Starting phenix.real_space_refine on Thu Nov 14 10:35:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgg_41235/11_2024/8tgg_41235_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgg_41235/11_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_41235/11_2024/8tgg_41235.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgg_41235/11_2024/8tgg_41235.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgg_41235/11_2024/8tgg_41235_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgg_41235/11_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. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 4.56, per 1000 atoms: 0.80 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: 1.65 Conformation dependent library (CDL) restraints added in 994.0 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: 0.66 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: 1.66 Time building geometry restraints manager: 1.88 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: 1.350 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.180 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.030 ------------------------------------------------------------------------------- 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 : 0.550 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: 23.6421 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 : 0.607 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 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 : 0.630 Fit side-chains REVERT: A 154 ASN cc_start: 0.7826 (m110) cc_final: 0.7613 (m-40) REVERT: A 177 MET cc_start: 0.6726 (tmm) cc_final: 0.5890 (tmm) REVERT: A 434 ASP cc_start: 0.7227 (t0) cc_final: 0.6866 (t0) REVERT: B 183 MET cc_start: 0.7126 (ptp) cc_final: 0.6776 (ptp) REVERT: B 291 THR cc_start: 0.8251 (p) cc_final: 0.8030 (t) outliers start: 32 outliers final: 20 residues processed: 148 average time/residue: 0.1206 time to fit residues: 25.7682 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 : 0.618 ------------------------------------------------------------------------------- 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 37 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 46 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 68 optimal weight: 0.0050 chunk 73 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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: 0.7023 moved from start: 0.1545 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= 0.242 Angle : 0.626 6.651 7982 Z= 0.307 Chirality : 0.042 0.153 957 Planarity : 0.005 0.039 973 Dihedral : 6.384 73.010 859 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 5.43 % Allowed : 31.74 % Favored : 62.83 % 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: 1.39 (0.31), residues: 746 helix: 1.50 (0.21), residues: 601 sheet: None (None), residues: 0 loop : -1.48 (0.51), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 366 HIS 0.002 0.001 HIS A 422 PHE 0.013 0.001 PHE A 294 TYR 0.009 0.001 TYR A 476 ARG 0.002 0.000 ARG A 225 *********************** 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 to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.524 Fit side-chains REVERT: A 177 MET cc_start: 0.6735 (tmm) cc_final: 0.5924 (tmm) REVERT: A 434 ASP cc_start: 0.7190 (t0) cc_final: 0.6832 (t0) REVERT: B 183 MET cc_start: 0.7087 (ptp) cc_final: 0.6587 (ptp) outliers start: 33 outliers final: 24 residues processed: 149 average time/residue: 0.1265 time to fit residues: 26.7658 Evaluate side-chains 151 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 333 SER 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7078 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 5860 Z= 0.362 Angle : 0.684 7.066 7982 Z= 0.338 Chirality : 0.045 0.158 957 Planarity : 0.005 0.039 973 Dihedral : 6.634 76.893 859 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 7.57 % Allowed : 31.25 % 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: 1.32 (0.31), residues: 746 helix: 1.46 (0.21), residues: 599 sheet: None (None), residues: 0 loop : -1.52 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 366 HIS 0.004 0.001 HIS B 422 PHE 0.016 0.002 PHE A 28 TYR 0.016 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 177 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 131 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 154 ASN cc_start: 0.8176 (m-40) cc_final: 0.7839 (m-40) REVERT: A 177 MET cc_start: 0.6765 (tmm) cc_final: 0.5840 (tmm) REVERT: A 434 ASP cc_start: 0.7248 (t0) cc_final: 0.7025 (t0) REVERT: B 183 MET cc_start: 0.7089 (ptp) cc_final: 0.6466 (ptp) REVERT: B 199 LEU cc_start: 0.7731 (mt) cc_final: 0.7424 (mt) outliers start: 46 outliers final: 34 residues processed: 154 average time/residue: 0.1295 time to fit residues: 28.5215 Evaluate side-chains 165 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 182 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 214 MET 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 333 SER 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 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 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 296 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7086 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5860 Z= 0.361 Angle : 0.682 6.808 7982 Z= 0.340 Chirality : 0.045 0.158 957 Planarity : 0.005 0.048 973 Dihedral : 6.693 78.364 859 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 7.24 % Allowed : 31.41 % 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: 1.39 (0.31), residues: 746 helix: 1.53 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.29 (0.49), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 366 HIS 0.002 0.001 HIS B 422 PHE 0.016 0.001 PHE A 28 TYR 0.016 0.002 TYR A 349 ARG 0.003 0.000 ARG A 225 *********************** 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 178 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 0.606 Fit side-chains REVERT: A 38 PHE cc_start: 0.7498 (t80) cc_final: 0.7262 (t80) REVERT: A 149 MET cc_start: 0.8001 (tpp) cc_final: 0.7390 (tpp) REVERT: A 231 THR cc_start: 0.7317 (OUTLIER) cc_final: 0.6973 (p) REVERT: A 434 ASP cc_start: 0.7269 (t0) cc_final: 0.6990 (t0) REVERT: B 36 MET cc_start: 0.6698 (mmm) cc_final: 0.6493 (tpp) REVERT: B 199 LEU cc_start: 0.7786 (mt) cc_final: 0.7421 (mt) outliers start: 44 outliers final: 33 residues processed: 154 average time/residue: 0.1292 time to fit residues: 27.9524 Evaluate side-chains 166 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 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 405 MET 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 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 145 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.0270 chunk 14 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.0870 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 223 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5860 Z= 0.267 Angle : 0.638 6.634 7982 Z= 0.314 Chirality : 0.043 0.159 957 Planarity : 0.005 0.040 973 Dihedral : 6.500 77.106 859 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.50 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: 1.49 (0.31), residues: 746 helix: 1.59 (0.21), residues: 595 sheet: None (None), residues: 0 loop : -1.41 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 336 HIS 0.002 0.001 HIS A 422 PHE 0.014 0.001 PHE B 178 TYR 0.010 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 167 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 130 time to evaluate : 0.614 Fit side-chains REVERT: A 149 MET cc_start: 0.8001 (tpp) cc_final: 0.7366 (tpp) REVERT: A 154 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7831 (m-40) REVERT: A 231 THR cc_start: 0.7223 (OUTLIER) cc_final: 0.6880 (p) REVERT: A 434 ASP cc_start: 0.7198 (t0) cc_final: 0.6989 (t0) REVERT: B 183 MET cc_start: 0.7020 (ptp) cc_final: 0.6562 (ptm) REVERT: B 199 LEU cc_start: 0.7745 (mt) cc_final: 0.7386 (mt) REVERT: B 439 MET cc_start: 0.6276 (mmt) cc_final: 0.6040 (mmt) outliers start: 37 outliers final: 27 residues processed: 146 average time/residue: 0.1244 time to fit residues: 25.9248 Evaluate side-chains 158 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 154 ASN 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 401 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 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 49 LEU 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 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 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 8 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 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 B 223 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5860 Z= 0.299 Angle : 0.653 7.630 7982 Z= 0.323 Chirality : 0.043 0.159 957 Planarity : 0.005 0.041 973 Dihedral : 6.556 78.037 859 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 7.73 % Allowed : 31.41 % 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: 1.44 (0.31), residues: 746 helix: 1.55 (0.21), residues: 595 sheet: None (None), residues: 0 loop : -1.44 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 336 HIS 0.010 0.001 HIS B 223 PHE 0.014 0.001 PHE A 28 TYR 0.012 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 177 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 130 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.8035 (tpp) cc_final: 0.7506 (tpp) REVERT: A 231 THR cc_start: 0.7318 (OUTLIER) cc_final: 0.6963 (p) REVERT: A 434 ASP cc_start: 0.7142 (t0) cc_final: 0.6892 (t0) REVERT: B 183 MET cc_start: 0.7064 (ptp) cc_final: 0.6627 (ptm) REVERT: B 199 LEU cc_start: 0.7760 (mt) cc_final: 0.7403 (mt) REVERT: B 439 MET cc_start: 0.6316 (mmt) cc_final: 0.6085 (mmt) outliers start: 47 outliers final: 38 residues processed: 155 average time/residue: 0.1239 time to fit residues: 27.3927 Evaluate side-chains 168 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 45 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 297 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 405 MET 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 47 THR Chi-restraints excluded: chain B residue 49 LEU 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 246 PHE Chi-restraints excluded: chain B residue 291 THR 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 380 LEU 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 21 optimal weight: 0.1980 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 49 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 65 optimal weight: 0.0670 chunk 69 optimal weight: 0.2980 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.3118 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5860 Z= 0.208 Angle : 0.623 8.409 7982 Z= 0.305 Chirality : 0.041 0.158 957 Planarity : 0.005 0.041 973 Dihedral : 6.378 75.506 859 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 7.40 % Allowed : 31.41 % 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: 1.62 (0.31), residues: 746 helix: 1.69 (0.21), residues: 595 sheet: None (None), residues: 0 loop : -1.40 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.013 0.001 HIS B 223 PHE 0.018 0.001 PHE B 178 TYR 0.009 0.001 TYR A 430 ARG 0.001 0.000 ARG B 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 170 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 125 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.8003 (tpp) cc_final: 0.7604 (tpp) REVERT: A 231 THR cc_start: 0.7180 (OUTLIER) cc_final: 0.6825 (p) REVERT: B 183 MET cc_start: 0.7050 (ptp) cc_final: 0.6659 (ptm) REVERT: B 439 MET cc_start: 0.6257 (mmt) cc_final: 0.6016 (mmt) outliers start: 45 outliers final: 38 residues processed: 148 average time/residue: 0.1262 time to fit residues: 26.6314 Evaluate side-chains 164 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 45 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 297 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 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 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 49 LEU 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 246 PHE Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 380 LEU 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 69 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 44 optimal weight: 0.0570 chunk 71 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.2388 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= 0.252 Angle : 0.634 8.813 7982 Z= 0.311 Chirality : 0.042 0.161 957 Planarity : 0.005 0.041 973 Dihedral : 6.388 75.617 859 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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: 1.61 (0.31), residues: 746 helix: 1.68 (0.21), residues: 595 sheet: None (None), residues: 0 loop : -1.38 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 366 HIS 0.015 0.001 HIS B 223 PHE 0.013 0.001 PHE A 28 TYR 0.010 0.001 TYR A 430 ARG 0.001 0.000 ARG A 197 *********************** 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 168 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.8033 (tpp) cc_final: 0.7610 (tpp) REVERT: A 231 THR cc_start: 0.7191 (OUTLIER) cc_final: 0.6841 (p) REVERT: B 183 MET cc_start: 0.7016 (ptp) cc_final: 0.6613 (ptm) REVERT: B 439 MET cc_start: 0.6298 (mmt) cc_final: 0.6052 (mmt) outliers start: 43 outliers final: 37 residues processed: 146 average time/residue: 0.1264 time to fit residues: 26.3869 Evaluate side-chains 163 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 125 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 45 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 297 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 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 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 49 LEU 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 246 PHE Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 380 LEU 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 49 optimal weight: 4.9990 chunk 74 optimal weight: 0.0170 chunk 68 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 6 optimal weight: 0.0270 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2426 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= 0.230 Angle : 0.630 8.561 7982 Z= 0.309 Chirality : 0.042 0.159 957 Planarity : 0.005 0.041 973 Dihedral : 6.345 74.754 859 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 6.25 % Allowed : 32.73 % 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: 1.64 (0.31), residues: 746 helix: 1.70 (0.21), residues: 595 sheet: None (None), residues: 0 loop : -1.34 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 366 HIS 0.016 0.001 HIS B 223 PHE 0.013 0.001 PHE A 356 TYR 0.010 0.001 TYR A 430 ARG 0.010 0.000 ARG A 479 ********************** 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 161 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: A 149 MET cc_start: 0.8031 (tpp) cc_final: 0.7606 (tpp) REVERT: A 231 THR cc_start: 0.7176 (OUTLIER) cc_final: 0.6823 (p) REVERT: B 183 MET cc_start: 0.7050 (ptp) cc_final: 0.6648 (ptm) REVERT: B 439 MET cc_start: 0.6293 (mmt) cc_final: 0.6048 (mmt) outliers start: 38 outliers final: 35 residues processed: 143 average time/residue: 0.1267 time to fit residues: 25.6481 Evaluate side-chains 159 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 45 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 297 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 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 455 ILE Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 49 LEU 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 246 PHE Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 380 LEU 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 54 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.144041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122386 restraints weight = 8206.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.124964 restraints weight = 4446.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.128265 restraints weight = 2832.933| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5860 Z= 0.289 Angle : 0.646 7.753 7982 Z= 0.317 Chirality : 0.043 0.161 957 Planarity : 0.005 0.041 973 Dihedral : 6.445 76.575 859 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 6.25 % Allowed : 33.06 % 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: 1.55 (0.31), residues: 746 helix: 1.63 (0.21), residues: 595 sheet: None (None), residues: 0 loop : -1.37 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 366 HIS 0.017 0.002 HIS B 223 PHE 0.014 0.001 PHE A 28 TYR 0.011 0.001 TYR A 349 ARG 0.009 0.001 ARG A 479 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1498.45 seconds wall clock time: 27 minutes 46.18 seconds (1666.18 seconds total)