Starting phenix.real_space_refine on Fri Jul 3 17:07:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jsk_22457/07_2026/7jsk_22457_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jsk_22457/07_2026/7jsk_22457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jsk_22457/07_2026/7jsk_22457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jsk_22457/07_2026/7jsk_22457.map" model { file = "/net/cci-nas-00/data/ceres_data/7jsk_22457/07_2026/7jsk_22457_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jsk_22457/07_2026/7jsk_22457_neut_trim.cif" } resolution = 3.04 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 16 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians S 64 5.16 5 Na 4 4.78 5 C 4920 2.51 5 N 1152 2.21 5 O 1232 1.98 5 H 7664 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15036 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7489 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 29, 'TRANS': 438} Chain breaks: 4 Chain: "B" Number of atoms: 7489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7489 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 29, 'TRANS': 438} Chain breaks: 4 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'CIT': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 27 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'CIT': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.50, per 1000 atoms: 0.17 Number of scatterers: 15036 At special positions: 0 Unit cell: (76.504, 103.752, 84.888, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 64 16.00 Na 4 11.00 O 1232 8.00 N 1152 7.00 C 4920 6.00 H 7664 1.00 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 562 " " NAG B 601 " - " ASN B 562 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 399.8 milliseconds 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1780 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 82.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 33 through 51 removed outlier: 4.032A pdb=" N ARG A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.783A pdb=" N THR A 59 " --> pdb=" O PRO A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 67 removed outlier: 3.710A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.792A pdb=" N VAL A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 84 through 103 removed outlier: 3.604A pdb=" N TRP A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 Processing helix chain 'A' and resid 120 through 137 Processing helix chain 'A' and resid 141 through 158 Proline residue: A 150 - end of helix removed outlier: 3.710A pdb=" N GLN A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 220 removed outlier: 4.127A pdb=" N LYS A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA A 207 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 227 through 241 removed outlier: 4.025A pdb=" N VAL A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 276 Proline residue: A 259 - end of helix removed outlier: 3.796A pdb=" N TYR A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 298 through 310 removed outlier: 3.740A pdb=" N GLU A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 310 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 333 removed outlier: 3.951A pdb=" N ILE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 367 removed outlier: 3.928A pdb=" N VAL A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 405 removed outlier: 4.393A pdb=" N THR A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 428 removed outlier: 3.635A pdb=" N VAL A 411 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 437 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.774A pdb=" N ALA A 442 " --> pdb=" O PRO A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 460 removed outlier: 3.510A pdb=" N ILE A 448 " --> pdb=" O PRO A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 483 Proline residue: A 474 - end of helix Processing helix chain 'A' and resid 487 through 499 Proline residue: A 493 - end of helix removed outlier: 4.005A pdb=" N SER A 499 " --> pdb=" O THR A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 516 removed outlier: 3.657A pdb=" N ALA A 512 " --> pdb=" O THR A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 547 removed outlier: 4.302A pdb=" N ILE A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET A 532 " --> pdb=" O THR A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 553 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 33 through 51 removed outlier: 4.031A pdb=" N ARG B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 removed outlier: 3.783A pdb=" N THR B 59 " --> pdb=" O PRO B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 67 removed outlier: 3.710A pdb=" N LEU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 80 removed outlier: 3.792A pdb=" N VAL B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 84 through 103 removed outlier: 3.604A pdb=" N TRP B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 118 Processing helix chain 'B' and resid 120 through 137 Processing helix chain 'B' and resid 141 through 158 Proline residue: B 150 - end of helix removed outlier: 3.710A pdb=" N GLN B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 220 removed outlier: 4.126A pdb=" N LYS B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 227 through 241 removed outlier: 4.024A pdb=" N VAL B 231 " --> pdb=" O THR B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 276 Proline residue: B 259 - end of helix removed outlier: 3.796A pdb=" N TYR B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 298 through 310 removed outlier: 3.740A pdb=" N GLU B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS B 308 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY B 310 " --> pdb=" O TYR B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 333 removed outlier: 3.951A pdb=" N ILE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 367 removed outlier: 3.929A pdb=" N VAL B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 405 removed outlier: 4.392A pdb=" N THR B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 428 removed outlier: 3.635A pdb=" N VAL B 411 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 437 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.775A pdb=" N ALA B 442 " --> pdb=" O PRO B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 460 removed outlier: 3.510A pdb=" N ILE B 448 " --> pdb=" O PRO B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 483 Proline residue: B 474 - end of helix Processing helix chain 'B' and resid 487 through 499 Proline residue: B 493 - end of helix removed outlier: 4.005A pdb=" N SER B 499 " --> pdb=" O THR B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 516 removed outlier: 3.657A pdb=" N ALA B 512 " --> pdb=" O THR B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 547 removed outlier: 4.301A pdb=" N ILE B 531 " --> pdb=" O LYS B 527 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET B 532 " --> pdb=" O THR B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 553 455 hydrogen bonds defined for protein. 1353 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 7644 1.03 - 1.22: 24 1.22 - 1.42: 3006 1.42 - 1.61: 4440 1.61 - 1.81: 108 Bond restraints: 15222 Sorted by residual: bond pdb=" C1 NAG B 601 " pdb=" C2 NAG B 601 " ideal model delta sigma weight residual 1.532 1.593 -0.061 2.00e-02 2.50e+03 9.20e+00 bond pdb=" C1 NAG A 601 " pdb=" C2 NAG A 601 " ideal model delta sigma weight residual 1.532 1.593 -0.061 2.00e-02 2.50e+03 9.17e+00 bond pdb=" C7 NAG B 601 " pdb=" N2 NAG B 601 " ideal model delta sigma weight residual 1.346 1.391 -0.045 2.00e-02 2.50e+03 5.08e+00 bond pdb=" C7 NAG A 601 " pdb=" N2 NAG A 601 " ideal model delta sigma weight residual 1.346 1.390 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" CA ALA A 119 " pdb=" CB ALA A 119 " ideal model delta sigma weight residual 1.525 1.495 0.030 1.47e-02 4.63e+03 4.04e+00 ... (remaining 15217 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.74: 27492 7.74 - 15.49: 37 15.49 - 23.23: 30 23.23 - 30.98: 120 30.98 - 38.72: 33 Bond angle restraints: 27712 Sorted by residual: angle pdb=" N VAL B 263 " pdb=" CA VAL B 263 " pdb=" HA VAL B 263 " ideal model delta sigma weight residual 110.00 71.28 38.72 3.00e+00 1.11e-01 1.67e+02 angle pdb=" N VAL A 263 " pdb=" CA VAL A 263 " pdb=" HA VAL A 263 " ideal model delta sigma weight residual 110.00 71.43 38.57 3.00e+00 1.11e-01 1.65e+02 angle pdb=" C PHE A 14 " pdb=" CA PHE A 14 " pdb=" HA PHE A 14 " ideal model delta sigma weight residual 109.00 72.35 36.65 3.00e+00 1.11e-01 1.49e+02 angle pdb=" C PHE B 14 " pdb=" CA PHE B 14 " pdb=" HA PHE B 14 " ideal model delta sigma weight residual 109.00 72.50 36.50 3.00e+00 1.11e-01 1.48e+02 angle pdb=" N SER A 13 " pdb=" CA SER A 13 " pdb=" HA SER A 13 " ideal model delta sigma weight residual 110.00 73.55 36.45 3.00e+00 1.11e-01 1.48e+02 ... (remaining 27707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.47: 6091 15.47 - 30.94: 759 30.94 - 46.42: 186 46.42 - 61.89: 136 61.89 - 77.36: 4 Dihedral angle restraints: 7176 sinusoidal: 3872 harmonic: 3304 Sorted by residual: dihedral pdb=" CA THR A 225 " pdb=" C THR A 225 " pdb=" N GLY A 226 " pdb=" CA GLY A 226 " ideal model delta harmonic sigma weight residual 180.00 151.23 28.77 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA THR B 225 " pdb=" C THR B 225 " pdb=" N GLY B 226 " pdb=" CA GLY B 226 " ideal model delta harmonic sigma weight residual 180.00 151.26 28.74 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA TYR A 353 " pdb=" C TYR A 353 " pdb=" N VAL A 354 " pdb=" CA VAL A 354 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 7173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.341: 1216 0.341 - 0.683: 8 0.683 - 1.024: 6 1.024 - 1.365: 2 1.365 - 1.707: 16 Chirality restraints: 1248 Sorted by residual: chirality pdb=" CG LEU A 440 " pdb=" CB LEU A 440 " pdb=" CD1 LEU A 440 " pdb=" CD2 LEU A 440 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.28e+01 chirality pdb=" CG LEU B 440 " pdb=" CB LEU B 440 " pdb=" CD1 LEU B 440 " pdb=" CD2 LEU B 440 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.24e+01 chirality pdb=" CG LEU A 111 " pdb=" CB LEU A 111 " pdb=" CD1 LEU A 111 " pdb=" CD2 LEU A 111 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.20e+01 ... (remaining 1245 not shown) Planarity restraints: 2102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 310 " -0.037 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO B 311 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 311 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 311 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 310 " 0.037 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO A 311 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 311 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 311 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 406 " 0.036 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO B 407 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 407 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 407 " 0.029 5.00e-02 4.00e+02 ... (remaining 2099 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 273 2.07 - 2.70: 25238 2.70 - 3.34: 45262 3.34 - 3.97: 55193 3.97 - 4.60: 89890 Nonbonded interactions: 215856 Sorted by model distance: nonbonded pdb=" OD1 ASN A 141 " pdb="NA NA A 603 " model vdw 1.439 3.090 nonbonded pdb=" OD1 ASN B 141 " pdb="NA NA B 603 " model vdw 1.442 3.090 nonbonded pdb=" O MET B 31 " pdb=" H ALA B 33 " model vdw 1.611 2.450 nonbonded pdb=" O MET A 31 " pdb=" H ALA A 33 " model vdw 1.618 2.450 nonbonded pdb=" O SER B 60 " pdb=" HH TYR B 82 " model vdw 1.626 2.450 ... (remaining 215851 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.110 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.390 Find NCS groups from input model: 0.100 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 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 : 0.011 0.063 7560 Z= 0.452 Angle : 1.160 16.678 10314 Z= 0.576 Chirality : 0.205 1.707 1248 Planarity : 0.006 0.055 1236 Dihedral : 14.761 77.359 2700 Min Nonbonded Distance : 1.439 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.17 % Favored : 90.61 % Rotamer: Outliers : 4.74 % Allowed : 10.10 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.67 (0.29), residues: 916 helix: 0.45 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -2.89 (0.42), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 201 TYR 0.009 0.002 TYR B 306 PHE 0.023 0.002 PHE A 35 TRP 0.015 0.002 TRP A 49 HIS 0.006 0.002 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.01126 / 0.45 ( 7558) covalent geometry : angle 1.15678 / 0.58 (10308) hydrogen bonds : bond 0.13158 / 8.45 ( 455) hydrogen bonds : angle 6.02506 / 4.36 ( 1353) link_NAG-ASN : bond 0.00966 / 0.49 ( 2) link_NAG-ASN : angle 3.95622 / 1.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.7726 (mtt) cc_final: 0.7486 (mtp) REVERT: A 157 GLN cc_start: 0.5901 (OUTLIER) cc_final: 0.5681 (tp40) REVERT: A 236 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7823 (mp10) REVERT: A 271 TRP cc_start: 0.7994 (t-100) cc_final: 0.7604 (t-100) REVERT: A 277 MET cc_start: 0.5352 (mmm) cc_final: 0.5120 (tpt) REVERT: A 300 LYS cc_start: 0.6924 (OUTLIER) cc_final: 0.6708 (ttmt) REVERT: B 208 MET cc_start: 0.6329 (mtm) cc_final: 0.6050 (mpp) outliers start: 38 outliers final: 13 residues processed: 208 average time/residue: 0.2113 time to fit residues: 59.0088 Evaluate side-chains 141 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 562 ASN Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 562 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 ASN B 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.133380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.121201 restraints weight = 32090.304| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.05 r_work: 0.3557 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7560 Z= 0.156 Angle : 0.968 16.017 10314 Z= 0.461 Chirality : 0.212 1.767 1248 Planarity : 0.006 0.057 1236 Dihedral : 8.472 70.623 1057 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.88 % Favored : 92.90 % Rotamer: Outliers : 3.49 % Allowed : 12.84 % Favored : 83.67 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.17 (0.30), residues: 916 helix: 1.04 (0.21), residues: 680 sheet: None (None), residues: 0 loop : -2.67 (0.44), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 108 TYR 0.018 0.002 TYR B 353 PHE 0.025 0.001 PHE A 314 TRP 0.008 0.001 TRP B 49 HIS 0.004 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 7558) covalent geometry : angle 0.96509 / 0.46 (10308) hydrogen bonds : bond 0.04514 / 2.93 ( 455) hydrogen bonds : angle 4.65705 / 3.30 ( 1353) link_NAG-ASN : bond 0.00463 / 0.23 ( 2) link_NAG-ASN : angle 2.99205 / 1.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.6779 (p90) cc_final: 0.6571 (p90) REVERT: A 62 MET cc_start: 0.8442 (mtt) cc_final: 0.8166 (mtp) REVERT: A 153 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7281 (mt-10) REVERT: A 157 GLN cc_start: 0.6683 (OUTLIER) cc_final: 0.6054 (tp40) REVERT: A 208 MET cc_start: 0.7856 (mtm) cc_final: 0.7229 (mmt) REVERT: A 236 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7729 (mp10) REVERT: A 264 MET cc_start: 0.8250 (mtp) cc_final: 0.7991 (mtp) REVERT: A 277 MET cc_start: 0.6133 (mmm) cc_final: 0.5603 (tpt) REVERT: A 300 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.7022 (ttmt) REVERT: B 354 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7711 (t) REVERT: B 461 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7730 (mm-30) REVERT: B 532 MET cc_start: 0.7824 (mtp) cc_final: 0.7609 (mtp) outliers start: 28 outliers final: 12 residues processed: 172 average time/residue: 0.1585 time to fit residues: 39.5782 Evaluate side-chains 148 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.131112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.118733 restraints weight = 33336.904| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.07 r_work: 0.3521 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7560 Z= 0.152 Angle : 0.947 15.878 10314 Z= 0.448 Chirality : 0.210 1.747 1248 Planarity : 0.006 0.054 1236 Dihedral : 7.782 65.748 1048 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.49 % Allowed : 14.84 % Favored : 82.67 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.54 (0.30), residues: 916 helix: 1.33 (0.21), residues: 680 sheet: None (None), residues: 0 loop : -2.60 (0.45), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 102 TYR 0.010 0.001 TYR B 353 PHE 0.021 0.001 PHE A 314 TRP 0.009 0.001 TRP A 49 HIS 0.004 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 ( 7558) covalent geometry : angle 0.94446 / 0.45 (10308) hydrogen bonds : bond 0.04164 / 2.71 ( 455) hydrogen bonds : angle 4.31798 / 3.05 ( 1353) link_NAG-ASN : bond 0.00776 / 0.39 ( 2) link_NAG-ASN : angle 3.07649 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8626 (mtt) cc_final: 0.8340 (mtp) REVERT: A 157 GLN cc_start: 0.6952 (OUTLIER) cc_final: 0.6150 (tp40) REVERT: A 208 MET cc_start: 0.7761 (mtm) cc_final: 0.7320 (mmt) REVERT: A 236 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7734 (mp10) REVERT: A 248 VAL cc_start: 0.8817 (OUTLIER) cc_final: 0.8526 (p) REVERT: A 277 MET cc_start: 0.6234 (mmm) cc_final: 0.5691 (tpt) REVERT: B 104 ASN cc_start: 0.6599 (p0) cc_final: 0.6376 (p0) REVERT: B 354 VAL cc_start: 0.8174 (OUTLIER) cc_final: 0.7930 (t) REVERT: B 532 MET cc_start: 0.8026 (mtp) cc_final: 0.7755 (mtp) outliers start: 20 outliers final: 10 residues processed: 156 average time/residue: 0.1509 time to fit residues: 33.8886 Evaluate side-chains 142 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 76 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 91 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.128187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.115801 restraints weight = 33661.533| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.06 r_work: 0.3490 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7560 Z= 0.161 Angle : 0.949 15.878 10314 Z= 0.449 Chirality : 0.211 1.794 1248 Planarity : 0.006 0.051 1236 Dihedral : 7.124 58.967 1042 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.37 % Allowed : 16.71 % Favored : 80.92 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.60 (0.30), residues: 916 helix: 1.31 (0.20), residues: 696 sheet: None (None), residues: 0 loop : -2.64 (0.47), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 102 TYR 0.011 0.001 TYR B 40 PHE 0.018 0.001 PHE A 314 TRP 0.011 0.001 TRP B 49 HIS 0.004 0.001 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 7558) covalent geometry : angle 0.94622 / 0.45 (10308) hydrogen bonds : bond 0.04199 / 2.76 ( 455) hydrogen bonds : angle 4.29201 / 3.02 ( 1353) link_NAG-ASN : bond 0.00721 / 0.36 ( 2) link_NAG-ASN : angle 3.03210 / 1.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8651 (mtt) cc_final: 0.8438 (mtp) REVERT: A 65 LEU cc_start: 0.8479 (tp) cc_final: 0.8260 (tp) REVERT: A 157 GLN cc_start: 0.7021 (OUTLIER) cc_final: 0.6216 (tp40) REVERT: A 208 MET cc_start: 0.7805 (mtm) cc_final: 0.7475 (mmt) REVERT: A 236 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.7659 (mp10) REVERT: A 248 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8575 (p) REVERT: A 276 TYR cc_start: 0.8221 (m-80) cc_final: 0.7998 (m-80) REVERT: A 277 MET cc_start: 0.6508 (mmm) cc_final: 0.5802 (tpt) REVERT: B 104 ASN cc_start: 0.6785 (p0) cc_final: 0.6551 (p0) REVERT: B 515 PHE cc_start: 0.7600 (t80) cc_final: 0.7362 (t80) outliers start: 19 outliers final: 12 residues processed: 155 average time/residue: 0.1590 time to fit residues: 35.6189 Evaluate side-chains 147 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 58 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.125380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.112861 restraints weight = 34065.277| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.08 r_work: 0.3449 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7560 Z= 0.177 Angle : 0.954 16.015 10314 Z= 0.453 Chirality : 0.211 1.798 1248 Planarity : 0.006 0.052 1236 Dihedral : 6.917 55.413 1041 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 2.74 % Allowed : 17.71 % Favored : 79.55 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.50 (0.30), residues: 916 helix: 1.31 (0.21), residues: 698 sheet: None (None), residues: 0 loop : -2.99 (0.45), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 102 TYR 0.008 0.001 TYR B 353 PHE 0.016 0.001 PHE A 314 TRP 0.012 0.001 TRP A 49 HIS 0.005 0.002 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 ( 7558) covalent geometry : angle 0.95123 / 0.45 (10308) hydrogen bonds : bond 0.04344 / 2.86 ( 455) hydrogen bonds : angle 4.27596 / 2.99 ( 1353) link_NAG-ASN : bond 0.00763 / 0.39 ( 2) link_NAG-ASN : angle 3.08094 / 1.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.6253 (tp-100) REVERT: A 208 MET cc_start: 0.7896 (mtm) cc_final: 0.7561 (mmt) REVERT: A 236 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7599 (mp10) REVERT: A 248 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8575 (p) REVERT: A 276 TYR cc_start: 0.8260 (m-80) cc_final: 0.7992 (m-80) REVERT: A 277 MET cc_start: 0.6626 (mmm) cc_final: 0.6042 (tpt) REVERT: B 104 ASN cc_start: 0.6741 (p0) cc_final: 0.6486 (p0) REVERT: B 515 PHE cc_start: 0.7638 (t80) cc_final: 0.7391 (t80) outliers start: 22 outliers final: 15 residues processed: 154 average time/residue: 0.1783 time to fit residues: 38.5576 Evaluate side-chains 144 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.124988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.112515 restraints weight = 33995.884| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.06 r_work: 0.3429 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7560 Z= 0.169 Angle : 0.949 15.950 10314 Z= 0.449 Chirality : 0.211 1.808 1248 Planarity : 0.006 0.051 1236 Dihedral : 6.858 56.607 1041 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.74 % Allowed : 17.58 % Favored : 79.68 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 (0.30), residues: 916 helix: 1.38 (0.21), residues: 698 sheet: None (None), residues: 0 loop : -3.07 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 102 TYR 0.009 0.001 TYR B 353 PHE 0.015 0.001 PHE A 314 TRP 0.011 0.001 TRP A 49 HIS 0.004 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 7558) covalent geometry : angle 0.94682 / 0.45 (10308) hydrogen bonds : bond 0.04246 / 2.80 ( 455) hydrogen bonds : angle 4.25368 / 2.97 ( 1353) link_NAG-ASN : bond 0.00754 / 0.38 ( 2) link_NAG-ASN : angle 3.07403 / 1.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6065 (tp-100) REVERT: A 208 MET cc_start: 0.7978 (mtm) cc_final: 0.7634 (mmt) REVERT: A 236 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.7601 (mp10) REVERT: A 248 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8587 (p) REVERT: A 276 TYR cc_start: 0.8278 (m-80) cc_final: 0.8050 (m-80) REVERT: A 277 MET cc_start: 0.6758 (mmm) cc_final: 0.6062 (tpt) REVERT: B 104 ASN cc_start: 0.6795 (p0) cc_final: 0.6505 (p0) outliers start: 22 outliers final: 17 residues processed: 149 average time/residue: 0.1597 time to fit residues: 34.0733 Evaluate side-chains 149 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 29 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.124891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.112513 restraints weight = 33918.021| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.05 r_work: 0.3437 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7560 Z= 0.157 Angle : 0.946 15.912 10314 Z= 0.446 Chirality : 0.211 1.801 1248 Planarity : 0.006 0.050 1236 Dihedral : 6.762 58.147 1041 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.74 % Allowed : 18.33 % Favored : 78.93 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.68 (0.30), residues: 916 helix: 1.46 (0.21), residues: 698 sheet: None (None), residues: 0 loop : -3.03 (0.45), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 102 TYR 0.010 0.001 TYR B 353 PHE 0.015 0.001 PHE A 314 TRP 0.012 0.001 TRP A 49 HIS 0.003 0.001 HIS A 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 ( 7558) covalent geometry : angle 0.94342 / 0.45 (10308) hydrogen bonds : bond 0.04084 / 2.69 ( 455) hydrogen bonds : angle 4.19781 / 2.93 ( 1353) link_NAG-ASN : bond 0.00774 / 0.39 ( 2) link_NAG-ASN : angle 3.10019 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6157 (tp-100) REVERT: A 208 MET cc_start: 0.7942 (mtm) cc_final: 0.7618 (mmt) REVERT: A 236 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.7581 (mp10) REVERT: A 248 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8634 (p) REVERT: B 104 ASN cc_start: 0.6749 (p0) cc_final: 0.6480 (p0) outliers start: 22 outliers final: 17 residues processed: 149 average time/residue: 0.1703 time to fit residues: 36.8308 Evaluate side-chains 148 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 260 ASN Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 30 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.125978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.113698 restraints weight = 33852.263| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.03 r_work: 0.3455 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7560 Z= 0.143 Angle : 0.941 15.853 10314 Z= 0.441 Chirality : 0.211 1.796 1248 Planarity : 0.005 0.053 1236 Dihedral : 6.653 59.535 1041 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.62 % Allowed : 18.83 % Favored : 78.55 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.82 (0.31), residues: 916 helix: 1.58 (0.21), residues: 698 sheet: None (None), residues: 0 loop : -3.01 (0.45), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 102 TYR 0.012 0.001 TYR A 276 PHE 0.014 0.001 PHE A 314 TRP 0.012 0.001 TRP A 49 HIS 0.003 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 ( 7558) covalent geometry : angle 0.93809 / 0.44 (10308) hydrogen bonds : bond 0.03860 / 2.55 ( 455) hydrogen bonds : angle 4.11054 / 2.87 ( 1353) link_NAG-ASN : bond 0.00788 / 0.40 ( 2) link_NAG-ASN : angle 3.11189 / 1.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6152 (tp-100) REVERT: A 208 MET cc_start: 0.7923 (mtm) cc_final: 0.7656 (mmt) REVERT: A 236 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.7425 (mp10) REVERT: A 248 VAL cc_start: 0.8905 (OUTLIER) cc_final: 0.8626 (p) REVERT: B 104 ASN cc_start: 0.6722 (p0) cc_final: 0.6432 (p0) REVERT: B 276 TYR cc_start: 0.8549 (m-80) cc_final: 0.8226 (m-80) REVERT: B 515 PHE cc_start: 0.7497 (t80) cc_final: 0.7268 (t80) outliers start: 21 outliers final: 17 residues processed: 146 average time/residue: 0.1630 time to fit residues: 34.3270 Evaluate side-chains 148 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.124136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.111898 restraints weight = 33662.970| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.00 r_work: 0.3426 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7560 Z= 0.167 Angle : 0.949 15.937 10314 Z= 0.448 Chirality : 0.211 1.811 1248 Planarity : 0.006 0.053 1236 Dihedral : 6.679 59.990 1041 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.99 % Allowed : 18.95 % Favored : 78.05 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.79 (0.31), residues: 916 helix: 1.54 (0.21), residues: 700 sheet: None (None), residues: 0 loop : -3.01 (0.46), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 102 TYR 0.011 0.001 TYR B 214 PHE 0.014 0.001 PHE A 314 TRP 0.015 0.001 TRP A 49 HIS 0.004 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 ( 7558) covalent geometry : angle 0.94660 / 0.45 (10308) hydrogen bonds : bond 0.04135 / 2.73 ( 455) hydrogen bonds : angle 4.18119 / 2.91 ( 1353) link_NAG-ASN : bond 0.00772 / 0.39 ( 2) link_NAG-ASN : angle 3.11428 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6208 (tp-100) REVERT: A 208 MET cc_start: 0.7894 (mtm) cc_final: 0.7652 (mmt) REVERT: A 236 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.7488 (mp10) REVERT: A 248 VAL cc_start: 0.8920 (OUTLIER) cc_final: 0.8647 (p) REVERT: B 104 ASN cc_start: 0.6752 (p0) cc_final: 0.6452 (p0) REVERT: B 515 PHE cc_start: 0.7530 (t80) cc_final: 0.7270 (t80) outliers start: 24 outliers final: 18 residues processed: 149 average time/residue: 0.1652 time to fit residues: 35.6166 Evaluate side-chains 146 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 58 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 59 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.125888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.113767 restraints weight = 33572.396| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.01 r_work: 0.3452 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7560 Z= 0.135 Angle : 0.935 15.860 10314 Z= 0.437 Chirality : 0.211 1.807 1248 Planarity : 0.006 0.067 1236 Dihedral : 6.551 58.312 1041 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.12 % Allowed : 20.20 % Favored : 77.68 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.93 (0.31), residues: 916 helix: 1.64 (0.21), residues: 700 sheet: None (None), residues: 0 loop : -2.95 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 102 TYR 0.014 0.001 TYR B 214 PHE 0.014 0.001 PHE A 314 TRP 0.015 0.001 TRP A 49 HIS 0.002 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.13 ( 7558) covalent geometry : angle 0.93215 / 0.44 (10308) hydrogen bonds : bond 0.03693 / 2.44 ( 455) hydrogen bonds : angle 4.04575 / 2.82 ( 1353) link_NAG-ASN : bond 0.00785 / 0.40 ( 2) link_NAG-ASN : angle 3.13083 / 1.43 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1832 Ramachandran restraints generated. 916 Oldfield, 0 Emsley, 916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6185 (tp-100) REVERT: A 236 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.7508 (mp10) REVERT: A 248 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8636 (p) REVERT: B 276 TYR cc_start: 0.8501 (m-80) cc_final: 0.8125 (m-80) outliers start: 17 outliers final: 14 residues processed: 138 average time/residue: 0.1790 time to fit residues: 35.1090 Evaluate side-chains 143 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 508 THR Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 519 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 75 optimal weight: 0.0770 chunk 79 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.126240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114162 restraints weight = 33721.633| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.00 r_work: 0.3461 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7560 Z= 0.140 Angle : 0.936 15.802 10314 Z= 0.439 Chirality : 0.211 1.809 1248 Planarity : 0.006 0.066 1236 Dihedral : 6.488 58.079 1041 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 2.12 % Allowed : 19.95 % Favored : 77.93 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.31), residues: 916 helix: 1.70 (0.21), residues: 700 sheet: None (None), residues: 0 loop : -2.95 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 102 TYR 0.010 0.001 TYR B 353 PHE 0.013 0.001 PHE A 314 TRP 0.014 0.001 TRP A 49 HIS 0.003 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 7558) covalent geometry : angle 0.93301 / 0.44 (10308) hydrogen bonds : bond 0.03760 / 2.48 ( 455) hydrogen bonds : angle 4.05081 / 2.83 ( 1353) link_NAG-ASN : bond 0.00794 / 0.40 ( 2) link_NAG-ASN : angle 3.11300 / 1.42 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3396.16 seconds wall clock time: 58 minutes 28.93 seconds (3508.93 seconds total)