Starting phenix.real_space_refine on Wed Feb 12 20:08:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z2g_14465/02_2025/7z2g_14465.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2g_14465/02_2025/7z2g_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7z2g_14465/02_2025/7z2g_14465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2g_14465/02_2025/7z2g_14465.map" model { file = "/net/cci-nas-00/data/ceres_data/7z2g_14465/02_2025/7z2g_14465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2g_14465/02_2025/7z2g_14465.cif" } resolution = 3.65 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= 0.026 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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:plan2': 1, ' DA%5*END:plan': 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: 5.14, per 1000 atoms: 0.61 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: 2.27 Conformation dependent library (CDL) restraints added in 964.8 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: 3.16 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: 2.80 Time building geometry restraints manager: 2.63 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: 0.200 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.380 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.320 ------------------------------------------------------------------------------- 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= 0.339 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 : 8.07 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 (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: -0.62 (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 TRP 0.050 0.001 TRP B 414 HIS 0.003 0.001 HIS A 315 PHE 0.011 0.001 PHE B 130 TYR 0.027 0.001 TYR A 405 ARG 0.003 0.000 ARG A 199 *********************** 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 : 0.862 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: 0.7121 (mm-40) outliers start: 2 outliers final: 0 residues processed: 115 average time/residue: 0.1874 time to fit residues: 30.9011 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 : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 75 optimal weight: 50.0000 chunk 29 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 GLN B 255 ASN B 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.190109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.162952 restraints weight = 9103.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.161008 restraints weight = 12191.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.159161 restraints weight = 11855.230| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8696 Z= 0.240 Angle : 0.589 8.557 11975 Z= 0.305 Chirality : 0.043 0.167 1306 Planarity : 0.005 0.093 1388 Dihedral : 15.667 77.900 1369 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.08 % Allowed : 10.24 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.44 (0.28), residues: 931 helix: 0.91 (0.30), residues: 322 sheet: -0.96 (0.39), residues: 156 loop : -0.88 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 383 HIS 0.004 0.001 HIS A 315 PHE 0.015 0.001 PHE B 61 TYR 0.011 0.001 TYR A 405 ARG 0.002 0.000 ARG A 72 *********************** 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 104 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 500 GLN cc_start: 0.7418 (mp10) cc_final: 0.7145 (mt0) REVERT: B 260 LEU cc_start: 0.8779 (tt) cc_final: 0.8557 (tp) outliers start: 9 outliers final: 7 residues processed: 99 average time/residue: 0.1894 time to fit residues: 26.9419 Evaluate side-chains 91 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 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 85 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 75 optimal weight: 50.0000 chunk 42 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN B 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.186770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.155853 restraints weight = 9339.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.154127 restraints weight = 14499.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.154612 restraints weight = 15046.147| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8696 Z= 0.319 Angle : 0.624 7.554 11975 Z= 0.320 Chirality : 0.044 0.167 1306 Planarity : 0.005 0.083 1388 Dihedral : 15.810 78.630 1369 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.05 % Allowed : 13.37 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.55 (0.27), residues: 931 helix: 0.79 (0.29), residues: 330 sheet: -0.87 (0.40), residues: 149 loop : -1.02 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 402 HIS 0.005 0.001 HIS A 315 PHE 0.018 0.002 PHE B 130 TYR 0.011 0.002 TYR A 181 ARG 0.004 0.000 ARG A 199 *********************** 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 106 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 500 GLN cc_start: 0.7588 (mp10) cc_final: 0.7211 (mt0) REVERT: B 260 LEU cc_start: 0.8743 (tt) cc_final: 0.8540 (tp) outliers start: 17 outliers final: 12 residues processed: 99 average time/residue: 0.1847 time to fit residues: 26.7464 Evaluate side-chains 95 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 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 120 LEU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 148 VAL 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 78 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 30 optimal weight: 5.9990 chunk 75 optimal weight: 40.0000 chunk 20 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3986 r_free = 0.3986 target = 0.189635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.159922 restraints weight = 9150.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.157708 restraints weight = 12836.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.157525 restraints weight = 13423.218| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8696 Z= 0.213 Angle : 0.555 6.379 11975 Z= 0.286 Chirality : 0.042 0.148 1306 Planarity : 0.004 0.072 1388 Dihedral : 15.704 77.801 1369 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.81 % Allowed : 14.58 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.33 (0.27), residues: 931 helix: 1.02 (0.30), residues: 330 sheet: -0.72 (0.41), residues: 149 loop : -0.94 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 153 HIS 0.003 0.001 HIS A 315 PHE 0.012 0.001 PHE B 130 TYR 0.019 0.001 TYR B 319 ARG 0.003 0.000 ARG A 199 *********************** 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 104 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.957 Fit side-chains REVERT: A 500 GLN cc_start: 0.7604 (mp10) cc_final: 0.7207 (mt0) outliers start: 15 outliers final: 12 residues processed: 100 average time/residue: 0.1779 time to fit residues: 26.5662 Evaluate side-chains 94 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 193 LEU 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 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 417 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 63 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 182 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 = 0.3961 r_free = 0.3961 target = 0.187008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.156210 restraints weight = 9193.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.153944 restraints weight = 15884.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.154400 restraints weight = 16532.430| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8696 Z= 0.306 Angle : 0.607 10.005 11975 Z= 0.311 Chirality : 0.043 0.145 1306 Planarity : 0.004 0.051 1388 Dihedral : 15.885 77.382 1369 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.65 % Allowed : 16.02 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.56 (0.27), residues: 931 helix: 0.90 (0.29), residues: 330 sheet: -0.92 (0.40), residues: 149 loop : -1.10 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 402 HIS 0.005 0.001 HIS A 315 PHE 0.028 0.002 PHE B 87 TYR 0.018 0.002 TYR B 319 ARG 0.003 0.000 ARG A 199 *********************** 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 103 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.823 Fit side-chains REVERT: A 500 GLN cc_start: 0.7590 (mp10) cc_final: 0.7205 (mt0) REVERT: B 346 PHE cc_start: 0.6187 (m-80) cc_final: 0.5594 (m-80) outliers start: 22 outliers final: 21 residues processed: 96 average time/residue: 0.1817 time to fit residues: 25.9770 Evaluate side-chains 98 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 11 LYS 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 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 417 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 28 optimal weight: 30.0000 chunk 40 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 79 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.189786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.160359 restraints weight = 9147.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.158031 restraints weight = 12606.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.158513 restraints weight = 13002.655| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.1597 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= 0.201 Angle : 0.545 9.197 11975 Z= 0.279 Chirality : 0.041 0.140 1306 Planarity : 0.004 0.051 1388 Dihedral : 15.768 76.331 1369 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.65 % Allowed : 16.87 % 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 (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: -0.36 (0.27), residues: 931 helix: 1.08 (0.30), residues: 332 sheet: -0.85 (0.39), residues: 149 loop : -1.00 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 383 HIS 0.003 0.001 HIS A 315 PHE 0.017 0.001 PHE B 87 TYR 0.014 0.001 TYR B 319 ARG 0.003 0.000 ARG A 199 *********************** 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 107 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.834 Fit side-chains REVERT: A 89 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6667 (pm20) REVERT: A 500 GLN cc_start: 0.7541 (mp10) cc_final: 0.7162 (mt0) REVERT: B 346 PHE cc_start: 0.6058 (m-80) cc_final: 0.5581 (m-80) outliers start: 22 outliers final: 14 residues processed: 103 average time/residue: 0.1790 time to fit residues: 27.2163 Evaluate side-chains 96 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 469 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 21 VAL 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 417 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 71 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 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 = 0.187198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.156925 restraints weight = 9217.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.155155 restraints weight = 13968.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.153044 restraints weight = 14105.213| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8696 Z= 0.296 Angle : 0.608 8.559 11975 Z= 0.311 Chirality : 0.044 0.281 1306 Planarity : 0.004 0.058 1388 Dihedral : 15.935 76.331 1369 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.01 % Allowed : 17.11 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.51 (0.27), residues: 931 helix: 0.95 (0.29), residues: 330 sheet: -0.98 (0.39), residues: 149 loop : -1.06 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 383 HIS 0.005 0.001 HIS A 315 PHE 0.017 0.001 PHE B 130 TYR 0.018 0.002 TYR B 319 ARG 0.004 0.000 ARG A 199 *********************** 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 105 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 89 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6264 (pm20) REVERT: A 500 GLN cc_start: 0.7621 (mp10) cc_final: 0.7201 (mt0) REVERT: B 346 PHE cc_start: 0.6106 (m-80) cc_final: 0.5582 (m-80) outliers start: 25 outliers final: 23 residues processed: 98 average time/residue: 0.1708 time to fit residues: 25.0528 Evaluate side-chains 100 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 161 GLN 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 11 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 40 optimal weight: 0.0980 chunk 8 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 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 ** 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 = 0.3970 r_free = 0.3970 target = 0.187990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.158468 restraints weight = 9280.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.157165 restraints weight = 13259.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.157436 restraints weight = 12984.331| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8696 Z= 0.260 Angle : 0.582 7.900 11975 Z= 0.299 Chirality : 0.043 0.266 1306 Planarity : 0.004 0.060 1388 Dihedral : 15.900 76.028 1369 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.65 % Allowed : 17.95 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.49 (0.27), residues: 931 helix: 0.98 (0.29), residues: 330 sheet: -1.00 (0.39), residues: 149 loop : -1.04 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 383 HIS 0.004 0.001 HIS A 315 PHE 0.027 0.002 PHE B 87 TYR 0.016 0.001 TYR B 319 ARG 0.004 0.000 ARG A 199 *********************** 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 99 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.835 Fit side-chains REVERT: A 89 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6281 (pm20) REVERT: A 500 GLN cc_start: 0.7553 (mp10) cc_final: 0.7181 (mt0) REVERT: B 346 PHE cc_start: 0.6141 (m-80) cc_final: 0.5651 (m-80) outliers start: 22 outliers final: 20 residues processed: 93 average time/residue: 0.1832 time to fit residues: 25.0310 Evaluate side-chains 98 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 161 GLN 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 469 LEU Chi-restraints excluded: chain A residue 497 THR Chi-restraints excluded: chain B residue 11 LYS 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 417 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 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 = 0.3965 r_free = 0.3965 target = 0.187379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.158559 restraints weight = 9273.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.157373 restraints weight = 14345.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.157426 restraints weight = 13911.794| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8696 Z= 0.291 Angle : 0.609 9.133 11975 Z= 0.314 Chirality : 0.044 0.259 1306 Planarity : 0.004 0.063 1388 Dihedral : 15.914 75.825 1369 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.73 % Allowed : 17.11 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.59 (0.27), residues: 931 helix: 0.84 (0.29), residues: 330 sheet: -1.03 (0.39), residues: 149 loop : -1.06 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 383 HIS 0.004 0.001 HIS A 315 PHE 0.020 0.001 PHE B 87 TYR 0.017 0.002 TYR B 319 ARG 0.004 0.000 ARG A 199 *********************** 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 110 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 89 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6297 (pm20) REVERT: A 376 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8142 (m) REVERT: A 500 GLN cc_start: 0.7614 (mp10) cc_final: 0.7274 (mt0) REVERT: B 346 PHE cc_start: 0.6182 (m-80) cc_final: 0.5692 (m-80) outliers start: 31 outliers final: 26 residues processed: 102 average time/residue: 0.1744 time to fit residues: 26.2717 Evaluate side-chains 105 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 161 GLN 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 376 THR 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 11 LYS 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 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 Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 60 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN B 198 HIS ** 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 = 0.3968 r_free = 0.3968 target = 0.187631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.158318 restraints weight = 9188.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.156807 restraints weight = 13198.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.156975 restraints weight = 13630.381| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8696 Z= 0.291 Angle : 0.611 9.311 11975 Z= 0.315 Chirality : 0.044 0.254 1306 Planarity : 0.004 0.064 1388 Dihedral : 15.908 75.583 1369 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.49 % Allowed : 17.59 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.60 (0.27), residues: 931 helix: 0.83 (0.29), residues: 330 sheet: -1.05 (0.39), residues: 149 loop : -1.06 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 383 HIS 0.004 0.001 HIS A 315 PHE 0.016 0.001 PHE B 130 TYR 0.017 0.002 TYR B 319 ARG 0.004 0.000 ARG A 199 ********************** 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 110 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6352 (pm20) REVERT: A 376 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8156 (m) REVERT: A 500 GLN cc_start: 0.7640 (mp10) cc_final: 0.7296 (mt0) REVERT: B 346 PHE cc_start: 0.6170 (m-80) cc_final: 0.5714 (m-80) outliers start: 29 outliers final: 26 residues processed: 101 average time/residue: 0.1809 time to fit residues: 26.9948 Evaluate side-chains 105 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 161 GLN 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 376 THR 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 11 LYS 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 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 Chi-restraints excluded: chain B residue 370 GLU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 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 = 0.3983 r_free = 0.3983 target = 0.189280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.158721 restraints weight = 9255.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.156394 restraints weight = 14913.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.157301 restraints weight = 14696.965| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8696 Z= 0.220 Angle : 0.585 9.974 11975 Z= 0.299 Chirality : 0.043 0.248 1306 Planarity : 0.004 0.063 1388 Dihedral : 15.756 74.576 1369 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.01 % Allowed : 18.07 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.48 (0.27), residues: 931 helix: 0.92 (0.30), residues: 332 sheet: -0.93 (0.40), residues: 149 loop : -1.00 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 383 HIS 0.003 0.001 HIS A 315 PHE 0.019 0.001 PHE B 87 TYR 0.013 0.001 TYR B 319 ARG 0.004 0.000 ARG A 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2225.47 seconds wall clock time: 41 minutes 5.50 seconds (2465.50 seconds total)