Starting phenix.real_space_refine on Tue Mar 3 19:20:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z2g_14465/03_2026/7z2g_14465.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2g_14465/03_2026/7z2g_14465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z2g_14465/03_2026/7z2g_14465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2g_14465/03_2026/7z2g_14465.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z2g_14465/03_2026/7z2g_14465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2g_14465/03_2026/7z2g_14465.map" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.026 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: 7 Type Number sf(0) Gaussians P 35 5.49 5 S 14 5.16 5 Cl 1 4.86 5 C 5323 2.51 5 N 1401 2.21 5 O 1629 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8406 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4324 Classifications: {'peptide': 536} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 34, 'TRANS': 499} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3333 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 30, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 720 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:plan': 1, ' DA%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'2KW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.37, per 1000 atoms: 0.28 Number of scatterers: 8406 At special positions: 0 Unit cell: (98.94, 109.61, 97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 14 16.00 P 35 15.00 F 3 9.00 O 1629 8.00 N 1401 7.00 C 5323 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: 0.76 Conformation dependent library (CDL) restraints added in 304.1 milliseconds 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 12 sheets defined 40.5% alpha, 15.4% beta 13 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 removed outlier: 3.581A pdb=" N GLU A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 84 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 114 through 118 removed outlier: 4.096A pdb=" N VAL A 118 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 removed outlier: 4.593A pdb=" N LYS A 126 " --> pdb=" O GLU A 122 " (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: 3.666A pdb=" N THR A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.768A 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 282 removed outlier: 3.872A pdb=" N LEU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) 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: 3.656A pdb=" N GLU A 404 " --> pdb=" O THR A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 489 Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.563A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.530A pdb=" N ASN A 519 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 4.537A pdb=" N GLN A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 552 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 removed outlier: 3.695A pdb=" N GLU B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU B 40 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 44 " --> pdb=" O GLU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 68 removed outlier: 3.932A pdb=" N ASP B 67 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 removed outlier: 3.765A pdb=" N LYS B 82 " --> pdb=" O ARG B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.794A pdb=" N LYS B 101 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.925A pdb=" N LYS B 126 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 154 through 175 removed outlier: 3.976A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 4.941A 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: 3.698A pdb=" N ARG B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 253 through 269 removed outlier: 4.142A pdb=" N GLN B 269 " --> pdb=" O ASN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 Processing helix chain 'B' and resid 296 through 312 removed outlier: 3.716A pdb=" N GLU B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 363 removed outlier: 4.470A pdb=" N ALA B 360 " --> pdb=" O ARG B 356 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS B 361 " --> pdb=" O MET B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 394 through 402 removed outlier: 3.835A pdb=" N TRP B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.673A pdb=" N GLN A 145 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG A 143 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 110 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 326 through 331 removed outlier: 3.898A pdb=" N GLU A 328 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN A 340 " --> pdb=" O GLU A 328 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TYR A 339 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR A 351 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLN A 343 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LYS A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.938A pdb=" N THR A 362 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.720A 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 389 through 391 removed outlier: 6.830A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 464 through 470 removed outlier: 4.373A pdb=" N GLU A 438 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL A 493 " --> pdb=" O TYR A 532 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ALA A 534 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE A 495 " --> pdb=" O ALA A 534 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AA9, first strand: chain 'B' and resid 60 through 63 Processing sheet with id=AB1, first strand: chain 'B' and resid 105 through 110 removed outlier: 3.554A pdb=" N SER B 105 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 347 through 351 removed outlier: 8.574A pdb=" N ASN B 348 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLN B 343 " --> pdb=" O ASN B 348 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 347 through 351 removed outlier: 8.574A pdb=" N ASN B 348 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLN B 343 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE B 389 " --> pdb=" O GLU B 415 " (cutoff:3.500A) 298 hydrogen bonds defined for protein. 822 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 35 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 1.44 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1316 1.27 - 1.40: 2137 1.40 - 1.54: 5024 1.54 - 1.67: 193 1.67 - 1.81: 26 Bond restraints: 8696 Sorted by residual: bond pdb=" C10 2KW A 601 " pdb=" C9 2KW A 601 " ideal model delta sigma weight residual 1.354 1.522 -0.168 2.00e-02 2.50e+03 7.04e+01 bond pdb=" C21 2KW A 601 " pdb=" N20 2KW A 601 " ideal model delta sigma weight residual 1.356 1.499 -0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" C10 2KW A 601 " pdb=" N11 2KW A 601 " ideal model delta sigma weight residual 1.355 1.489 -0.134 2.00e-02 2.50e+03 4.51e+01 bond pdb=" C7 2KW A 601 " pdb=" C8 2KW A 601 " ideal model delta sigma weight residual 1.359 1.481 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C18 2KW A 601 " pdb=" N19 2KW A 601 " ideal model delta sigma weight residual 1.287 1.402 -0.115 2.00e-02 2.50e+03 3.28e+01 ... (remaining 8691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 11854 3.06 - 6.11: 109 6.11 - 9.17: 10 9.17 - 12.23: 1 12.23 - 15.28: 1 Bond angle restraints: 11975 Sorted by residual: angle pdb=" C ASP A 186 " pdb=" CA ASP A 186 " pdb=" CB ASP A 186 " ideal model delta sigma weight residual 109.38 94.10 15.28 2.03e+00 2.43e-01 5.67e+01 angle pdb=" C CYS A 63 " pdb=" CA CYS A 63 " pdb=" CB CYS A 63 " ideal model delta sigma weight residual 109.66 120.31 -10.65 1.94e+00 2.66e-01 3.01e+01 angle pdb=" N ASP A 186 " pdb=" CA ASP A 186 " pdb=" C ASP A 186 " ideal model delta sigma weight residual 109.06 117.88 -8.82 1.70e+00 3.46e-01 2.69e+01 angle pdb=" N GLY B 155 " pdb=" CA GLY B 155 " pdb=" C GLY B 155 " ideal model delta sigma weight residual 113.86 107.18 6.68 1.50e+00 4.44e-01 1.98e+01 angle pdb=" C5' DG E 33 " pdb=" C4' DG E 33 " pdb=" O4' DG E 33 " ideal model delta sigma weight residual 109.40 115.87 -6.47 1.50e+00 4.44e-01 1.86e+01 ... (remaining 11970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 4321 17.27 - 34.55: 560 34.55 - 51.82: 159 51.82 - 69.09: 45 69.09 - 86.37: 10 Dihedral angle restraints: 5095 sinusoidal: 2344 harmonic: 2751 Sorted by residual: dihedral pdb=" C ASP A 186 " pdb=" N ASP A 186 " pdb=" CA ASP A 186 " pdb=" CB ASP A 186 " ideal model delta harmonic sigma weight residual -122.60 -107.57 -15.03 0 2.50e+00 1.60e-01 3.61e+01 dihedral pdb=" CA ILE A 411 " pdb=" C ILE A 411 " pdb=" N PRO A 412 " pdb=" CA PRO A 412 " ideal model delta harmonic sigma weight residual -180.00 -160.56 -19.44 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA PHE A 77 " pdb=" C PHE A 77 " pdb=" N ARG A 78 " pdb=" CA ARG A 78 " ideal model delta harmonic sigma weight residual -180.00 -161.62 -18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 5092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1181 0.083 - 0.166: 115 0.166 - 0.249: 7 0.249 - 0.332: 1 0.332 - 0.415: 2 Chirality restraints: 1306 Sorted by residual: chirality pdb=" C4' DG E 32 " pdb=" C5' DG E 32 " pdb=" O4' DG E 32 " pdb=" C3' DG E 32 " both_signs ideal model delta sigma weight residual False -2.53 -2.11 -0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" C4' DG E 33 " pdb=" C5' DG E 33 " pdb=" O4' DG E 33 " pdb=" C3' DG E 33 " both_signs ideal model delta sigma weight residual False -2.53 -2.15 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" C4' DC E 22 " pdb=" C5' DC E 22 " pdb=" O4' DC E 22 " pdb=" C3' DC E 22 " both_signs ideal model delta sigma weight residual False -2.53 -2.26 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1303 not shown) Planarity restraints: 1388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 358 " 0.492 9.50e-02 1.11e+02 2.20e-01 2.97e+01 pdb=" NE ARG A 358 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 358 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 358 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 358 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 467 " -0.087 5.00e-02 4.00e+02 1.30e-01 2.70e+01 pdb=" N PRO A 468 " 0.225 5.00e-02 4.00e+02 pdb=" CA PRO A 468 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO A 468 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 414 " 0.014 2.00e-02 2.50e+03 1.92e-02 9.19e+00 pdb=" CG TRP B 414 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 414 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP B 414 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 414 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 414 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 414 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 414 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 414 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 414 " 0.001 2.00e-02 2.50e+03 ... (remaining 1385 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2631 2.84 - 3.35: 7457 3.35 - 3.87: 13733 3.87 - 4.38: 15986 4.38 - 4.90: 26814 Nonbonded interactions: 66621 Sorted by model distance: nonbonded pdb=" O VAL A 35 " pdb=" OG1 THR A 39 " model vdw 2.324 3.040 nonbonded pdb=" OH TYR B 115 " pdb=" OE1 GLN B 182 " model vdw 2.360 3.040 nonbonded pdb=" OG1 THR A 107 " pdb=" NE2 HIS A 198 " model vdw 2.371 3.120 nonbonded pdb=" O LYS B 366 " pdb=" OE1 GLU B 370 " model vdw 2.382 3.040 nonbonded pdb=" O LYS A 103 " pdb=" N20 2KW A 601 " model vdw 2.383 3.120 ... (remaining 66616 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 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: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.490 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 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 0.168 8696 Z= 0.295 Angle : 0.743 15.282 11975 Z= 0.412 Chirality : 0.049 0.415 1306 Planarity : 0.008 0.220 1388 Dihedral : 16.930 86.367 3319 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.24 % Allowed : 1.57 % Favored : 98.19 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.27), residues: 931 helix: 0.63 (0.31), residues: 316 sheet: -0.91 (0.40), residues: 151 loop : -0.91 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 199 TYR 0.027 0.001 TYR A 405 PHE 0.011 0.001 PHE B 130 TRP 0.050 0.001 TRP B 414 HIS 0.003 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00602 ( 8696) covalent geometry : angle 0.74280 (11975) hydrogen bonds : bond 0.13888 ( 331) hydrogen bonds : angle 6.79310 ( 892) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.305 Fit side-chains REVERT: A 164 MET cc_start: 0.8586 (tpp) cc_final: 0.7881 (tpp) REVERT: A 500 GLN cc_start: 0.7479 (mp10) cc_final: 0.7122 (mm-40) outliers start: 2 outliers final: 0 residues processed: 115 average time/residue: 0.0807 time to fit residues: 13.4541 Evaluate side-chains 83 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.0770 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN A 547 GLN B 255 ASN B 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.188192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.160000 restraints weight = 9194.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.157881 restraints weight = 12625.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.157060 restraints weight = 13851.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.155855 restraints weight = 12630.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.155923 restraints weight = 12020.563| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8696 Z= 0.199 Angle : 0.622 8.443 11975 Z= 0.321 Chirality : 0.044 0.176 1306 Planarity : 0.005 0.094 1388 Dihedral : 15.802 78.509 1369 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.08 % Allowed : 11.20 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.27), residues: 931 helix: 0.82 (0.30), residues: 322 sheet: -0.98 (0.39), residues: 154 loop : -0.92 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 199 TYR 0.013 0.002 TYR A 405 PHE 0.018 0.002 PHE B 61 TRP 0.012 0.002 TRP B 383 HIS 0.005 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 8696) covalent geometry : angle 0.62176 (11975) hydrogen bonds : bond 0.04493 ( 331) hydrogen bonds : angle 4.71590 ( 892) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.8612 (tpp) cc_final: 0.8056 (tpp) REVERT: A 500 GLN cc_start: 0.7554 (mp10) cc_final: 0.7220 (mt0) outliers start: 9 outliers final: 6 residues processed: 96 average time/residue: 0.0829 time to fit residues: 11.4957 Evaluate side-chains 88 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 19 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 30 optimal weight: 0.0000 chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.189021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.159035 restraints weight = 9146.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.156639 restraints weight = 13316.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.156212 restraints weight = 13751.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.154906 restraints weight = 12101.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.155727 restraints weight = 11009.816| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8696 Z= 0.162 Angle : 0.580 9.010 11975 Z= 0.298 Chirality : 0.042 0.163 1306 Planarity : 0.004 0.081 1388 Dihedral : 15.731 78.482 1369 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.69 % Allowed : 13.98 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.27), residues: 931 helix: 1.00 (0.30), residues: 324 sheet: -0.75 (0.40), residues: 149 loop : -0.91 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 199 TYR 0.010 0.001 TYR B 319 PHE 0.013 0.001 PHE B 130 TRP 0.012 0.001 TRP B 383 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8696) covalent geometry : angle 0.58025 (11975) hydrogen bonds : bond 0.03928 ( 331) hydrogen bonds : angle 4.53002 ( 892) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.8593 (tpp) cc_final: 0.8071 (tpp) REVERT: A 500 GLN cc_start: 0.7630 (mp10) cc_final: 0.7206 (mt0) outliers start: 14 outliers final: 10 residues processed: 100 average time/residue: 0.0763 time to fit residues: 11.2219 Evaluate side-chains 92 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 39 optimal weight: 0.0980 chunk 19 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.188169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.158236 restraints weight = 9247.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.155897 restraints weight = 13244.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.156419 restraints weight = 14030.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.154803 restraints weight = 11358.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.155545 restraints weight = 11080.268| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8696 Z= 0.174 Angle : 0.582 8.072 11975 Z= 0.300 Chirality : 0.043 0.150 1306 Planarity : 0.004 0.074 1388 Dihedral : 15.764 77.826 1369 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.29 % Allowed : 15.06 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.27), residues: 931 helix: 0.95 (0.30), residues: 330 sheet: -0.79 (0.40), residues: 149 loop : -0.99 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 199 TYR 0.018 0.001 TYR B 319 PHE 0.019 0.001 PHE B 87 TRP 0.010 0.001 TRP B 402 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 8696) covalent geometry : angle 0.58193 (11975) hydrogen bonds : bond 0.03847 ( 331) hydrogen bonds : angle 4.52015 ( 892) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.260 Fit side-chains REVERT: A 500 GLN cc_start: 0.7621 (mp10) cc_final: 0.7214 (mt0) outliers start: 19 outliers final: 16 residues processed: 96 average time/residue: 0.0717 time to fit residues: 10.3845 Evaluate side-chains 92 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 2 optimal weight: 0.0020 chunk 33 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 27 optimal weight: 0.3980 chunk 54 optimal weight: 7.9990 overall best weight: 2.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.190085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.159168 restraints weight = 9310.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.156734 restraints weight = 15400.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.158317 restraints weight = 16061.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.158288 restraints weight = 12127.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.158449 restraints weight = 10381.982| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8696 Z= 0.141 Angle : 0.548 10.367 11975 Z= 0.281 Chirality : 0.041 0.142 1306 Planarity : 0.004 0.049 1388 Dihedral : 15.697 76.834 1369 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.81 % Allowed : 16.27 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.27), residues: 931 helix: 1.08 (0.30), residues: 332 sheet: -0.73 (0.40), residues: 149 loop : -0.97 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 199 TYR 0.012 0.001 TYR B 319 PHE 0.025 0.001 PHE B 87 TRP 0.013 0.001 TRP B 383 HIS 0.002 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8696) covalent geometry : angle 0.54840 (11975) hydrogen bonds : bond 0.03503 ( 331) hydrogen bonds : angle 4.35364 ( 892) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.329 Fit side-chains REVERT: A 500 GLN cc_start: 0.7563 (mp10) cc_final: 0.7170 (mt0) REVERT: B 346 PHE cc_start: 0.6048 (m-80) cc_final: 0.5489 (m-80) outliers start: 15 outliers final: 13 residues processed: 98 average time/residue: 0.0710 time to fit residues: 10.4845 Evaluate side-chains 96 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 21 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 82 optimal weight: 0.0470 chunk 80 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.189366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.159756 restraints weight = 9171.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.157226 restraints weight = 13357.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.157406 restraints weight = 13998.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.156467 restraints weight = 11342.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.157117 restraints weight = 10508.140| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8696 Z= 0.155 Angle : 0.562 9.141 11975 Z= 0.286 Chirality : 0.042 0.141 1306 Planarity : 0.004 0.051 1388 Dihedral : 15.755 76.132 1369 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.13 % Allowed : 16.02 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.27), residues: 931 helix: 1.08 (0.29), residues: 332 sheet: -0.78 (0.40), residues: 149 loop : -0.99 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 199 TYR 0.010 0.001 TYR B 144 PHE 0.013 0.001 PHE B 130 TRP 0.014 0.001 TRP B 383 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 8696) covalent geometry : angle 0.56163 (11975) hydrogen bonds : bond 0.03556 ( 331) hydrogen bonds : angle 4.34130 ( 892) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 500 GLN cc_start: 0.7601 (mp10) cc_final: 0.7193 (mt0) REVERT: B 346 PHE cc_start: 0.6011 (m-80) cc_final: 0.5464 (m-80) outliers start: 26 outliers final: 22 residues processed: 101 average time/residue: 0.0696 time to fit residues: 10.6509 Evaluate side-chains 102 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 89 optimal weight: 4.9990 chunk 44 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 55 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.188719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.158026 restraints weight = 9296.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.155312 restraints weight = 15631.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.155667 restraints weight = 15599.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.153141 restraints weight = 12463.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.154341 restraints weight = 12056.421| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8696 Z= 0.169 Angle : 0.571 8.346 11975 Z= 0.293 Chirality : 0.043 0.285 1306 Planarity : 0.004 0.057 1388 Dihedral : 15.832 76.057 1369 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.89 % Allowed : 16.63 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.27), residues: 931 helix: 1.11 (0.29), residues: 330 sheet: -0.84 (0.40), residues: 149 loop : -0.98 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 199 TYR 0.015 0.001 TYR B 319 PHE 0.014 0.001 PHE B 130 TRP 0.009 0.001 TRP A 410 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 8696) covalent geometry : angle 0.57138 (11975) hydrogen bonds : bond 0.03606 ( 331) hydrogen bonds : angle 4.36330 ( 892) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.326 Fit side-chains REVERT: A 500 GLN cc_start: 0.7590 (mp10) cc_final: 0.7197 (mt0) REVERT: B 346 PHE cc_start: 0.6071 (m-80) cc_final: 0.5564 (m-80) outliers start: 24 outliers final: 21 residues processed: 101 average time/residue: 0.0746 time to fit residues: 11.3245 Evaluate side-chains 101 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 418 ASN Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 59 optimal weight: 0.1980 chunk 49 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 53 optimal weight: 0.0020 chunk 11 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.194616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.165098 restraints weight = 9123.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.162554 restraints weight = 13674.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.163131 restraints weight = 13223.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.161029 restraints weight = 12860.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.161847 restraints weight = 11761.619| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8696 Z= 0.105 Angle : 0.527 8.235 11975 Z= 0.268 Chirality : 0.041 0.266 1306 Planarity : 0.004 0.057 1388 Dihedral : 15.468 72.765 1369 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.93 % Allowed : 18.07 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.28), residues: 931 helix: 1.45 (0.30), residues: 327 sheet: -0.58 (0.40), residues: 149 loop : -0.84 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 358 TYR 0.008 0.001 TYR B 319 PHE 0.007 0.001 PHE A 171 TRP 0.008 0.001 TRP B 383 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8696) covalent geometry : angle 0.52712 (11975) hydrogen bonds : bond 0.02946 ( 331) hydrogen bonds : angle 4.06407 ( 892) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6391 (pm20) REVERT: A 500 GLN cc_start: 0.7564 (mp10) cc_final: 0.7161 (mt0) REVERT: B 346 PHE cc_start: 0.5981 (m-80) cc_final: 0.5581 (m-80) outliers start: 16 outliers final: 12 residues processed: 112 average time/residue: 0.0766 time to fit residues: 12.8355 Evaluate side-chains 102 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 265 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 91 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 27 optimal weight: 0.2980 chunk 21 optimal weight: 7.9990 chunk 89 optimal weight: 0.0970 chunk 28 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 GLN ** B 265 ASN ** 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 = 0.4013 r_free = 0.4013 target = 0.192338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.164356 restraints weight = 9205.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.162218 restraints weight = 12837.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.161319 restraints weight = 13998.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.160005 restraints weight = 13263.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.160827 restraints weight = 11837.577| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8696 Z= 0.129 Angle : 0.528 7.543 11975 Z= 0.269 Chirality : 0.042 0.257 1306 Planarity : 0.004 0.061 1388 Dihedral : 15.461 72.994 1369 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.05 % Allowed : 18.31 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.28), residues: 931 helix: 1.44 (0.29), residues: 332 sheet: -0.62 (0.39), residues: 149 loop : -0.83 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 199 TYR 0.011 0.001 TYR B 319 PHE 0.024 0.001 PHE B 87 TRP 0.012 0.001 TRP B 383 HIS 0.002 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8696) covalent geometry : angle 0.52837 (11975) hydrogen bonds : bond 0.03117 ( 331) hydrogen bonds : angle 4.02725 ( 892) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.6432 (pm20) REVERT: A 500 GLN cc_start: 0.7575 (mp10) cc_final: 0.7173 (mt0) REVERT: B 346 PHE cc_start: 0.6057 (m-80) cc_final: 0.5619 (m-80) outliers start: 17 outliers final: 16 residues processed: 99 average time/residue: 0.0679 time to fit residues: 10.2926 Evaluate side-chains 100 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 363 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 70 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.187003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.157319 restraints weight = 9137.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.154270 restraints weight = 15964.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.153717 restraints weight = 16282.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.150862 restraints weight = 13626.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.152159 restraints weight = 13070.676| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8696 Z= 0.218 Angle : 0.615 10.273 11975 Z= 0.313 Chirality : 0.045 0.251 1306 Planarity : 0.004 0.065 1388 Dihedral : 15.700 75.623 1369 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.17 % Allowed : 18.80 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.27), residues: 931 helix: 1.10 (0.29), residues: 330 sheet: -0.93 (0.39), residues: 149 loop : -0.99 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 199 TYR 0.015 0.002 TYR B 319 PHE 0.018 0.002 PHE B 130 TRP 0.016 0.002 TRP B 383 HIS 0.005 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 8696) covalent geometry : angle 0.61521 (11975) hydrogen bonds : bond 0.03915 ( 331) hydrogen bonds : angle 4.36437 ( 892) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1862 Ramachandran restraints generated. 931 Oldfield, 0 Emsley, 931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 89 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6485 (pm20) REVERT: A 500 GLN cc_start: 0.7658 (mp10) cc_final: 0.7293 (mt0) REVERT: B 346 PHE cc_start: 0.6230 (m-80) cc_final: 0.5740 (m-80) outliers start: 18 outliers final: 14 residues processed: 93 average time/residue: 0.0763 time to fit residues: 10.6854 Evaluate side-chains 89 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 363 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 33 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 75 optimal weight: 0.0470 chunk 47 optimal weight: 10.0000 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.187414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.157478 restraints weight = 9224.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.155758 restraints weight = 13613.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.155784 restraints weight = 13832.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.153017 restraints weight = 13463.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.153716 restraints weight = 13688.688| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8696 Z= 0.198 Angle : 0.592 7.358 11975 Z= 0.304 Chirality : 0.044 0.249 1306 Planarity : 0.004 0.064 1388 Dihedral : 15.698 75.928 1369 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.05 % Allowed : 18.67 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.27), residues: 931 helix: 1.03 (0.29), residues: 330 sheet: -1.04 (0.38), residues: 149 loop : -1.02 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 199 TYR 0.012 0.002 TYR B 319 PHE 0.021 0.002 PHE B 87 TRP 0.015 0.001 TRP B 383 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 8696) covalent geometry : angle 0.59245 (11975) hydrogen bonds : bond 0.03763 ( 331) hydrogen bonds : angle 4.37579 ( 892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1253.24 seconds wall clock time: 22 minutes 26.07 seconds (1346.07 seconds total)