Starting phenix.real_space_refine on Fri Sep 11 06:45:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z2g_14465/09_2026/7z2g_14465.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2g_14465/09_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_14465/09_2026/7z2g_14465.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2g_14465/09_2026/7z2g_14465.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7z2g_14465/09_2026/7z2g_14465.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z2g_14465/09_2026/7z2g_14465.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z2g_14465/09_2026/7z2g_14465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2g_14465/09_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 1.71, per 1000 atoms: 0.20 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: 0.86 Conformation dependent library (CDL) restraints added in 174.1 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: 0.91 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: 1.38 Time building geometry restraints manager: 1.04 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=" C4' DG E 32 " pdb=" O4' DG E 32 " ideal model delta sigma weight residual 1.446 1.364 0.082 1.00e-02 1.00e+04 6.71e+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 ... (remaining 8691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 11859 3.06 - 6.11: 104 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=" O4' DA E 26 " pdb=" C4' DA E 26 " pdb=" C3' DA E 26 " ideal model delta sigma weight residual 106.00 102.73 3.27 6.00e-01 2.78e+00 2.97e+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 ... (remaining 11970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 4308 17.27 - 34.55: 560 34.55 - 51.82: 159 51.82 - 69.09: 45 69.09 - 86.37: 10 Dihedral angle restraints: 5082 sinusoidal: 2331 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 5079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1173 0.084 - 0.168: 123 0.168 - 0.253: 7 0.253 - 0.337: 1 0.337 - 0.421: 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 -0.42 2.00e-01 2.50e+01 4.43e+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 -0.38 2.00e-01 2.50e+01 3.60e+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 -0.27 2.00e-01 2.50e+01 1.83e+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: 0.100 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.850 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 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= 0.316 Angle : 0.721 15.282 11975 Z= 0.412 Chirality : 0.051 0.421 1306 Planarity : 0.008 0.220 1388 Dihedral : 16.962 86.367 3306 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/Z covalent geometry : bond 0.00589 / 0.32 ( 8696) covalent geometry : angle 0.72121 / 0.41 (11975) hydrogen bonds : bond 0.13888 / 9.08 ( 331) hydrogen bonds : angle 6.79310 / 4.58 ( 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 : 0.260 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: 0.0664 time to fit residues: 11.2108 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 : 0.260 ------------------------------------------------------------------------------- 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... B 255 ASN 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 = 0.189156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.158438 restraints weight = 9189.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.155840 restraints weight = 15024.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.152523 restraints weight = 16069.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.151419 restraints weight = 11453.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.152439 restraints weight = 9871.107| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.0865 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 : 0.636 8.945 11975 Z= 0.335 Chirality : 0.046 0.243 1306 Planarity : 0.005 0.092 1388 Dihedral : 15.849 80.415 1356 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.08 % Allowed : 10.60 % Favored : 88.31 % 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: -0.56 (0.28), residues: 931 helix: 0.76 (0.30), residues: 322 sheet: -1.00 (0.39), residues: 154 loop : -0.91 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 358 TYR 0.013 0.001 TYR A 405 PHE 0.020 0.002 PHE B 61 TRP 0.012 0.002 TRP B 414 HIS 0.005 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 ( 8696) covalent geometry : angle 0.63637 / 0.34 (11975) hydrogen bonds : bond 0.04962 / 3.22 ( 331) hydrogen bonds : angle 4.90596 / 3.42 ( 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 : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 500 GLN cc_start: 0.7534 (mp10) cc_final: 0.7104 (mt0) outliers start: 9 outliers final: 7 residues processed: 96 average time/residue: 0.0766 time to fit residues: 10.6709 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 : 0.229 ------------------------------------------------------------------------------- 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 19 optimal weight: 20.0000 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 0.0270 chunk 3 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 71 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.0644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.192346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.165165 restraints weight = 9073.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.161635 restraints weight = 12081.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.159374 restraints weight = 12834.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.158872 restraints weight = 12757.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.158867 restraints weight = 11766.503| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8696 Z= 0.120 Angle : 0.563 8.870 11975 Z= 0.296 Chirality : 0.042 0.142 1306 Planarity : 0.004 0.075 1388 Dihedral : 15.822 78.765 1356 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.20 % Allowed : 11.45 % Favored : 87.35 % 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: -0.18 (0.28), residues: 931 helix: 1.12 (0.31), residues: 322 sheet: -0.56 (0.41), residues: 149 loop : -0.82 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 199 TYR 0.012 0.001 TYR B 319 PHE 0.019 0.001 PHE B 87 TRP 0.009 0.001 TRP B 153 HIS 0.002 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 8696) covalent geometry : angle 0.56333 / 0.30 (11975) hydrogen bonds : bond 0.04024 / 2.60 ( 331) hydrogen bonds : angle 4.55998 / 3.17 ( 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 108 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.8581 (tpp) cc_final: 0.7921 (tpp) REVERT: A 500 GLN cc_start: 0.7456 (mp10) cc_final: 0.7087 (mt0) REVERT: B 87 PHE cc_start: 0.7057 (t80) cc_final: 0.6811 (t80) outliers start: 10 outliers final: 7 residues processed: 105 average time/residue: 0.0659 time to fit residues: 10.2660 Evaluate side-chains 96 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU 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 189 VAL Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL 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: 8.9990 chunk 48 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 89 optimal weight: 0.4980 chunk 80 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN B 182 GLN B 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.187846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.157915 restraints weight = 9302.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.155737 restraints weight = 14064.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.152680 restraints weight = 14627.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.149704 restraints weight = 13070.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.150497 restraints weight = 12187.754| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1217 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= 0.208 Angle : 0.610 8.276 11975 Z= 0.320 Chirality : 0.044 0.146 1306 Planarity : 0.004 0.070 1388 Dihedral : 15.906 78.804 1356 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.57 % Allowed : 13.86 % 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 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: -0.52 (0.27), residues: 931 helix: 0.82 (0.30), residues: 328 sheet: -0.83 (0.40), residues: 149 loop : -1.01 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 199 TYR 0.021 0.002 TYR B 319 PHE 0.017 0.002 PHE B 87 TRP 0.010 0.002 TRP B 337 HIS 0.005 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 ( 8696) covalent geometry : angle 0.60962 / 0.32 (11975) hydrogen bonds : bond 0.04307 / 2.85 ( 331) hydrogen bonds : angle 4.64344 / 3.24 ( 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: 13 poor density : 89 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 500 GLN cc_start: 0.7641 (mp10) cc_final: 0.7251 (mt0) REVERT: B 87 PHE cc_start: 0.7092 (t80) cc_final: 0.6817 (t80) outliers start: 13 outliers final: 12 residues processed: 97 average time/residue: 0.0846 time to fit residues: 12.0858 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 : 0.321 ------------------------------------------------------------------------------- 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 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 265 ASN Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 2 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 27 optimal weight: 0.0030 chunk 54 optimal weight: 10.0000 overall best weight: 4.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.187683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.156984 restraints weight = 9328.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.154828 restraints weight = 15280.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.155601 restraints weight = 14495.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.155622 restraints weight = 11361.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.155643 restraints weight = 10934.579| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1338 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= 0.195 Angle : 0.604 8.790 11975 Z= 0.316 Chirality : 0.044 0.148 1306 Planarity : 0.004 0.051 1388 Dihedral : 15.955 78.727 1356 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.89 % Allowed : 14.34 % Favored : 82.77 % 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: -0.59 (0.27), residues: 931 helix: 0.81 (0.29), residues: 328 sheet: -0.88 (0.40), residues: 149 loop : -1.08 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 284 TYR 0.020 0.002 TYR B 319 PHE 0.016 0.002 PHE B 130 TRP 0.012 0.001 TRP B 266 HIS 0.005 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 ( 8696) covalent geometry : angle 0.60426 / 0.32 (11975) hydrogen bonds : bond 0.04163 / 2.77 ( 331) hydrogen bonds : angle 4.63590 / 3.22 ( 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 111 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 500 GLN cc_start: 0.7628 (mp10) cc_final: 0.7234 (mt0) REVERT: B 87 PHE cc_start: 0.7083 (t80) cc_final: 0.6854 (t80) outliers start: 24 outliers final: 20 residues processed: 105 average time/residue: 0.0833 time to fit residues: 12.8150 Evaluate side-chains 104 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 193 LEU Chi-restraints excluded: chain A residue 204 GLU 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 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 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: 7.9990 chunk 49 optimal weight: 2.9990 chunk 82 optimal weight: 0.0000 chunk 80 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 overall best weight: 2.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.190324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.160485 restraints weight = 9181.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.157986 restraints weight = 13296.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.158538 restraints weight = 13207.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.156007 restraints weight = 12233.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.156929 restraints weight = 12083.483| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8696 Z= 0.131 Angle : 0.554 8.776 11975 Z= 0.289 Chirality : 0.042 0.142 1306 Planarity : 0.004 0.050 1388 Dihedral : 15.881 78.024 1356 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.93 % Allowed : 15.90 % Favored : 82.17 % 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: 1.03 (0.29), residues: 330 sheet: -0.73 (0.40), residues: 149 loop : -1.01 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 199 TYR 0.010 0.001 TYR B 144 PHE 0.012 0.001 PHE B 87 TRP 0.012 0.001 TRP B 383 HIS 0.003 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 8696) covalent geometry : angle 0.55405 / 0.29 (11975) hydrogen bonds : bond 0.03709 / 2.46 ( 331) hydrogen bonds : angle 4.45711 / 3.10 ( 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 106 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 500 GLN cc_start: 0.7614 (mp10) cc_final: 0.7220 (mt0) outliers start: 16 outliers final: 14 residues processed: 101 average time/residue: 0.0858 time to fit residues: 12.5391 Evaluate side-chains 98 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 204 GLU 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 89 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 37 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 55 optimal weight: 0.0570 chunk 73 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 overall best weight: 1.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.191337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.161821 restraints weight = 9287.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.159407 restraints weight = 13670.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.159648 restraints weight = 13416.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.158338 restraints weight = 12279.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.158698 restraints weight = 11168.590| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1504 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= 0.121 Angle : 0.554 10.021 11975 Z= 0.286 Chirality : 0.042 0.138 1306 Planarity : 0.004 0.053 1388 Dihedral : 15.818 77.311 1356 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.53 % Allowed : 16.14 % 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 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: -0.20 (0.27), residues: 931 helix: 1.16 (0.30), residues: 332 sheet: -0.57 (0.40), residues: 149 loop : -0.94 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 284 TYR 0.009 0.001 TYR B 144 PHE 0.009 0.001 PHE B 130 TRP 0.010 0.001 TRP B 383 HIS 0.002 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 8696) covalent geometry : angle 0.55378 / 0.29 (11975) hydrogen bonds : bond 0.03520 / 2.32 ( 331) hydrogen bonds : angle 4.34640 / 3.04 ( 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 112 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 500 GLN cc_start: 0.7673 (mp10) cc_final: 0.7243 (mt0) REVERT: B 363 ASN cc_start: 0.5869 (m-40) cc_final: 0.5607 (m-40) outliers start: 21 outliers final: 18 residues processed: 107 average time/residue: 0.0762 time to fit residues: 12.0653 Evaluate side-chains 103 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 193 LEU Chi-restraints excluded: chain A residue 204 GLU 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 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 265 ASN 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: 4.9990 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 37 optimal weight: 0.0370 chunk 15 optimal weight: 7.9990 chunk 41 optimal weight: 0.2980 chunk 14 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 overall best weight: 2.4664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 332 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 = 0.3996 r_free = 0.3996 target = 0.190906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.161337 restraints weight = 9171.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.158476 restraints weight = 13568.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.158103 restraints weight = 14150.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.156430 restraints weight = 14544.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.157257 restraints weight = 12883.956| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8696 Z= 0.134 Angle : 0.552 8.219 11975 Z= 0.289 Chirality : 0.043 0.284 1306 Planarity : 0.004 0.055 1388 Dihedral : 15.807 77.171 1356 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.17 % Allowed : 16.27 % Favored : 81.57 % 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: -0.20 (0.27), residues: 931 helix: 1.16 (0.29), residues: 332 sheet: -0.59 (0.40), residues: 149 loop : -0.93 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 284 TYR 0.009 0.001 TYR B 144 PHE 0.011 0.001 PHE B 130 TRP 0.010 0.001 TRP B 383 HIS 0.003 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 8696) covalent geometry : angle 0.55250 / 0.29 (11975) hydrogen bonds : bond 0.03560 / 2.37 ( 331) hydrogen bonds : angle 4.34683 / 3.04 ( 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 106 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 500 GLN cc_start: 0.7677 (mp10) cc_final: 0.7258 (mt0) outliers start: 18 outliers final: 17 residues processed: 102 average time/residue: 0.0811 time to fit residues: 12.1940 Evaluate side-chains 104 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 193 LEU Chi-restraints excluded: chain A residue 204 GLU 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 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 91 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.191738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.162537 restraints weight = 9203.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.160780 restraints weight = 13010.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.160069 restraints weight = 14003.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.159051 restraints weight = 12563.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.159527 restraints weight = 11954.328| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8696 Z= 0.120 Angle : 0.547 8.032 11975 Z= 0.288 Chirality : 0.042 0.276 1306 Planarity : 0.004 0.056 1388 Dihedral : 15.802 76.718 1356 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.17 % Allowed : 16.51 % 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 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: -0.16 (0.27), residues: 931 helix: 1.19 (0.30), residues: 332 sheet: -0.51 (0.40), residues: 149 loop : -0.92 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 199 TYR 0.009 0.001 TYR B 144 PHE 0.009 0.001 PHE B 130 TRP 0.011 0.001 TRP B 383 HIS 0.002 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8696) covalent geometry : angle 0.54660 / 0.29 (11975) hydrogen bonds : bond 0.03440 / 2.30 ( 331) hydrogen bonds : angle 4.31272 / 3.02 ( 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 107 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.7004 (pt0) cc_final: 0.6729 (pm20) REVERT: A 500 GLN cc_start: 0.7681 (mp10) cc_final: 0.7310 (mt0) REVERT: B 346 PHE cc_start: 0.6108 (m-80) cc_final: 0.5566 (m-80) outliers start: 18 outliers final: 16 residues processed: 102 average time/residue: 0.0825 time to fit residues: 12.2778 Evaluate side-chains 102 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 193 LEU Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 257 ILE 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 137 ASN Chi-restraints excluded: chain B residue 184 MET 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 Chi-restraints excluded: chain B residue 417 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 70 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.189240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.159764 restraints weight = 9193.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.157272 restraints weight = 13517.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.157346 restraints weight = 13202.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.155821 restraints weight = 12648.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.156439 restraints weight = 11386.590| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8696 Z= 0.191 Angle : 0.594 10.081 11975 Z= 0.309 Chirality : 0.044 0.276 1306 Planarity : 0.004 0.059 1388 Dihedral : 15.854 77.326 1356 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.29 % Allowed : 16.63 % Favored : 81.08 % 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: -0.33 (0.27), residues: 931 helix: 1.05 (0.29), residues: 332 sheet: -0.71 (0.39), residues: 149 loop : -0.98 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 199 TYR 0.010 0.002 TYR A 181 PHE 0.016 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/Z covalent geometry : bond 0.00451 / 0.19 ( 8696) covalent geometry : angle 0.59376 / 0.31 (11975) hydrogen bonds : bond 0.03779 / 2.55 ( 331) hydrogen bonds : angle 4.41315 / 3.09 ( 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 104 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.6978 (pt0) cc_final: 0.6711 (pm20) REVERT: A 500 GLN cc_start: 0.7706 (mp10) cc_final: 0.7324 (mt0) outliers start: 19 outliers final: 18 residues processed: 98 average time/residue: 0.0856 time to fit residues: 12.3068 Evaluate side-chains 101 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 193 LEU Chi-restraints excluded: chain A residue 204 GLU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 33 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 93 optimal weight: 30.0000 chunk 86 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 GLN ** 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 = 0.3964 r_free = 0.3964 target = 0.187520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.157492 restraints weight = 9253.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.155420 restraints weight = 15333.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.155923 restraints weight = 15256.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.155938 restraints weight = 12775.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.156145 restraints weight = 11590.642| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1655 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= 0.207 Angle : 0.615 7.529 11975 Z= 0.322 Chirality : 0.045 0.276 1306 Planarity : 0.004 0.060 1388 Dihedral : 15.993 77.637 1356 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.17 % Allowed : 16.75 % Favored : 81.08 % 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: -0.51 (0.27), residues: 931 helix: 0.91 (0.29), residues: 330 sheet: -0.93 (0.39), residues: 149 loop : -1.04 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 284 TYR 0.012 0.002 TYR A 181 PHE 0.018 0.001 PHE B 130 TRP 0.018 0.002 TRP B 383 HIS 0.005 0.001 HIS A 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 ( 8696) covalent geometry : angle 0.61495 / 0.32 (11975) hydrogen bonds : bond 0.04035 / 2.72 ( 331) hydrogen bonds : angle 4.56018 / 3.19 ( 892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1320.13 seconds wall clock time: 23 minutes 38.88 seconds (1418.88 seconds total)