Starting phenix.real_space_refine on Wed Mar 12 18:38:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z29_14458/03_2025/7z29_14458.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z29_14458/03_2025/7z29_14458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z29_14458/03_2025/7z29_14458.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z29_14458/03_2025/7z29_14458.map" model { file = "/net/cci-nas-00/data/ceres_data/7z29_14458/03_2025/7z29_14458.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z29_14458/03_2025/7z29_14458.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 35 5.49 5 S 12 5.16 5 C 5264 2.51 5 N 1388 2.21 5 O 1608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8307 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4268 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 494} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3298 Classifications: {'peptide': 405} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 30, 'TRANS': 374} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 721 Classifications: {'DNA': 34, 'RNA': 2} Modifications used: {'5*END': 1, 'rna3p': 2} Link IDs: {'rna3p': 35} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan2': 1, ' DA%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'NVP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.81, per 1000 atoms: 0.58 Number of scatterers: 8307 At special positions: 0 Unit cell: (98.94, 109.61, 95.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 35 15.00 O 1608 8.00 N 1388 7.00 C 5264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 888.5 milliseconds 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1766 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 38.8% alpha, 15.2% beta 13 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 30 through 44 removed outlier: 3.892A pdb=" N LEU A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 121 through 128 removed outlier: 3.969A pdb=" N LYS A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.516A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 296 through 311 Processing helix chain 'A' and resid 363 through 383 Processing helix chain 'A' and resid 394 through 404 removed outlier: 3.734A pdb=" N GLU A 404 " --> pdb=" O THR A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 488 removed outlier: 4.220A pdb=" N ILE A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.604A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.740A pdb=" N ASN A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 528 " --> pdb=" O GLN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.713A pdb=" N VAL A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A 549 " --> pdb=" O ASN A 545 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 43 removed outlier: 4.121A pdb=" N LEU B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 89 removed outlier: 5.543A pdb=" N ASP B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 103 removed outlier: 3.527A pdb=" N LYS B 101 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 102 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 103 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.852A pdb=" N LYS B 126 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.641A pdb=" N ASN B 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 138 " --> pdb=" O ILE B 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 134 through 138' Processing helix chain 'B' and resid 154 through 175 removed outlier: 4.081A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 212 removed outlier: 3.802A pdb=" N THR B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 removed outlier: 3.525A pdb=" N TRP B 239 " --> pdb=" O PRO B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 271 removed outlier: 4.186A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE B 270 " --> pdb=" O TRP B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 403 through 406 removed outlier: 3.568A pdb=" N TRP B 406 " --> pdb=" O THR B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 406' Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 131 Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 229 Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 354 removed outlier: 7.228A pdb=" N LYS A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN A 343 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR A 351 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR A 339 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS A 353 " --> pdb=" O TRP A 337 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP A 337 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 340 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 328 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A 390 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.706A pdb=" N THR A 362 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 512 " --> pdb=" O THR A 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 464 through 470 removed outlier: 3.968A pdb=" N GLY A 456 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 443 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU A 438 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 493 " --> pdb=" O LYS A 530 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AA8, first strand: chain 'B' and resid 61 through 64 Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 183 removed outlier: 3.582A pdb=" N SER B 191 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 105 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 252 through 253 removed outlier: 4.305A pdb=" N TRP B 252 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 347 through 348 removed outlier: 4.139A pdb=" N GLU B 344 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 339 " --> pdb=" O GLY B 352 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 347 through 348 removed outlier: 4.139A pdb=" N GLU B 344 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA B 327 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) 287 hydrogen bonds defined for protein. 798 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 2.47 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1309 1.31 - 1.44: 2388 1.44 - 1.56: 4808 1.56 - 1.68: 69 1.68 - 1.81: 21 Bond restraints: 8595 Sorted by residual: bond pdb=" CA LYS B 138 " pdb=" C LYS B 138 " ideal model delta sigma weight residual 1.523 1.472 0.052 1.30e-02 5.92e+03 1.58e+01 bond pdb=" N ILE B 132 " pdb=" CA ILE B 132 " ideal model delta sigma weight residual 1.460 1.489 -0.029 7.50e-03 1.78e+04 1.52e+01 bond pdb=" CA LEU A 260 " pdb=" C LEU A 260 " ideal model delta sigma weight residual 1.524 1.481 0.042 1.26e-02 6.30e+03 1.13e+01 bond pdb=" C4' DG E 19 " pdb=" O4' DG E 19 " ideal model delta sigma weight residual 1.450 1.515 -0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" O3' DC E 3 " pdb=" P OMC E 4 " ideal model delta sigma weight residual 1.607 1.558 0.049 1.50e-02 4.44e+03 1.05e+01 ... (remaining 8590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.85: 11646 2.85 - 5.70: 177 5.70 - 8.55: 18 8.55 - 11.40: 1 11.40 - 14.25: 2 Bond angle restraints: 11844 Sorted by residual: angle pdb=" C5' DG E 19 " pdb=" C4' DG E 19 " pdb=" O4' DG E 19 " ideal model delta sigma weight residual 109.40 121.13 -11.73 1.50e+00 4.44e-01 6.12e+01 angle pdb=" N PRO A 412 " pdb=" CA PRO A 412 " pdb=" C PRO A 412 " ideal model delta sigma weight residual 112.47 126.72 -14.25 2.06e+00 2.36e-01 4.79e+01 angle pdb=" C5' DC E 3 " pdb=" C4' DC E 3 " pdb=" O4' DC E 3 " ideal model delta sigma weight residual 109.40 119.40 -10.00 1.50e+00 4.44e-01 4.45e+01 angle pdb=" CA GLY B 333 " pdb=" C GLY B 333 " pdb=" O GLY B 333 " ideal model delta sigma weight residual 122.24 117.62 4.62 8.70e-01 1.32e+00 2.82e+01 angle pdb=" C THR B 131 " pdb=" N ILE B 132 " pdb=" CA ILE B 132 " ideal model delta sigma weight residual 122.59 118.81 3.78 7.20e-01 1.93e+00 2.76e+01 ... (remaining 11839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 4309 17.69 - 35.38: 544 35.38 - 53.07: 126 53.07 - 70.76: 45 70.76 - 88.46: 10 Dihedral angle restraints: 5034 sinusoidal: 2301 harmonic: 2733 Sorted by residual: dihedral pdb=" C TYR A 183 " pdb=" N TYR A 183 " pdb=" CA TYR A 183 " pdb=" CB TYR A 183 " ideal model delta harmonic sigma weight residual -122.60 -111.33 -11.27 0 2.50e+00 1.60e-01 2.03e+01 dihedral pdb=" C LYS B 424 " pdb=" N LYS B 424 " pdb=" CA LYS B 424 " pdb=" CB LYS B 424 " ideal model delta harmonic sigma weight residual -122.60 -133.72 11.12 0 2.50e+00 1.60e-01 1.98e+01 dihedral pdb=" CA GLU B 44 " pdb=" C GLU B 44 " pdb=" N GLY B 45 " pdb=" CA GLY B 45 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 5031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1110 0.074 - 0.148: 150 0.148 - 0.222: 28 0.222 - 0.297: 10 0.297 - 0.371: 6 Chirality restraints: 1304 Sorted by residual: chirality pdb=" CA GLU B 415 " pdb=" N GLU B 415 " pdb=" C GLU B 415 " pdb=" CB GLU B 415 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA TYR A 183 " pdb=" N TYR A 183 " pdb=" C TYR A 183 " pdb=" CB TYR A 183 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CA LYS B 101 " pdb=" N LYS B 101 " pdb=" C LYS B 101 " pdb=" CB LYS B 101 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 1301 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 307 " 0.465 9.50e-02 1.11e+02 2.09e-01 2.66e+01 pdb=" NE ARG A 307 " -0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 307 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 307 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 307 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 156 " 0.059 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO B 157 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 130 " 0.018 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C PHE B 130 " -0.060 2.00e-02 2.50e+03 pdb=" O PHE B 130 " 0.022 2.00e-02 2.50e+03 pdb=" N THR B 131 " 0.020 2.00e-02 2.50e+03 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2406 2.82 - 3.34: 7260 3.34 - 3.86: 13458 3.86 - 4.38: 15856 4.38 - 4.90: 26301 Nonbonded interactions: 65281 Sorted by model distance: nonbonded pdb=" O LYS B 323 " pdb=" NZ LYS B 385 " model vdw 2.304 3.120 nonbonded pdb=" OH TYR A 457 " pdb=" OD2 ASP A 488 " model vdw 2.361 3.040 nonbonded pdb=" NZ LYS A 104 " pdb=" O LEU A 193 " model vdw 2.364 3.120 nonbonded pdb=" OD1 ASP B 17 " pdb=" N GLY B 18 " model vdw 2.369 3.120 nonbonded pdb=" OE1 GLN A 547 " pdb=" OG1 THR B 286 " model vdw 2.372 3.040 ... (remaining 65276 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 0.180 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.420 Find NCS groups from input model: 0.060 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 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 : 0.005 0.065 8595 Z= 0.331 Angle : 0.836 14.254 11844 Z= 0.523 Chirality : 0.061 0.371 1304 Planarity : 0.008 0.209 1371 Dihedral : 17.032 88.455 3268 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.04 % Favored : 96.85 % Rotamer: Outliers : 1.96 % Allowed : 1.96 % Favored : 96.09 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 3.08 % 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: -0.47 (0.28), residues: 921 helix: 0.95 (0.31), residues: 325 sheet: -1.19 (0.39), residues: 171 loop : -0.85 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 402 HIS 0.003 0.001 HIS A 235 PHE 0.007 0.001 PHE A 389 TYR 0.030 0.002 TYR A 319 ARG 0.004 0.000 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.876 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 4 residues processed: 132 average time/residue: 0.2031 time to fit residues: 37.2978 Evaluate side-chains 99 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 30.0000 chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 547 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.207514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.163214 restraints weight = 8761.863| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.80 r_work: 0.3632 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8595 Z= 0.348 Angle : 0.670 7.862 11844 Z= 0.352 Chirality : 0.047 0.240 1304 Planarity : 0.005 0.057 1371 Dihedral : 16.220 78.147 1365 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.13 % Favored : 95.66 % Rotamer: Outliers : 1.34 % Allowed : 11.49 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.88 (0.27), residues: 921 helix: 0.61 (0.29), residues: 328 sheet: -1.21 (0.40), residues: 162 loop : -1.23 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 402 HIS 0.004 0.001 HIS A 235 PHE 0.011 0.002 PHE B 130 TYR 0.024 0.002 TYR A 339 ARG 0.003 0.001 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.909 Fit side-chains REVERT: A 182 GLN cc_start: 0.8130 (pt0) cc_final: 0.7773 (pt0) REVERT: B 102 LYS cc_start: 0.7406 (mppt) cc_final: 0.6779 (mppt) REVERT: B 382 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.7953 (mp) REVERT: B 410 TRP cc_start: 0.7705 (p-90) cc_final: 0.7418 (p90) outliers start: 11 outliers final: 7 residues processed: 102 average time/residue: 0.1933 time to fit residues: 27.9268 Evaluate side-chains 96 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 32 optimal weight: 0.0010 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 63 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 3 optimal weight: 30.0000 chunk 16 optimal weight: 9.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.214334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.171544 restraints weight = 8781.874| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.91 r_work: 0.3776 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8595 Z= 0.157 Angle : 0.531 6.372 11844 Z= 0.277 Chirality : 0.042 0.200 1304 Planarity : 0.004 0.050 1371 Dihedral : 15.836 79.120 1365 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.06 % Favored : 97.83 % Rotamer: Outliers : 1.22 % Allowed : 13.20 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.23 (0.27), residues: 921 helix: 1.32 (0.30), residues: 322 sheet: -1.08 (0.39), residues: 174 loop : -0.83 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 212 HIS 0.002 0.001 HIS A 96 PHE 0.008 0.001 PHE B 116 TYR 0.016 0.001 TYR A 232 ARG 0.003 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8145 (pt0) cc_final: 0.7743 (pt0) REVERT: A 281 LYS cc_start: 0.7925 (ttmt) cc_final: 0.7503 (tttt) REVERT: A 319 TYR cc_start: 0.7539 (t80) cc_final: 0.7309 (t80) REVERT: A 425 LEU cc_start: 0.8438 (mt) cc_final: 0.8152 (mp) REVERT: A 428 GLN cc_start: 0.7173 (OUTLIER) cc_final: 0.6723 (mm110) REVERT: B 382 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.7857 (mp) REVERT: B 410 TRP cc_start: 0.7607 (p-90) cc_final: 0.7399 (p90) outliers start: 10 outliers final: 5 residues processed: 111 average time/residue: 0.1996 time to fit residues: 30.8380 Evaluate side-chains 99 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 94 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 27 optimal weight: 30.0000 chunk 75 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 87 optimal weight: 10.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN A 480 GLN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.209311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.164735 restraints weight = 8786.959| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 1.82 r_work: 0.3681 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8595 Z= 0.265 Angle : 0.575 6.824 11844 Z= 0.300 Chirality : 0.043 0.191 1304 Planarity : 0.004 0.047 1371 Dihedral : 15.865 77.934 1363 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.69 % Favored : 96.20 % Rotamer: Outliers : 2.44 % Allowed : 13.69 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.46 (0.27), residues: 921 helix: 1.11 (0.29), residues: 324 sheet: -1.27 (0.39), residues: 175 loop : -0.93 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 402 HIS 0.003 0.001 HIS A 235 PHE 0.008 0.001 PHE B 130 TYR 0.020 0.002 TYR A 339 ARG 0.003 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8160 (pt0) cc_final: 0.7755 (pt0) REVERT: B 382 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.7937 (mp) outliers start: 20 outliers final: 13 residues processed: 108 average time/residue: 0.2887 time to fit residues: 45.0477 Evaluate side-chains 100 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 0 optimal weight: 30.0000 chunk 88 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 24 optimal weight: 0.4980 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 ASN ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.211797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.167639 restraints weight = 8712.532| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.81 r_work: 0.3695 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8595 Z= 0.185 Angle : 0.533 6.546 11844 Z= 0.277 Chirality : 0.042 0.146 1304 Planarity : 0.004 0.046 1371 Dihedral : 15.608 77.998 1363 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.04 % Favored : 96.85 % Rotamer: Outliers : 2.20 % Allowed : 16.14 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.31 (0.28), residues: 921 helix: 1.30 (0.30), residues: 324 sheet: -1.27 (0.39), residues: 175 loop : -0.86 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 402 HIS 0.002 0.001 HIS A 235 PHE 0.006 0.001 PHE B 416 TYR 0.018 0.002 TYR A 232 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8155 (pt0) cc_final: 0.7776 (pt0) REVERT: A 281 LYS cc_start: 0.8058 (ttmt) cc_final: 0.7598 (tttt) REVERT: A 425 LEU cc_start: 0.7953 (mp) cc_final: 0.7679 (mt) REVERT: B 40 GLU cc_start: 0.7511 (tt0) cc_final: 0.7270 (tt0) REVERT: B 203 GLU cc_start: 0.7568 (pp20) cc_final: 0.7337 (pp20) REVERT: B 382 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.7899 (mp) outliers start: 18 outliers final: 14 residues processed: 111 average time/residue: 0.1980 time to fit residues: 30.8877 Evaluate side-chains 107 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN A 480 GLN ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.209730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.165180 restraints weight = 8708.482| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.82 r_work: 0.3676 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8595 Z= 0.250 Angle : 0.572 6.850 11844 Z= 0.296 Chirality : 0.043 0.154 1304 Planarity : 0.004 0.048 1371 Dihedral : 15.445 77.306 1360 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.47 % Favored : 96.42 % Rotamer: Outliers : 2.69 % Allowed : 16.99 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.46 (0.27), residues: 921 helix: 1.12 (0.30), residues: 323 sheet: -1.36 (0.39), residues: 175 loop : -0.90 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 402 HIS 0.003 0.001 HIS A 235 PHE 0.007 0.001 PHE B 130 TYR 0.020 0.002 TYR A 232 ARG 0.003 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8136 (pt0) cc_final: 0.7784 (pt0) REVERT: B 203 GLU cc_start: 0.7507 (pp20) cc_final: 0.7257 (pp20) REVERT: B 382 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.7964 (mp) outliers start: 22 outliers final: 18 residues processed: 110 average time/residue: 0.2234 time to fit residues: 34.9552 Evaluate side-chains 107 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 22 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 0.0970 chunk 30 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 11 optimal weight: 0.3980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.214472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.170055 restraints weight = 8750.050| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 1.84 r_work: 0.3745 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8595 Z= 0.148 Angle : 0.516 6.340 11844 Z= 0.263 Chirality : 0.041 0.153 1304 Planarity : 0.004 0.048 1371 Dihedral : 14.965 78.223 1360 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.82 % Favored : 97.07 % Rotamer: Outliers : 1.71 % Allowed : 18.46 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.07 (0.28), residues: 921 helix: 1.51 (0.30), residues: 327 sheet: -1.15 (0.39), residues: 175 loop : -0.75 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 402 HIS 0.002 0.000 HIS A 235 PHE 0.005 0.001 PHE A 171 TYR 0.019 0.001 TYR A 232 ARG 0.002 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.880 Fit side-chains REVERT: A 104 LYS cc_start: 0.7733 (tmmt) cc_final: 0.7515 (tmmt) REVERT: A 182 GLN cc_start: 0.8098 (pt0) cc_final: 0.7776 (pt0) REVERT: A 281 LYS cc_start: 0.7969 (ttmt) cc_final: 0.7499 (tttt) REVERT: B 40 GLU cc_start: 0.7405 (tt0) cc_final: 0.7173 (tt0) REVERT: B 203 GLU cc_start: 0.7556 (pp20) cc_final: 0.7295 (pp20) REVERT: B 342 TYR cc_start: 0.7955 (p90) cc_final: 0.7484 (p90) REVERT: B 382 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.7848 (mp) outliers start: 14 outliers final: 10 residues processed: 113 average time/residue: 0.2178 time to fit residues: 35.0376 Evaluate side-chains 100 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 51 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 42 optimal weight: 40.0000 chunk 16 optimal weight: 10.0000 chunk 31 optimal weight: 0.3980 chunk 67 optimal weight: 9.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN B 363 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.210973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.167053 restraints weight = 8813.412| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.88 r_work: 0.3691 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8595 Z= 0.229 Angle : 0.564 6.594 11844 Z= 0.289 Chirality : 0.043 0.172 1304 Planarity : 0.004 0.051 1371 Dihedral : 15.091 77.585 1360 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.58 % Favored : 96.31 % Rotamer: Outliers : 2.20 % Allowed : 18.34 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.28 (0.28), residues: 921 helix: 1.32 (0.30), residues: 327 sheet: -1.22 (0.39), residues: 175 loop : -0.88 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 402 HIS 0.003 0.001 HIS A 235 PHE 0.007 0.001 PHE B 130 TYR 0.020 0.002 TYR A 232 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.8104 (pt0) cc_final: 0.7632 (pt0) REVERT: A 305 GLU cc_start: 0.7720 (tp30) cc_final: 0.7354 (pt0) REVERT: B 203 GLU cc_start: 0.7495 (pp20) cc_final: 0.7280 (pp20) REVERT: B 342 TYR cc_start: 0.8111 (p90) cc_final: 0.7627 (p90) REVERT: B 382 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.7940 (mp) outliers start: 18 outliers final: 12 residues processed: 106 average time/residue: 0.1929 time to fit residues: 28.8279 Evaluate side-chains 104 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 92 optimal weight: 0.0030 chunk 74 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 7 optimal weight: 0.0670 chunk 83 optimal weight: 0.4980 chunk 39 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.5132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN B 363 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.214047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.170683 restraints weight = 8849.262| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.90 r_work: 0.3758 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8595 Z= 0.155 Angle : 0.522 7.874 11844 Z= 0.267 Chirality : 0.041 0.171 1304 Planarity : 0.004 0.051 1371 Dihedral : 14.952 78.273 1360 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.82 % Favored : 97.07 % Rotamer: Outliers : 1.47 % Allowed : 18.95 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.01 (0.28), residues: 921 helix: 1.59 (0.30), residues: 326 sheet: -1.07 (0.39), residues: 175 loop : -0.76 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 402 HIS 0.002 0.000 HIS A 235 PHE 0.004 0.001 PHE B 416 TYR 0.019 0.001 TYR A 232 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 104 LYS cc_start: 0.7763 (tmmt) cc_final: 0.7537 (tmmt) REVERT: A 182 GLN cc_start: 0.7987 (pt0) cc_final: 0.7128 (pt0) REVERT: A 281 LYS cc_start: 0.7948 (ttmt) cc_final: 0.7471 (tttt) REVERT: A 305 GLU cc_start: 0.7684 (tp30) cc_final: 0.7353 (pt0) REVERT: A 374 LYS cc_start: 0.8090 (tmtt) cc_final: 0.7745 (ttpp) REVERT: B 16 MET cc_start: 0.5969 (tpt) cc_final: 0.5670 (tpp) REVERT: B 40 GLU cc_start: 0.7415 (tt0) cc_final: 0.7173 (tt0) REVERT: B 203 GLU cc_start: 0.7523 (pp20) cc_final: 0.7307 (pp20) REVERT: B 342 TYR cc_start: 0.8037 (p90) cc_final: 0.7543 (p90) REVERT: B 382 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.7858 (mp) outliers start: 12 outliers final: 11 residues processed: 101 average time/residue: 0.2046 time to fit residues: 28.5993 Evaluate side-chains 102 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 74 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN B 363 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.208445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.164536 restraints weight = 8875.134| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 1.88 r_work: 0.3702 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8595 Z= 0.196 Angle : 0.548 9.127 11844 Z= 0.279 Chirality : 0.042 0.187 1304 Planarity : 0.004 0.051 1371 Dihedral : 15.030 77.915 1360 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.74 % Rotamer: Outliers : 1.71 % Allowed : 18.95 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.13 (0.28), residues: 921 helix: 1.47 (0.30), residues: 327 sheet: -1.09 (0.39), residues: 175 loop : -0.84 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 402 HIS 0.003 0.001 HIS A 235 PHE 0.006 0.001 PHE B 130 TYR 0.022 0.002 TYR A 232 ARG 0.004 0.000 ARG B 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1842 Ramachandran restraints generated. 921 Oldfield, 0 Emsley, 921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 104 LYS cc_start: 0.7812 (tmmt) cc_final: 0.7537 (tmmt) REVERT: A 182 GLN cc_start: 0.8026 (pt0) cc_final: 0.7183 (pt0) REVERT: A 281 LYS cc_start: 0.7998 (ttmt) cc_final: 0.7542 (tttt) REVERT: A 305 GLU cc_start: 0.7656 (tp30) cc_final: 0.7315 (pt0) REVERT: B 203 GLU cc_start: 0.7494 (pp20) cc_final: 0.7267 (pp20) REVERT: B 342 TYR cc_start: 0.8102 (p90) cc_final: 0.7614 (p90) REVERT: B 382 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.7917 (mp) outliers start: 14 outliers final: 9 residues processed: 100 average time/residue: 0.1982 time to fit residues: 27.9497 Evaluate side-chains 99 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 414 TRP Chi-restraints excluded: chain B residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 29 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.212384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.168533 restraints weight = 8793.339| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.90 r_work: 0.3697 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8595 Z= 0.202 Angle : 0.552 9.103 11844 Z= 0.282 Chirality : 0.042 0.182 1304 Planarity : 0.004 0.050 1371 Dihedral : 15.080 77.703 1360 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.93 % Favored : 96.96 % Rotamer: Outliers : 1.59 % Allowed : 19.07 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.21 (0.28), residues: 921 helix: 1.35 (0.30), residues: 327 sheet: -1.12 (0.39), residues: 175 loop : -0.84 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 402 HIS 0.003 0.001 HIS A 235 PHE 0.006 0.001 PHE B 130 TYR 0.021 0.002 TYR A 232 ARG 0.004 0.000 ARG B 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4620.44 seconds wall clock time: 81 minutes 38.16 seconds (4898.16 seconds total)