 seconds (2085.34 seconds total)