Starting phenix.real_space_refine on Fri Aug 7 03:51:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9okk_70567/08_2026/9okk_70567.cif Found real_map, /net/cci-nas-00/data/ceres_data/9okk_70567/08_2026/9okk_70567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9okk_70567/08_2026/9okk_70567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9okk_70567/08_2026/9okk_70567.map" model { file = "/net/cci-nas-00/data/ceres_data/9okk_70567/08_2026/9okk_70567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9okk_70567/08_2026/9okk_70567.cif" } resolution = 3.23 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 34 5.16 5 C 5977 2.51 5 N 1577 2.21 5 O 1755 1.98 5 H 9344 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18687 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2302 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "I" Number of atoms: 5752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5752 Classifications: {'peptide': 354} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 337} Chain: "K" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1934 Classifications: {'peptide': 123} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "L" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 3880 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 5, 'TRANS': 233} Chain breaks: 4 Chain: "M" Number of atoms: 2635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 2635 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 159} Chain: "N" Number of atoms: 1976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1976 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 114} Chain breaks: 1 Chain: "T" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 208 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Time building chain proxies: 3.15, per 1000 atoms: 0.17 Number of scatterers: 18687 At special positions: 0 Unit cell: (98.046, 108.102, 128.214, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 O 1755 8.00 N 1577 7.00 C 5977 6.00 H 9344 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 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 481.3 milliseconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2260 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 4 sheets defined 67.6% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'H' and resid 33 through 61 removed outlier: 3.626A pdb=" N SER H 39 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 63 through 68 Processing helix chain 'H' and resid 73 through 108 removed outlier: 4.008A pdb=" N LYS H 77 " --> pdb=" O GLU H 73 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS H 90 " --> pdb=" O LYS H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 170 removed outlier: 3.910A pdb=" N LYS H 170 " --> pdb=" O LEU H 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 309 through 313 Processing helix chain 'I' and resid 315 through 334 removed outlier: 3.641A pdb=" N HIS I 328 " --> pdb=" O HIS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 341 through 360 Processing helix chain 'I' and resid 363 through 374 Processing helix chain 'I' and resid 375 through 377 No H-bonds generated for 'chain 'I' and resid 375 through 377' Processing helix chain 'I' and resid 382 through 391 removed outlier: 3.672A pdb=" N GLU I 391 " --> pdb=" O LEU I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 413 removed outlier: 4.210A pdb=" N LEU I 401 " --> pdb=" O SER I 397 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY I 402 " --> pdb=" O PRO I 398 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR I 403 " --> pdb=" O ASP I 399 " (cutoff:3.500A) Proline residue: I 407 - end of helix Processing helix chain 'I' and resid 416 through 438 Processing helix chain 'I' and resid 451 through 477 removed outlier: 4.061A pdb=" N TYR I 455 " --> pdb=" O PRO I 451 " (cutoff:3.500A) Proline residue: I 460 - end of helix removed outlier: 3.619A pdb=" N TYR I 476 " --> pdb=" O LYS I 472 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN I 477 " --> pdb=" O ALA I 473 " (cutoff:3.500A) Processing helix chain 'I' and resid 480 through 501 Processing helix chain 'I' and resid 510 through 520 removed outlier: 3.586A pdb=" N LEU I 514 " --> pdb=" O GLY I 510 " (cutoff:3.500A) Proline residue: I 517 - end of helix Processing helix chain 'I' and resid 522 through 547 removed outlier: 3.868A pdb=" N ILE I 526 " --> pdb=" O SER I 522 " (cutoff:3.500A) Processing helix chain 'I' and resid 550 through 573 removed outlier: 3.625A pdb=" N LEU I 570 " --> pdb=" O ASP I 566 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N TYR I 571 " --> pdb=" O LEU I 567 " (cutoff:3.500A) Processing helix chain 'I' and resid 578 through 582 Processing helix chain 'I' and resid 584 through 588 Processing helix chain 'I' and resid 589 through 600 Processing helix chain 'I' and resid 602 through 607 removed outlier: 3.564A pdb=" N LYS I 606 " --> pdb=" O GLU I 602 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU I 607 " --> pdb=" O PRO I 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 602 through 607' Processing helix chain 'I' and resid 612 through 618 removed outlier: 4.550A pdb=" N ALA I 617 " --> pdb=" O ALA I 614 " (cutoff:3.500A) Processing helix chain 'I' and resid 619 through 624 Processing helix chain 'I' and resid 627 through 632 removed outlier: 3.579A pdb=" N ALA I 631 " --> pdb=" O ASP I 627 " (cutoff:3.500A) Processing helix chain 'I' and resid 633 through 645 removed outlier: 3.706A pdb=" N TYR I 637 " --> pdb=" O ASN I 633 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N HIS I 643 " --> pdb=" O ALA I 639 " (cutoff:3.500A) Processing helix chain 'I' and resid 645 through 656 Processing helix chain 'I' and resid 656 through 661 removed outlier: 3.540A pdb=" N ARG I 660 " --> pdb=" O VAL I 656 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET I 661 " --> pdb=" O PRO I 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 656 through 661' Processing helix chain 'K' and resid 3 through 34 Processing helix chain 'K' and resid 42 through 62 Processing helix chain 'K' and resid 71 through 123 removed outlier: 3.640A pdb=" N LYS K 84 " --> pdb=" O LEU K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 67 Processing helix chain 'L' and resid 142 through 158 Processing helix chain 'L' and resid 167 through 182 Processing helix chain 'L' and resid 211 through 221 Processing helix chain 'L' and resid 227 through 248 Processing helix chain 'L' and resid 250 through 254 removed outlier: 4.157A pdb=" N VAL L 253 " --> pdb=" O ASP L 250 " (cutoff:3.500A) Processing helix chain 'L' and resid 276 through 291 Processing helix chain 'M' and resid 31 through 49 Processing helix chain 'M' and resid 63 through 73 removed outlier: 3.921A pdb=" N VAL M 67 " --> pdb=" O LEU M 63 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP M 71 " --> pdb=" O VAL M 67 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU M 72 " --> pdb=" O LYS M 68 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 102 removed outlier: 3.566A pdb=" N TRP M 95 " --> pdb=" O PHE M 91 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN M 102 " --> pdb=" O LYS M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 109 removed outlier: 5.948A pdb=" N ASP M 106 " --> pdb=" O VAL M 103 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG M 109 " --> pdb=" O ASP M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 139 Processing helix chain 'M' and resid 150 through 170 Processing helix chain 'N' and resid 198 through 207 Processing helix chain 'N' and resid 238 through 250 Processing helix chain 'N' and resid 288 through 299 Processing helix chain 'N' and resid 306 through 312 removed outlier: 3.837A pdb=" N PHE N 309 " --> pdb=" O SER N 306 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE N 311 " --> pdb=" O PHE N 308 " (cutoff:3.500A) Processing helix chain 'N' and resid 323 through 327 Processing helix chain 'T' and resid 813 through 836 Processing sheet with id=AA1, first strand: chain 'L' and resid 35 through 37 removed outlier: 4.148A pdb=" N GLY L 271 " --> pdb=" O LYS L 267 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL L 193 " --> pdb=" O SER L 257 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE L 259 " --> pdb=" O THR L 191 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR L 191 " --> pdb=" O ILE L 259 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS N 285 " --> pdb=" O LYS L 204 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP L 210 " --> pdb=" O ASN N 279 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ASN N 279 " --> pdb=" O ASP L 210 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 77 through 84 removed outlier: 6.168A pdb=" N SER L 103 " --> pdb=" O VAL L 113 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL L 113 " --> pdb=" O SER L 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 54 through 60 removed outlier: 8.156A pdb=" N ILE M 82 " --> pdb=" O THR M 24 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE M 26 " --> pdb=" O ILE M 82 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ALA M 84 " --> pdb=" O ILE M 26 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU M 28 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'N' and resid 228 through 229 623 hydrogen bonds defined for protein. 1812 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: 3.75 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9331 1.03 - 1.23: 13 1.23 - 1.42: 3805 1.42 - 1.62: 5638 1.62 - 1.81: 55 Bond restraints: 18842 Sorted by residual: bond pdb=" N MET K 1 " pdb=" H2 MET K 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N MET K 1 " pdb=" H3 MET K 1 " ideal model delta sigma weight residual 0.890 0.959 -0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" N MET K 1 " pdb=" CA MET K 1 " ideal model delta sigma weight residual 1.491 1.458 0.033 2.10e-02 2.27e+03 2.48e+00 bond pdb=" N MET K 1 " pdb=" H1 MET K 1 " ideal model delta sigma weight residual 0.890 0.860 0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C GLU I 602 " pdb=" O GLU I 602 " ideal model delta sigma weight residual 1.235 1.231 0.004 4.70e-03 4.53e+04 6.53e-01 ... (remaining 18837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.20: 34081 5.20 - 10.40: 2 10.40 - 15.60: 2 15.60 - 20.80: 1 20.80 - 26.00: 7 Bond angle restraints: 34093 Sorted by residual: angle pdb=" CG2 ILE N 246 " pdb=" CB ILE N 246 " pdb=" HB ILE N 246 " ideal model delta sigma weight residual 109.00 83.00 26.00 3.00e+00 1.11e-01 7.51e+01 angle pdb=" CG1 ILE N 246 " pdb=" CB ILE N 246 " pdb=" HB ILE N 246 " ideal model delta sigma weight residual 109.00 83.60 25.40 3.00e+00 1.11e-01 7.17e+01 angle pdb=" CG2 ILE I 508 " pdb=" CB ILE I 508 " pdb=" HB ILE I 508 " ideal model delta sigma weight residual 109.00 83.78 25.22 3.00e+00 1.11e-01 7.07e+01 angle pdb=" CG1 ILE I 508 " pdb=" CB ILE I 508 " pdb=" HB ILE I 508 " ideal model delta sigma weight residual 109.00 84.05 24.95 3.00e+00 1.11e-01 6.92e+01 angle pdb=" CA ILE N 246 " pdb=" CB ILE N 246 " pdb=" HB ILE N 246 " ideal model delta sigma weight residual 109.00 85.95 23.05 3.00e+00 1.11e-01 5.91e+01 ... (remaining 34088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 8108 17.87 - 35.74: 524 35.74 - 53.61: 135 53.61 - 71.48: 42 71.48 - 89.35: 15 Dihedral angle restraints: 8824 sinusoidal: 4870 harmonic: 3954 Sorted by residual: dihedral pdb=" CA TYR I 618 " pdb=" C TYR I 618 " pdb=" N THR I 619 " pdb=" CA THR I 619 " ideal model delta harmonic sigma weight residual -180.00 -161.35 -18.65 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA ASP H 36 " pdb=" CB ASP H 36 " pdb=" CG ASP H 36 " pdb=" OD1 ASP H 36 " ideal model delta sinusoidal sigma weight residual -30.00 -89.42 59.42 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CG ARG I 414 " pdb=" CD ARG I 414 " pdb=" NE ARG I 414 " pdb=" CZ ARG I 414 " ideal model delta sinusoidal sigma weight residual -180.00 -135.29 -44.71 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 8821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.365: 1519 0.365 - 0.730: 0 0.730 - 1.095: 0 1.095 - 1.460: 0 1.460 - 1.825: 2 Chirality restraints: 1521 Sorted by residual: chirality pdb=" CB ILE I 508 " pdb=" CA ILE I 508 " pdb=" CG1 ILE I 508 " pdb=" CG2 ILE I 508 " both_signs ideal model delta sigma weight residual False 2.64 0.82 1.82 2.00e-01 2.50e+01 8.32e+01 chirality pdb=" CB ILE N 246 " pdb=" CA ILE N 246 " pdb=" CG1 ILE N 246 " pdb=" CG2 ILE N 246 " both_signs ideal model delta sigma weight residual False 2.64 0.96 1.68 2.00e-01 2.50e+01 7.08e+01 chirality pdb=" CA ILE I 363 " pdb=" N ILE I 363 " pdb=" C ILE I 363 " pdb=" CB ILE I 363 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 1518 not shown) Planarity restraints: 2707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA N 243 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C ALA N 243 " -0.029 2.00e-02 2.50e+03 pdb=" O ALA N 243 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU N 244 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 82 " 0.006 2.00e-02 2.50e+03 1.19e-02 1.42e+00 pdb=" C VAL H 82 " -0.021 2.00e-02 2.50e+03 pdb=" O VAL H 82 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA H 83 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE N 199 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO N 200 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO N 200 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO N 200 " 0.016 5.00e-02 4.00e+02 ... (remaining 2704 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1514 2.23 - 2.82: 42149 2.82 - 3.41: 48357 3.41 - 4.01: 64657 4.01 - 4.60: 102000 Nonbonded interactions: 258677 Sorted by model distance: nonbonded pdb="HH11 ARG H 167 " pdb=" O ALA I 312 " model vdw 1.637 2.450 nonbonded pdb=" O LEU I 511 " pdb=" HG SER I 515 " model vdw 1.638 2.450 nonbonded pdb=" OE1 GLU I 379 " pdb=" HZ1 LYS M 160 " model vdw 1.638 2.450 nonbonded pdb=" H ASN N 323 " pdb=" OD2 ASP N 326 " model vdw 1.646 2.450 nonbonded pdb=" O PHE M 135 " pdb="HD22 ASN M 139 " model vdw 1.658 2.450 ... (remaining 258672 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.760 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: 0.130 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 16.240 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 : 0.003 0.033 9498 Z= 0.138 Angle : 0.503 16.266 12850 Z= 0.268 Chirality : 0.074 1.825 1521 Planarity : 0.003 0.032 1615 Dihedral : 13.585 89.355 3572 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 2.87 (0.26), residues: 1144 helix: 3.10 (0.20), residues: 683 sheet: -0.23 (0.50), residues: 113 loop : 0.19 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 195 TYR 0.010 0.001 TYR I 618 PHE 0.013 0.001 PHE I 334 TRP 0.007 0.001 TRP I 392 HIS 0.004 0.001 HIS I 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 ( 9498) covalent geometry : angle 0.50263 / 0.27 (12850) hydrogen bonds : bond 0.12240 / 7.95 ( 623) hydrogen bonds : angle 5.23561 / 3.88 ( 1812) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.532 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: I 388 GLN cc_start: 0.8324 (mt0) cc_final: 0.8087 (mt0) REVERT: I 579 ARG cc_start: 0.8158 (ptt-90) cc_final: 0.7898 (ptm-80) REVERT: L 40 LYS cc_start: 0.7458 (ttpt) cc_final: 0.6849 (tttp) REVERT: L 240 GLN cc_start: 0.7563 (tm-30) cc_final: 0.7158 (tm-30) REVERT: T 824 MET cc_start: 0.7460 (mmt) cc_final: 0.6627 (ptt) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2986 time to fit residues: 93.4853 Evaluate side-chains 154 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.0050 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 153 ASN I 378 ASN L 198 GLN M 134 ASN N 313 HIS ** T 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 819 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.183559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.139544 restraints weight = 32136.061| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.51 r_work: 0.3427 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9498 Z= 0.150 Angle : 0.538 15.534 12850 Z= 0.277 Chirality : 0.072 1.761 1521 Planarity : 0.003 0.033 1615 Dihedral : 4.156 75.930 1249 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.38 % Allowed : 5.81 % Favored : 93.81 % 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: 2.96 (0.25), residues: 1144 helix: 3.22 (0.19), residues: 688 sheet: -0.38 (0.48), residues: 113 loop : 0.14 (0.36), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 610 TYR 0.020 0.001 TYR M 136 PHE 0.010 0.001 PHE L 209 TRP 0.005 0.001 TRP I 392 HIS 0.003 0.001 HIS M 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 9498) covalent geometry : angle 0.53772 / 0.28 (12850) hydrogen bonds : bond 0.05053 / 3.39 ( 623) hydrogen bonds : angle 4.11151 / 3.10 ( 1812) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 168 time to evaluate : 0.620 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: I 388 GLN cc_start: 0.8451 (mt0) cc_final: 0.8130 (mt0) REVERT: I 442 ARG cc_start: 0.7764 (ptm160) cc_final: 0.7553 (ptm160) REVERT: I 579 ARG cc_start: 0.8092 (ptt-90) cc_final: 0.7801 (ptm-80) REVERT: L 56 GLN cc_start: 0.6852 (mt0) cc_final: 0.6633 (mt0) REVERT: M 36 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7475 (mm-30) REVERT: T 824 MET cc_start: 0.7311 (mmt) cc_final: 0.6790 (ptt) outliers start: 4 outliers final: 4 residues processed: 170 average time/residue: 0.3083 time to fit residues: 68.3013 Evaluate side-chains 148 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain L residue 155 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 74 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 813 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 = 0.4108 r_free = 0.4108 target = 0.181377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.136156 restraints weight = 32069.308| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.43 r_work: 0.3387 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9498 Z= 0.156 Angle : 0.522 15.566 12850 Z= 0.268 Chirality : 0.072 1.761 1521 Planarity : 0.003 0.034 1615 Dihedral : 4.209 79.855 1249 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.76 % Allowed : 6.95 % Favored : 92.29 % 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: 2.79 (0.25), residues: 1144 helix: 3.14 (0.19), residues: 684 sheet: -0.47 (0.48), residues: 113 loop : -0.01 (0.35), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 494 TYR 0.018 0.001 TYR M 136 PHE 0.010 0.001 PHE I 373 TRP 0.005 0.001 TRP I 377 HIS 0.004 0.001 HIS M 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 9498) covalent geometry : angle 0.52207 / 0.27 (12850) hydrogen bonds : bond 0.04907 / 3.27 ( 623) hydrogen bonds : angle 3.98454 / 2.98 ( 1812) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.578 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: H 169 MET cc_start: 0.6749 (ttm) cc_final: 0.6273 (ttm) REVERT: I 388 GLN cc_start: 0.8691 (mt0) cc_final: 0.8379 (mt0) REVERT: I 579 ARG cc_start: 0.8110 (ptt-90) cc_final: 0.7761 (ptm-80) REVERT: I 602 GLU cc_start: 0.8186 (mp0) cc_final: 0.7635 (pt0) REVERT: L 230 ASP cc_start: 0.8018 (m-30) cc_final: 0.7756 (m-30) REVERT: T 824 MET cc_start: 0.7381 (mmt) cc_final: 0.6729 (ptt) outliers start: 8 outliers final: 5 residues processed: 151 average time/residue: 0.3038 time to fit residues: 60.4202 Evaluate side-chains 141 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain L residue 155 THR Chi-restraints excluded: chain L residue 262 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 109 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** T 813 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 = 0.4109 r_free = 0.4109 target = 0.179753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.137190 restraints weight = 31301.966| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.34 r_work: 0.3391 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9498 Z= 0.142 Angle : 0.516 15.712 12850 Z= 0.262 Chirality : 0.069 1.634 1521 Planarity : 0.003 0.035 1615 Dihedral : 4.203 80.128 1249 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.86 % Allowed : 6.95 % Favored : 92.19 % 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: 2.83 (0.25), residues: 1144 helix: 3.19 (0.19), residues: 686 sheet: -0.48 (0.48), residues: 113 loop : -0.06 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 494 TYR 0.019 0.001 TYR M 136 PHE 0.010 0.001 PHE I 373 TRP 0.005 0.001 TRP I 377 HIS 0.004 0.001 HIS M 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 9498) covalent geometry : angle 0.51648 / 0.26 (12850) hydrogen bonds : bond 0.04676 / 3.11 ( 623) hydrogen bonds : angle 3.86882 / 2.89 ( 1812) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 169 MET cc_start: 0.6738 (ttm) cc_final: 0.6398 (ttm) REVERT: I 388 GLN cc_start: 0.8709 (mt0) cc_final: 0.8422 (mt0) REVERT: I 579 ARG cc_start: 0.8148 (ptt-90) cc_final: 0.7789 (ptm-80) REVERT: I 602 GLU cc_start: 0.8258 (mp0) cc_final: 0.7741 (pt0) REVERT: K 109 MET cc_start: 0.7741 (mtp) cc_final: 0.7474 (mtm) REVERT: L 230 ASP cc_start: 0.8024 (m-30) cc_final: 0.7769 (m-30) REVERT: L 240 GLN cc_start: 0.7530 (tm-30) cc_final: 0.7048 (tm-30) REVERT: N 266 LYS cc_start: 0.8150 (mtpp) cc_final: 0.7478 (mmtt) REVERT: T 824 MET cc_start: 0.7278 (mmt) cc_final: 0.6656 (ptt) outliers start: 9 outliers final: 7 residues processed: 150 average time/residue: 0.2867 time to fit residues: 56.8168 Evaluate side-chains 141 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain K residue 4 LYS Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain L residue 155 THR Chi-restraints excluded: chain L residue 262 THR Chi-restraints excluded: chain N residue 264 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 94 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 813 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.176179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.124891 restraints weight = 32099.358| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.49 r_work: 0.3296 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9498 Z= 0.220 Angle : 0.556 15.627 12850 Z= 0.288 Chirality : 0.071 1.650 1521 Planarity : 0.004 0.036 1615 Dihedral : 4.407 85.719 1249 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.24 % Allowed : 7.43 % Favored : 91.33 % 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: 2.50 (0.25), residues: 1144 helix: 2.95 (0.18), residues: 686 sheet: -0.59 (0.48), residues: 113 loop : -0.27 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 494 TYR 0.020 0.002 TYR M 136 PHE 0.019 0.002 PHE L 157 TRP 0.006 0.001 TRP I 392 HIS 0.006 0.001 HIS M 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.22 ( 9498) covalent geometry : angle 0.55638 / 0.29 (12850) hydrogen bonds : bond 0.05227 / 3.48 ( 623) hydrogen bonds : angle 3.97214 / 2.94 ( 1812) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.525 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: H 169 MET cc_start: 0.6590 (ttm) cc_final: 0.6302 (ttm) REVERT: I 388 GLN cc_start: 0.8788 (mt0) cc_final: 0.8491 (mt0) REVERT: I 579 ARG cc_start: 0.8140 (ptt-90) cc_final: 0.7763 (ptm-80) REVERT: I 602 GLU cc_start: 0.8307 (mp0) cc_final: 0.7756 (pt0) REVERT: K 109 MET cc_start: 0.7753 (mtp) cc_final: 0.7482 (mtm) REVERT: L 230 ASP cc_start: 0.8034 (m-30) cc_final: 0.7777 (m-30) REVERT: L 240 GLN cc_start: 0.7613 (tm-30) cc_final: 0.7078 (tm-30) REVERT: M 64 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7767 (mm-30) REVERT: N 266 LYS cc_start: 0.8137 (mtpp) cc_final: 0.7441 (mmtt) REVERT: T 824 MET cc_start: 0.7230 (mmt) cc_final: 0.6573 (ptt) outliers start: 13 outliers final: 11 residues processed: 160 average time/residue: 0.2809 time to fit residues: 60.1875 Evaluate side-chains 153 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain I residue 336 ASP Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain I residue 646 SER Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 38 ILE Chi-restraints excluded: chain L residue 155 THR Chi-restraints excluded: chain L residue 262 THR Chi-restraints excluded: chain N residue 264 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 94 optimal weight: 0.0030 chunk 61 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 105 optimal weight: 0.1980 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 87 optimal weight: 0.4980 chunk 95 optimal weight: 0.8980 overall best weight: 0.4590 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.178457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.127488 restraints weight = 31979.754| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.51 r_work: 0.3336 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9498 Z= 0.113 Angle : 0.508 15.611 12850 Z= 0.258 Chirality : 0.069 1.631 1521 Planarity : 0.003 0.036 1615 Dihedral : 4.198 78.605 1249 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.86 % Allowed : 8.10 % Favored : 91.05 % 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: 2.84 (0.25), residues: 1144 helix: 3.21 (0.18), residues: 685 sheet: -0.37 (0.49), residues: 113 loop : -0.11 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 195 TYR 0.017 0.001 TYR M 136 PHE 0.016 0.001 PHE N 312 TRP 0.004 0.001 TRP M 95 HIS 0.004 0.001 HIS I 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 9498) covalent geometry : angle 0.50792 / 0.26 (12850) hydrogen bonds : bond 0.04472 / 2.98 ( 623) hydrogen bonds : angle 3.78908 / 2.81 ( 1812) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 169 MET cc_start: 0.6571 (ttm) cc_final: 0.6235 (ttm) REVERT: I 388 GLN cc_start: 0.8702 (mt0) cc_final: 0.8409 (mt0) REVERT: I 579 ARG cc_start: 0.8103 (ptt-90) cc_final: 0.7740 (ptm-80) REVERT: I 602 GLU cc_start: 0.8301 (mp0) cc_final: 0.7770 (pt0) REVERT: K 109 MET cc_start: 0.7729 (mtp) cc_final: 0.7456 (mtm) REVERT: L 215 ARG cc_start: 0.8470 (ttm170) cc_final: 0.8158 (mtp180) REVERT: L 230 ASP cc_start: 0.7965 (m-30) cc_final: 0.7708 (m-30) REVERT: L 240 GLN cc_start: 0.7545 (tm-30) cc_final: 0.7083 (tm-30) REVERT: L 276 THR cc_start: 0.8233 (t) cc_final: 0.7997 (t) REVERT: N 266 LYS cc_start: 0.8034 (mtpp) cc_final: 0.7371 (mmtt) REVERT: N 324 ILE cc_start: 0.2379 (OUTLIER) cc_final: 0.2141 (mt) REVERT: T 824 MET cc_start: 0.7214 (mmt) cc_final: 0.6572 (ptt) outliers start: 9 outliers final: 7 residues processed: 148 average time/residue: 0.2913 time to fit residues: 57.0436 Evaluate side-chains 146 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain I residue 336 ASP Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 155 THR Chi-restraints excluded: chain N residue 264 THR Chi-restraints excluded: chain N residue 324 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 21 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 28 optimal weight: 0.0470 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- 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 = 0.4067 r_free = 0.4067 target = 0.177171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.126108 restraints weight = 32346.700| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.49 r_work: 0.3320 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9498 Z= 0.144 Angle : 0.513 15.463 12850 Z= 0.261 Chirality : 0.070 1.637 1521 Planarity : 0.003 0.036 1615 Dihedral : 4.258 83.084 1249 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.86 % Allowed : 8.48 % Favored : 90.67 % 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: 2.84 (0.25), residues: 1144 helix: 3.20 (0.18), residues: 685 sheet: -0.24 (0.50), residues: 110 loop : -0.15 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 610 TYR 0.018 0.001 TYR M 136 PHE 0.011 0.001 PHE I 373 TRP 0.004 0.001 TRP L 36 HIS 0.005 0.001 HIS I 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.14 ( 9498) covalent geometry : angle 0.51327 / 0.26 (12850) hydrogen bonds : bond 0.04580 / 3.05 ( 623) hydrogen bonds : angle 3.78569 / 2.81 ( 1812) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 169 MET cc_start: 0.6541 (ttm) cc_final: 0.6340 (ttm) REVERT: I 388 GLN cc_start: 0.8704 (mt0) cc_final: 0.8411 (mt0) REVERT: I 579 ARG cc_start: 0.8130 (ptt-90) cc_final: 0.7767 (ptm-80) REVERT: I 602 GLU cc_start: 0.8312 (mp0) cc_final: 0.7769 (pt0) REVERT: K 109 MET cc_start: 0.7766 (mtp) cc_final: 0.7499 (mtm) REVERT: L 215 ARG cc_start: 0.8493 (ttm170) cc_final: 0.8185 (mtp180) REVERT: L 230 ASP cc_start: 0.7958 (m-30) cc_final: 0.7701 (m-30) REVERT: L 240 GLN cc_start: 0.7604 (tm-30) cc_final: 0.7050 (tm-30) REVERT: N 266 LYS cc_start: 0.8029 (mtpp) cc_final: 0.7407 (mmtt) REVERT: N 324 ILE cc_start: 0.2443 (OUTLIER) cc_final: 0.2190 (mt) REVERT: T 824 MET cc_start: 0.7196 (mmt) cc_final: 0.6549 (ptt) outliers start: 9 outliers final: 8 residues processed: 146 average time/residue: 0.2741 time to fit residues: 53.0831 Evaluate side-chains 146 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain I residue 336 ASP Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 155 THR Chi-restraints excluded: chain N residue 228 ILE Chi-restraints excluded: chain N residue 264 THR Chi-restraints excluded: chain N residue 324 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 107 optimal weight: 0.5980 chunk 75 optimal weight: 0.2980 chunk 54 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.177158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.129415 restraints weight = 31033.744| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.31 r_work: 0.3332 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9498 Z= 0.123 Angle : 0.504 15.537 12850 Z= 0.255 Chirality : 0.070 1.639 1521 Planarity : 0.003 0.036 1615 Dihedral : 4.199 81.763 1249 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.14 % Allowed : 8.48 % Favored : 90.38 % 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: 2.92 (0.25), residues: 1144 helix: 3.26 (0.18), residues: 685 sheet: -0.16 (0.50), residues: 110 loop : -0.13 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 610 TYR 0.017 0.001 TYR M 136 PHE 0.009 0.001 PHE I 373 TRP 0.004 0.001 TRP L 36 HIS 0.005 0.001 HIS I 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 ( 9498) covalent geometry : angle 0.50372 / 0.26 (12850) hydrogen bonds : bond 0.04393 / 2.92 ( 623) hydrogen bonds : angle 3.73396 / 2.77 ( 1812) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 169 MET cc_start: 0.6556 (ttm) cc_final: 0.6270 (ttm) REVERT: I 388 GLN cc_start: 0.8667 (mt0) cc_final: 0.8369 (mt0) REVERT: I 579 ARG cc_start: 0.8124 (ptt-90) cc_final: 0.7781 (ptm-80) REVERT: I 602 GLU cc_start: 0.8300 (mp0) cc_final: 0.7820 (pt0) REVERT: K 109 MET cc_start: 0.7720 (mtp) cc_final: 0.7448 (mtm) REVERT: L 215 ARG cc_start: 0.8480 (ttm170) cc_final: 0.8166 (mtp180) REVERT: L 230 ASP cc_start: 0.7920 (m-30) cc_final: 0.7666 (m-30) REVERT: L 240 GLN cc_start: 0.7606 (tm-30) cc_final: 0.7066 (tm-30) REVERT: N 266 LYS cc_start: 0.7983 (mtpp) cc_final: 0.7395 (mmtt) REVERT: N 324 ILE cc_start: 0.2351 (OUTLIER) cc_final: 0.2111 (mt) REVERT: T 824 MET cc_start: 0.7203 (mmt) cc_final: 0.6567 (ptt) outliers start: 12 outliers final: 9 residues processed: 145 average time/residue: 0.2209 time to fit residues: 43.2505 Evaluate side-chains 146 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain I residue 336 ASP Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 155 THR Chi-restraints excluded: chain N residue 228 ILE Chi-restraints excluded: chain N residue 264 THR Chi-restraints excluded: chain N residue 324 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 81 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.176229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.134445 restraints weight = 31346.063| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.30 r_work: 0.3320 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9498 Z= 0.142 Angle : 0.514 15.469 12850 Z= 0.262 Chirality : 0.070 1.633 1521 Planarity : 0.004 0.047 1615 Dihedral : 4.245 84.801 1249 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.95 % Allowed : 8.57 % Favored : 90.48 % 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: 2.85 (0.25), residues: 1144 helix: 3.24 (0.18), residues: 686 sheet: -0.27 (0.50), residues: 113 loop : -0.21 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 494 TYR 0.017 0.001 TYR M 136 PHE 0.011 0.001 PHE I 373 TRP 0.005 0.001 TRP M 53 HIS 0.006 0.001 HIS I 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 9498) covalent geometry : angle 0.51383 / 0.26 (12850) hydrogen bonds : bond 0.04486 / 2.99 ( 623) hydrogen bonds : angle 3.73733 / 2.78 ( 1812) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 169 MET cc_start: 0.6584 (ttm) cc_final: 0.6358 (ttm) REVERT: I 388 GLN cc_start: 0.8651 (mt0) cc_final: 0.8357 (mt0) REVERT: I 579 ARG cc_start: 0.8106 (ptt-90) cc_final: 0.7767 (ptm-80) REVERT: I 602 GLU cc_start: 0.8248 (mp0) cc_final: 0.7795 (pt0) REVERT: K 109 MET cc_start: 0.7684 (mtp) cc_final: 0.7412 (mtm) REVERT: L 215 ARG cc_start: 0.8495 (ttm170) cc_final: 0.8173 (mtp180) REVERT: L 230 ASP cc_start: 0.7896 (m-30) cc_final: 0.7635 (m-30) REVERT: L 240 GLN cc_start: 0.7635 (tm-30) cc_final: 0.7077 (tm-30) REVERT: N 266 LYS cc_start: 0.7963 (mtpp) cc_final: 0.7377 (mmtt) REVERT: N 324 ILE cc_start: 0.2318 (OUTLIER) cc_final: 0.2077 (mt) REVERT: T 824 MET cc_start: 0.7192 (mmt) cc_final: 0.6582 (ptt) outliers start: 10 outliers final: 9 residues processed: 142 average time/residue: 0.2340 time to fit residues: 44.5482 Evaluate side-chains 146 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain I residue 336 ASP Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 155 THR Chi-restraints excluded: chain N residue 228 ILE Chi-restraints excluded: chain N residue 264 THR Chi-restraints excluded: chain N residue 324 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 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 = 0.4136 r_free = 0.4136 target = 0.182825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.138475 restraints weight = 31994.625| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.47 r_work: 0.3396 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9498 Z= 0.119 Angle : 0.502 15.602 12850 Z= 0.254 Chirality : 0.070 1.648 1521 Planarity : 0.003 0.037 1615 Dihedral : 4.183 82.438 1249 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.95 % Allowed : 8.57 % Favored : 90.48 % 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: 2.97 (0.25), residues: 1144 helix: 3.28 (0.18), residues: 692 sheet: -0.09 (0.50), residues: 110 loop : -0.15 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 610 TYR 0.017 0.001 TYR M 136 PHE 0.009 0.001 PHE I 373 TRP 0.004 0.001 TRP M 53 HIS 0.006 0.001 HIS I 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 9498) covalent geometry : angle 0.50212 / 0.25 (12850) hydrogen bonds : bond 0.04281 / 2.85 ( 623) hydrogen bonds : angle 3.66278 / 2.73 ( 1812) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 169 MET cc_start: 0.6644 (ttm) cc_final: 0.6412 (ttm) REVERT: I 388 GLN cc_start: 0.8758 (mt0) cc_final: 0.8480 (mt0) REVERT: I 579 ARG cc_start: 0.8215 (ptt-90) cc_final: 0.7669 (ptm-80) REVERT: I 595 LYS cc_start: 0.8288 (mmtt) cc_final: 0.8024 (tptt) REVERT: I 602 GLU cc_start: 0.8318 (mp0) cc_final: 0.7941 (pt0) REVERT: K 109 MET cc_start: 0.7745 (mtp) cc_final: 0.7490 (mtm) REVERT: L 230 ASP cc_start: 0.7868 (m-30) cc_final: 0.7610 (m-30) REVERT: L 240 GLN cc_start: 0.7712 (tm-30) cc_final: 0.7162 (tm-30) REVERT: N 266 LYS cc_start: 0.7849 (mtpp) cc_final: 0.7335 (mmtt) REVERT: T 824 MET cc_start: 0.7269 (mmt) cc_final: 0.6646 (ptt) outliers start: 10 outliers final: 9 residues processed: 142 average time/residue: 0.2463 time to fit residues: 46.7562 Evaluate side-chains 145 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain I residue 336 ASP Chi-restraints excluded: chain I residue 500 LEU Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain K residue 100 SER Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 155 THR Chi-restraints excluded: chain N residue 228 ILE Chi-restraints excluded: chain N residue 264 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 111 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4129 r_free = 0.4129 target = 0.182082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.137348 restraints weight = 32162.565| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.49 r_work: 0.3379 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9498 Z= 0.137 Angle : 0.511 15.501 12850 Z= 0.260 Chirality : 0.070 1.634 1521 Planarity : 0.003 0.036 1615 Dihedral : 4.222 85.063 1249 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.86 % Allowed : 8.86 % Favored : 90.29 % 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: 2.95 (0.25), residues: 1144 helix: 3.26 (0.18), residues: 692 sheet: -0.05 (0.51), residues: 110 loop : -0.18 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 52 TYR 0.017 0.001 TYR M 136 PHE 0.010 0.001 PHE I 373 TRP 0.005 0.001 TRP I 636 HIS 0.006 0.001 HIS I 589 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 9498) covalent geometry : angle 0.51102 / 0.26 (12850) hydrogen bonds : bond 0.04395 / 2.93 ( 623) hydrogen bonds : angle 3.68125 / 2.74 ( 1812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5189.64 seconds wall clock time: 88 minutes 40.55 seconds (5320.55 seconds total)