Starting phenix.real_space_refine on Wed Feb 4 06:16:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vh1_65052/02_2026/9vh1_65052.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vh1_65052/02_2026/9vh1_65052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vh1_65052/02_2026/9vh1_65052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vh1_65052/02_2026/9vh1_65052.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vh1_65052/02_2026/9vh1_65052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vh1_65052/02_2026/9vh1_65052.map" } resolution = 3.4 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= 0.080 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 22 5.16 5 C 2863 2.51 5 N 768 2.21 5 O 850 1.98 5 H 4500 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9004 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2815 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain breaks: 3 Chain: "E" Number of atoms: 2851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2851 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 7, 'TRANS': 165} Chain breaks: 3 Chain: "F" Number of atoms: 3337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 3337 Classifications: {'peptide': 210} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 201} Chain breaks: 1 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6342 SG CYS F 43 35.183 50.872 55.716 1.00 60.72 S ATOM 6383 SG CYS F 46 36.186 50.965 51.963 1.00 61.69 S ATOM 6926 SG CYS F 78 34.988 47.748 53.629 1.00 62.94 S ATOM 7046 SG CYS F 90 38.389 49.376 54.441 1.00 57.44 S Time building chain proxies: 1.24, per 1000 atoms: 0.14 Number of scatterers: 9004 At special positions: 0 Unit cell: (77.456, 94.76, 93.112, 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) Zn 1 29.99 S 22 16.00 O 850 8.00 N 768 7.00 C 2863 6.00 H 4500 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: 0.73 Conformation dependent library (CDL) restraints added in 151.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 90 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 46 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 43 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 78 " Number of angles added : 6 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1062 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 4 sheets defined 53.5% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'D' and resid 362 through 378 removed outlier: 3.837A pdb=" N SER D 366 " --> pdb=" O ARG D 362 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU D 367 " --> pdb=" O VAL D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 409 removed outlier: 4.146A pdb=" N VAL D 409 " --> pdb=" O GLN D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 417 removed outlier: 3.510A pdb=" N VAL D 416 " --> pdb=" O ASN D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 433 Processing helix chain 'D' and resid 436 through 440 Processing helix chain 'D' and resid 467 through 473 removed outlier: 3.522A pdb=" N GLU D 471 " --> pdb=" O ALA D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 498 Processing helix chain 'D' and resid 505 through 518 removed outlier: 3.691A pdb=" N GLU D 509 " --> pdb=" O ASN D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 527 Processing helix chain 'D' and resid 527 through 545 Processing helix chain 'E' and resid 362 through 377 Processing helix chain 'E' and resid 402 through 406 Processing helix chain 'E' and resid 409 through 417 removed outlier: 3.518A pdb=" N ARG E 414 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER E 415 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL E 416 " --> pdb=" O ASN E 412 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE E 417 " --> pdb=" O LEU E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 438 No H-bonds generated for 'chain 'E' and resid 436 through 438' Processing helix chain 'E' and resid 470 through 475 Processing helix chain 'E' and resid 483 through 499 removed outlier: 4.006A pdb=" N HIS E 487 " --> pdb=" O ILE E 483 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TRP E 488 " --> pdb=" O ALA E 484 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU E 489 " --> pdb=" O GLU E 485 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY E 490 " --> pdb=" O SER E 486 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU E 494 " --> pdb=" O GLY E 490 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN E 499 " --> pdb=" O LEU E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 518 removed outlier: 3.921A pdb=" N LEU E 510 " --> pdb=" O GLN E 506 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS E 513 " --> pdb=" O GLU E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 544 removed outlier: 3.532A pdb=" N ARG E 533 " --> pdb=" O ASP E 529 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 15 removed outlier: 3.689A pdb=" N GLN F 15 " --> pdb=" O ILE F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 26 Processing helix chain 'F' and resid 27 through 30 Processing helix chain 'F' and resid 31 through 40 removed outlier: 4.113A pdb=" N GLU F 37 " --> pdb=" O PRO F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 72 No H-bonds generated for 'chain 'F' and resid 70 through 72' Processing helix chain 'F' and resid 91 through 96 removed outlier: 3.588A pdb=" N ASP F 95 " --> pdb=" O GLY F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 106 Processing helix chain 'F' and resid 134 through 147 removed outlier: 3.548A pdb=" N LYS F 138 " --> pdb=" O GLY F 134 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA F 140 " --> pdb=" O ALA F 136 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG F 145 " --> pdb=" O GLN F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 165 removed outlier: 3.542A pdb=" N SER F 158 " --> pdb=" O LYS F 154 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR F 161 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA F 162 " --> pdb=" O SER F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 176 removed outlier: 3.536A pdb=" N LEU F 173 " --> pdb=" O ASN F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 194 Processing helix chain 'F' and resid 195 through 199 removed outlier: 3.619A pdb=" N SER F 198 " --> pdb=" O LYS F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 210 Processing sheet with id=AA1, first strand: chain 'D' and resid 88 through 92 removed outlier: 3.520A pdb=" N THR D 426 " --> pdb=" O ILE D 91 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL D 392 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N THR D 425 " --> pdb=" O VAL D 392 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE D 394 " --> pdb=" O THR D 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 90 through 91 removed outlier: 6.670A pdb=" N VAL E 90 " --> pdb=" O ARG E 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'F' and resid 54 through 57 Processing sheet with id=AA4, first strand: chain 'F' and resid 119 through 120 162 hydrogen bonds defined for protein. 441 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: 1.44 Time building geometry restraints manager: 1.01 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: 4495 1.03 - 1.23: 6 1.23 - 1.42: 1865 1.42 - 1.61: 2679 1.61 - 1.81: 37 Bond restraints: 9082 Sorted by residual: bond pdb=" N PHE F 64 " pdb=" CA PHE F 64 " ideal model delta sigma weight residual 1.464 1.455 0.009 1.07e-02 8.73e+03 7.67e-01 bond pdb=" C SER D 428 " pdb=" O SER D 428 " ideal model delta sigma weight residual 1.248 1.238 0.010 1.26e-02 6.30e+03 6.75e-01 bond pdb=" CA ASN E 419 " pdb=" CB ASN E 419 " ideal model delta sigma weight residual 1.527 1.547 -0.020 2.48e-02 1.63e+03 6.62e-01 bond pdb=" CA ILE D 420 " pdb=" CB ILE D 420 " ideal model delta sigma weight residual 1.548 1.539 0.009 1.13e-02 7.83e+03 6.49e-01 bond pdb=" CB PHE E 443 " pdb=" CG PHE E 443 " ideal model delta sigma weight residual 1.502 1.518 -0.016 2.30e-02 1.89e+03 4.70e-01 ... (remaining 9077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 14980 1.02 - 2.03: 1391 2.03 - 3.05: 72 3.05 - 4.06: 23 4.06 - 5.08: 6 Bond angle restraints: 16472 Sorted by residual: angle pdb=" N ASN F 51 " pdb=" CA ASN F 51 " pdb=" C ASN F 51 " ideal model delta sigma weight residual 113.43 108.35 5.08 1.26e+00 6.30e-01 1.62e+01 angle pdb=" N VAL D 473 " pdb=" CA VAL D 473 " pdb=" C VAL D 473 " ideal model delta sigma weight residual 112.96 109.57 3.39 1.00e+00 1.00e+00 1.15e+01 angle pdb=" N TRP E 405 " pdb=" CA TRP E 405 " pdb=" C TRP E 405 " ideal model delta sigma weight residual 114.09 109.87 4.22 1.55e+00 4.16e-01 7.40e+00 angle pdb=" N ILE D 544 " pdb=" CA ILE D 544 " pdb=" C ILE D 544 " ideal model delta sigma weight residual 112.35 108.85 3.50 1.41e+00 5.03e-01 6.16e+00 angle pdb=" N SER E 522 " pdb=" CA SER E 522 " pdb=" C SER E 522 " ideal model delta sigma weight residual 110.53 113.66 -3.13 1.29e+00 6.01e-01 5.88e+00 ... (remaining 16467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3617 17.98 - 35.97: 415 35.97 - 53.95: 137 53.95 - 71.94: 30 71.94 - 89.92: 9 Dihedral angle restraints: 4208 sinusoidal: 2336 harmonic: 1872 Sorted by residual: dihedral pdb=" CA PHE F 147 " pdb=" C PHE F 147 " pdb=" N ASN F 148 " pdb=" CA ASN F 148 " ideal model delta harmonic sigma weight residual -180.00 -149.63 -30.37 0 5.00e+00 4.00e-02 3.69e+01 dihedral pdb=" CA ASP E 521 " pdb=" C ASP E 521 " pdb=" N SER E 522 " pdb=" CA SER E 522 " ideal model delta harmonic sigma weight residual -180.00 -152.48 -27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA ILE E 520 " pdb=" C ILE E 520 " pdb=" N ASP E 521 " pdb=" CA ASP E 521 " ideal model delta harmonic sigma weight residual 180.00 158.31 21.69 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 4205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 392 0.025 - 0.051: 189 0.051 - 0.076: 70 0.076 - 0.101: 17 0.101 - 0.126: 29 Chirality restraints: 697 Sorted by residual: chirality pdb=" CA ILE E 520 " pdb=" N ILE E 520 " pdb=" C ILE E 520 " pdb=" CB ILE E 520 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA VAL E 392 " pdb=" N VAL E 392 " pdb=" C VAL E 392 " pdb=" CB VAL E 392 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA ILE E 420 " pdb=" N ILE E 420 " pdb=" C ILE E 420 " pdb=" CB ILE E 420 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 694 not shown) Planarity restraints: 1317 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 402 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO E 403 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO E 403 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 403 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN F 113 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO F 114 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO F 114 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 114 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 414 " -0.111 9.50e-02 1.11e+02 3.72e-02 1.58e+00 pdb=" NE ARG E 414 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG E 414 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG E 414 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG E 414 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG E 414 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG E 414 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG E 414 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG E 414 " -0.001 2.00e-02 2.50e+03 ... (remaining 1314 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.36: 3137 2.36 - 2.92: 20958 2.92 - 3.48: 22559 3.48 - 4.04: 31564 4.04 - 4.60: 46860 Nonbonded interactions: 125078 Sorted by model distance: nonbonded pdb=" H ASP E 521 " pdb=" H SER E 522 " model vdw 1.795 2.100 nonbonded pdb=" H TRP E 405 " pdb=" H GLN E 406 " model vdw 1.846 2.100 nonbonded pdb=" O ASN E 499 " pdb="HD21 ASN E 499 " model vdw 1.874 2.450 nonbonded pdb=" HG2 ARG E 414 " pdb="HH11 ARG E 414 " model vdw 1.879 2.270 nonbonded pdb=" HD1 HIS D 402 " pdb=" H LYS D 404 " model vdw 1.890 2.100 ... (remaining 125073 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 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 85 through 92 or resid 361 through 377 or resid 391 throug \ h 545)) selection = (chain 'E' and ((resid 85 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 86 through 443 or (resid 454 and (name N or \ name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or nam \ e HA or name HB2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 o \ r name HD21 or name HD22 or name HD23)) or resid 455 through 545)) } 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: 1.350 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: 0.050 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.660 Find NCS groups from input model: 0.050 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 0.031 4586 Z= 0.150 Angle : 0.593 5.079 6187 Z= 0.332 Chirality : 0.040 0.126 697 Planarity : 0.004 0.048 794 Dihedral : 19.451 89.919 1740 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 5.16 % Allowed : 26.19 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.08 (0.36), residues: 535 helix: -2.03 (0.32), residues: 254 sheet: -2.48 (0.72), residues: 42 loop : -1.80 (0.42), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 414 TYR 0.006 0.001 TYR F 117 PHE 0.011 0.001 PHE E 417 TRP 0.008 0.001 TRP F 185 HIS 0.004 0.001 HIS F 54 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 4582) covalent geometry : angle 0.58604 ( 6181) hydrogen bonds : bond 0.23832 ( 162) hydrogen bonds : angle 10.51773 ( 441) metal coordination : bond 0.00725 ( 4) metal coordination : angle 2.90200 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 362 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.4597 (ttp-170) REVERT: D 404 LYS cc_start: 0.8804 (tttt) cc_final: 0.8425 (tttm) REVERT: D 419 ASN cc_start: 0.8481 (m-40) cc_final: 0.8149 (p0) REVERT: D 420 ILE cc_start: 0.9239 (tt) cc_final: 0.9012 (tt) REVERT: D 458 ASP cc_start: 0.7993 (t0) cc_final: 0.7644 (t0) REVERT: D 471 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7128 (tm-30) REVERT: E 393 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8453 (pp) REVERT: E 506 GLN cc_start: 0.8710 (tt0) cc_final: 0.8477 (tt0) REVERT: F 34 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8404 (mmmm) REVERT: F 141 GLN cc_start: 0.8775 (mt0) cc_final: 0.8572 (mt0) REVERT: F 191 ASP cc_start: 0.8712 (t70) cc_final: 0.8346 (t0) REVERT: F 194 GLU cc_start: 0.7891 (tt0) cc_final: 0.7043 (tm-30) outliers start: 26 outliers final: 21 residues processed: 113 average time/residue: 0.1293 time to fit residues: 18.3847 Evaluate side-chains 121 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 ARG Chi-restraints excluded: chain D residue 421 GLN Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 464 SER Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 398 GLU Chi-restraints excluded: chain E residue 443 PHE Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 20 GLN Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 34 LYS Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 180 PHE Chi-restraints excluded: chain F residue 203 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 53 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 499 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.120271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.099375 restraints weight = 16958.730| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.79 r_work: 0.2886 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4586 Z= 0.128 Angle : 0.554 4.733 6187 Z= 0.290 Chirality : 0.040 0.123 697 Planarity : 0.004 0.038 794 Dihedral : 10.376 69.852 633 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 5.16 % Allowed : 24.60 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.48 (0.37), residues: 535 helix: -1.33 (0.32), residues: 260 sheet: -2.45 (0.71), residues: 42 loop : -1.71 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 414 TYR 0.007 0.001 TYR F 117 PHE 0.006 0.001 PHE F 147 TRP 0.007 0.001 TRP F 185 HIS 0.003 0.001 HIS F 54 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 4582) covalent geometry : angle 0.54758 ( 6181) hydrogen bonds : bond 0.03964 ( 162) hydrogen bonds : angle 6.01483 ( 441) metal coordination : bond 0.00655 ( 4) metal coordination : angle 2.78655 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 362 ARG cc_start: 0.7118 (OUTLIER) cc_final: 0.4584 (ttp-110) REVERT: D 419 ASN cc_start: 0.8466 (m-40) cc_final: 0.8149 (p0) REVERT: D 420 ILE cc_start: 0.9247 (tt) cc_final: 0.8997 (tt) REVERT: D 458 ASP cc_start: 0.8117 (t0) cc_final: 0.7759 (t0) REVERT: D 471 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: D 500 SER cc_start: 0.8439 (t) cc_final: 0.7932 (p) REVERT: E 393 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8425 (pp) REVERT: E 506 GLN cc_start: 0.8688 (tt0) cc_final: 0.8485 (tt0) REVERT: F 178 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: F 191 ASP cc_start: 0.8689 (t70) cc_final: 0.8252 (t0) REVERT: F 194 GLU cc_start: 0.7953 (tt0) cc_final: 0.7097 (tm-30) outliers start: 26 outliers final: 14 residues processed: 113 average time/residue: 0.1759 time to fit residues: 24.8823 Evaluate side-chains 114 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 ARG Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 398 GLU Chi-restraints excluded: chain E residue 443 PHE Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 20 GLN Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 180 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 499 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.119959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.098616 restraints weight = 17073.151| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.82 r_work: 0.2880 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4586 Z= 0.140 Angle : 0.537 4.739 6187 Z= 0.280 Chirality : 0.040 0.124 697 Planarity : 0.004 0.039 794 Dihedral : 9.163 71.193 614 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 5.56 % Allowed : 24.01 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.03 (0.37), residues: 535 helix: -0.78 (0.33), residues: 261 sheet: -2.24 (0.73), residues: 42 loop : -1.73 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 414 TYR 0.007 0.001 TYR F 117 PHE 0.007 0.001 PHE F 147 TRP 0.007 0.001 TRP F 185 HIS 0.003 0.001 HIS F 54 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 4582) covalent geometry : angle 0.53055 ( 6181) hydrogen bonds : bond 0.03536 ( 162) hydrogen bonds : angle 5.35432 ( 441) metal coordination : bond 0.00722 ( 4) metal coordination : angle 2.73201 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 362 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.4565 (ttp-110) REVERT: D 419 ASN cc_start: 0.8472 (m-40) cc_final: 0.8226 (p0) REVERT: D 455 ASP cc_start: 0.6467 (OUTLIER) cc_final: 0.6059 (p0) REVERT: D 458 ASP cc_start: 0.8111 (t0) cc_final: 0.7732 (t0) REVERT: D 500 SER cc_start: 0.8436 (t) cc_final: 0.7913 (p) REVERT: E 393 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8417 (pp) REVERT: F 88 SER cc_start: 0.8714 (t) cc_final: 0.8377 (t) REVERT: F 191 ASP cc_start: 0.8663 (t70) cc_final: 0.8320 (t0) REVERT: F 194 GLU cc_start: 0.7930 (tt0) cc_final: 0.7076 (tm-30) outliers start: 28 outliers final: 21 residues processed: 122 average time/residue: 0.1828 time to fit residues: 27.8775 Evaluate side-chains 121 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 ARG Chi-restraints excluded: chain D residue 421 GLN Chi-restraints excluded: chain D residue 427 HIS Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 486 SER Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 398 GLU Chi-restraints excluded: chain E residue 443 PHE Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 20 GLN Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 180 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 13 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 499 ASN E 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.120660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.099708 restraints weight = 16948.058| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.78 r_work: 0.2898 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4586 Z= 0.114 Angle : 0.518 4.595 6187 Z= 0.269 Chirality : 0.039 0.123 697 Planarity : 0.004 0.040 794 Dihedral : 8.736 72.553 609 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 5.36 % Allowed : 24.01 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.71 (0.38), residues: 535 helix: -0.47 (0.34), residues: 261 sheet: -2.06 (0.75), residues: 42 loop : -1.63 (0.43), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 414 TYR 0.007 0.001 TYR F 117 PHE 0.008 0.001 PHE E 417 TRP 0.007 0.001 TRP F 185 HIS 0.003 0.001 HIS F 54 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 4582) covalent geometry : angle 0.51086 ( 6181) hydrogen bonds : bond 0.03051 ( 162) hydrogen bonds : angle 4.97800 ( 441) metal coordination : bond 0.00574 ( 4) metal coordination : angle 2.73571 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 362 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.4536 (ttp-110) REVERT: D 419 ASN cc_start: 0.8402 (m-40) cc_final: 0.8180 (p0) REVERT: D 420 ILE cc_start: 0.9230 (tt) cc_final: 0.8988 (tt) REVERT: D 458 ASP cc_start: 0.8047 (t0) cc_final: 0.7697 (t0) REVERT: D 500 SER cc_start: 0.8427 (t) cc_final: 0.7917 (p) REVERT: E 393 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8415 (pp) REVERT: F 88 SER cc_start: 0.8710 (t) cc_final: 0.8377 (t) REVERT: F 191 ASP cc_start: 0.8611 (t70) cc_final: 0.8298 (t0) REVERT: F 194 GLU cc_start: 0.7900 (tt0) cc_final: 0.7101 (tm-30) outliers start: 27 outliers final: 19 residues processed: 123 average time/residue: 0.1648 time to fit residues: 25.4127 Evaluate side-chains 122 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 ARG Chi-restraints excluded: chain D residue 421 GLN Chi-restraints excluded: chain D residue 427 HIS Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 398 GLU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 521 ASP Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 180 PHE Chi-restraints excluded: chain F residue 203 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 10 optimal weight: 0.0040 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 0.0770 chunk 50 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 0.4150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 499 ASN F 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.122239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.101604 restraints weight = 16708.514| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.75 r_work: 0.2926 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4586 Z= 0.096 Angle : 0.498 4.481 6187 Z= 0.257 Chirality : 0.039 0.122 697 Planarity : 0.004 0.046 794 Dihedral : 7.922 61.755 604 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 4.56 % Allowed : 25.40 % Favored : 70.04 % 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: -1.30 (0.38), residues: 535 helix: -0.09 (0.35), residues: 258 sheet: -1.82 (0.77), residues: 42 loop : -1.49 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 414 TYR 0.007 0.001 TYR F 117 PHE 0.004 0.001 PHE D 518 TRP 0.006 0.000 TRP F 185 HIS 0.003 0.001 HIS F 54 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 4582) covalent geometry : angle 0.49115 ( 6181) hydrogen bonds : bond 0.02721 ( 162) hydrogen bonds : angle 4.63391 ( 441) metal coordination : bond 0.00430 ( 4) metal coordination : angle 2.73823 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 362 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.4539 (ttp-110) REVERT: D 404 LYS cc_start: 0.8672 (tttt) cc_final: 0.8361 (tttm) REVERT: D 458 ASP cc_start: 0.7964 (t0) cc_final: 0.7629 (t0) REVERT: D 500 SER cc_start: 0.8416 (t) cc_final: 0.7915 (p) REVERT: E 377 MET cc_start: 0.6974 (tpt) cc_final: 0.6764 (tpt) REVERT: E 393 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8415 (pp) REVERT: F 88 SER cc_start: 0.8664 (t) cc_final: 0.8335 (t) REVERT: F 191 ASP cc_start: 0.8600 (t70) cc_final: 0.8319 (t0) REVERT: F 194 GLU cc_start: 0.7833 (tt0) cc_final: 0.7105 (tm-30) outliers start: 23 outliers final: 19 residues processed: 117 average time/residue: 0.1677 time to fit residues: 24.3622 Evaluate side-chains 112 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 ARG Chi-restraints excluded: chain D residue 421 GLN Chi-restraints excluded: chain D residue 427 HIS Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 398 GLU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 521 ASP Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 117 TYR Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 180 PHE Chi-restraints excluded: chain F residue 203 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 499 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.121275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.100328 restraints weight = 16748.374| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.77 r_work: 0.2905 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 4586 Z= 0.130 Angle : 0.513 4.905 6187 Z= 0.265 Chirality : 0.040 0.124 697 Planarity : 0.004 0.042 794 Dihedral : 7.880 61.655 604 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 5.56 % Allowed : 23.81 % Favored : 70.63 % 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: -1.19 (0.39), residues: 535 helix: 0.03 (0.35), residues: 258 sheet: -1.78 (0.77), residues: 42 loop : -1.47 (0.44), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 414 TYR 0.007 0.001 TYR F 117 PHE 0.011 0.001 PHE E 417 TRP 0.006 0.001 TRP F 185 HIS 0.003 0.001 HIS F 54 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 4582) covalent geometry : angle 0.50624 ( 6181) hydrogen bonds : bond 0.02776 ( 162) hydrogen bonds : angle 4.56708 ( 441) metal coordination : bond 0.00669 ( 4) metal coordination : angle 2.72155 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 362 ARG cc_start: 0.7106 (OUTLIER) cc_final: 0.4557 (ttp-110) REVERT: D 455 ASP cc_start: 0.6403 (OUTLIER) cc_final: 0.6106 (p0) REVERT: D 458 ASP cc_start: 0.8002 (t0) cc_final: 0.7642 (t0) REVERT: D 500 SER cc_start: 0.8421 (t) cc_final: 0.7910 (p) REVERT: E 377 MET cc_start: 0.6923 (tpt) cc_final: 0.6721 (tpt) REVERT: E 393 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8420 (pp) REVERT: F 88 SER cc_start: 0.8745 (t) cc_final: 0.8423 (t) REVERT: F 191 ASP cc_start: 0.8612 (t70) cc_final: 0.8330 (t0) REVERT: F 194 GLU cc_start: 0.7832 (tt0) cc_final: 0.7087 (tm-30) outliers start: 28 outliers final: 20 residues processed: 117 average time/residue: 0.1823 time to fit residues: 26.3487 Evaluate side-chains 117 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 ARG Chi-restraints excluded: chain D residue 421 GLN Chi-restraints excluded: chain D residue 427 HIS Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 398 GLU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 521 ASP Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 180 PHE Chi-restraints excluded: chain F residue 203 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 499 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.120242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.099380 restraints weight = 16973.902| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.76 r_work: 0.2895 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 4586 Z= 0.135 Angle : 0.520 4.929 6187 Z= 0.268 Chirality : 0.040 0.125 697 Planarity : 0.004 0.047 794 Dihedral : 7.848 61.736 604 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 5.36 % Allowed : 23.21 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.13 (0.39), residues: 535 helix: 0.12 (0.35), residues: 258 sheet: -1.73 (0.78), residues: 42 loop : -1.49 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 414 TYR 0.008 0.001 TYR F 117 PHE 0.005 0.001 PHE F 147 TRP 0.007 0.001 TRP F 185 HIS 0.003 0.001 HIS F 54 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 4582) covalent geometry : angle 0.51309 ( 6181) hydrogen bonds : bond 0.02755 ( 162) hydrogen bonds : angle 4.51339 ( 441) metal coordination : bond 0.00746 ( 4) metal coordination : angle 2.77164 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 362 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.4576 (ttp-110) REVERT: D 455 ASP cc_start: 0.6420 (OUTLIER) cc_final: 0.6137 (p0) REVERT: D 458 ASP cc_start: 0.7998 (t0) cc_final: 0.7634 (t0) REVERT: D 500 SER cc_start: 0.8423 (t) cc_final: 0.7906 (p) REVERT: E 393 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8414 (pp) REVERT: F 88 SER cc_start: 0.8719 (t) cc_final: 0.8397 (t) REVERT: F 191 ASP cc_start: 0.8637 (t70) cc_final: 0.8353 (t0) REVERT: F 194 GLU cc_start: 0.7822 (tt0) cc_final: 0.7095 (tm-30) outliers start: 27 outliers final: 21 residues processed: 115 average time/residue: 0.1557 time to fit residues: 22.1464 Evaluate side-chains 116 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 ARG Chi-restraints excluded: chain D residue 421 GLN Chi-restraints excluded: chain D residue 427 HIS Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 398 GLU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 507 SER Chi-restraints excluded: chain E residue 521 ASP Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 22 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 180 PHE Chi-restraints excluded: chain F residue 203 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 3 optimal weight: 0.1980 chunk 44 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 499 ASN E 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.121373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.100327 restraints weight = 16772.928| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.77 r_work: 0.2907 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 4586 Z= 0.112 Angle : 0.513 4.914 6187 Z= 0.263 Chirality : 0.039 0.125 697 Planarity : 0.004 0.048 794 Dihedral : 7.760 61.631 604 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 4.96 % Allowed : 23.41 % Favored : 71.63 % 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: -0.95 (0.39), residues: 535 helix: 0.28 (0.35), residues: 258 sheet: -1.61 (0.79), residues: 42 loop : -1.42 (0.44), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 414 TYR 0.007 0.001 TYR F 117 PHE 0.005 0.001 PHE F 180 TRP 0.007 0.000 TRP F 185 HIS 0.003 0.001 HIS F 54 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 4582) covalent geometry : angle 0.50593 ( 6181) hydrogen bonds : bond 0.02628 ( 162) hydrogen bonds : angle 4.45567 ( 441) metal coordination : bond 0.00571 ( 4) metal coordination : angle 2.73207 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 362 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.4577 (ttp-110) REVERT: D 455 ASP cc_start: 0.6399 (OUTLIER) cc_final: 0.6123 (p0) REVERT: D 458 ASP cc_start: 0.7986 (t0) cc_final: 0.7641 (t0) REVERT: D 500 SER cc_start: 0.8421 (t) cc_final: 0.7908 (p) REVERT: E 393 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8390 (pp) REVERT: F 88 SER cc_start: 0.8748 (t) cc_final: 0.8431 (t) REVERT: F 191 ASP cc_start: 0.8641 (t70) cc_final: 0.8349 (t0) REVERT: F 194 GLU cc_start: 0.7815 (tt0) cc_final: 0.7077 (tm-30) outliers start: 25 outliers final: 20 residues processed: 113 average time/residue: 0.1466 time to fit residues: 20.6027 Evaluate side-chains 117 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 ARG Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 421 GLN Chi-restraints excluded: chain D residue 427 HIS Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 398 GLU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 443 PHE Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 521 ASP Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 180 PHE Chi-restraints excluded: chain F residue 203 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 35 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 499 ASN E 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.120831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.099688 restraints weight = 16915.205| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.78 r_work: 0.2898 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 4586 Z= 0.130 Angle : 0.533 9.912 6187 Z= 0.270 Chirality : 0.040 0.126 697 Planarity : 0.004 0.051 794 Dihedral : 7.650 61.467 604 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 5.56 % Allowed : 22.82 % Favored : 71.63 % 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: -0.91 (0.39), residues: 535 helix: 0.33 (0.35), residues: 258 sheet: -1.62 (0.79), residues: 42 loop : -1.42 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 414 TYR 0.008 0.001 TYR F 117 PHE 0.006 0.001 PHE F 180 TRP 0.007 0.001 TRP F 185 HIS 0.003 0.001 HIS F 54 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4582) covalent geometry : angle 0.52543 ( 6181) hydrogen bonds : bond 0.02655 ( 162) hydrogen bonds : angle 4.41415 ( 441) metal coordination : bond 0.00728 ( 4) metal coordination : angle 2.83367 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 362 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.4608 (ttp-110) REVERT: D 455 ASP cc_start: 0.6395 (OUTLIER) cc_final: 0.6116 (p0) REVERT: D 458 ASP cc_start: 0.8008 (t0) cc_final: 0.7656 (t0) REVERT: D 500 SER cc_start: 0.8430 (t) cc_final: 0.7916 (p) REVERT: E 393 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8378 (pp) REVERT: F 88 SER cc_start: 0.8718 (t) cc_final: 0.8403 (t) REVERT: F 191 ASP cc_start: 0.8655 (t70) cc_final: 0.8355 (t0) REVERT: F 194 GLU cc_start: 0.7847 (tt0) cc_final: 0.7100 (tm-30) outliers start: 28 outliers final: 22 residues processed: 118 average time/residue: 0.1553 time to fit residues: 22.6354 Evaluate side-chains 121 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 ARG Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 421 GLN Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 398 GLU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 443 PHE Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 521 ASP Chi-restraints excluded: chain F residue 17 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 180 PHE Chi-restraints excluded: chain F residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 29 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 506 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.120742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.099403 restraints weight = 16904.887| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.81 r_work: 0.2892 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 4586 Z= 0.129 Angle : 0.526 6.220 6187 Z= 0.269 Chirality : 0.040 0.124 697 Planarity : 0.004 0.054 794 Dihedral : 7.581 61.606 604 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 4.56 % Allowed : 24.21 % Favored : 71.23 % 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: -0.84 (0.39), residues: 535 helix: 0.38 (0.35), residues: 258 sheet: -1.59 (0.80), residues: 42 loop : -1.38 (0.44), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 414 TYR 0.007 0.001 TYR F 117 PHE 0.005 0.001 PHE F 147 TRP 0.007 0.001 TRP F 185 HIS 0.003 0.001 HIS F 54 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 4582) covalent geometry : angle 0.51932 ( 6181) hydrogen bonds : bond 0.02635 ( 162) hydrogen bonds : angle 4.40224 ( 441) metal coordination : bond 0.00701 ( 4) metal coordination : angle 2.74540 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1070 Ramachandran restraints generated. 535 Oldfield, 0 Emsley, 535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 362 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.4614 (ttp-110) REVERT: D 455 ASP cc_start: 0.6369 (OUTLIER) cc_final: 0.6057 (p0) REVERT: D 458 ASP cc_start: 0.8013 (t0) cc_final: 0.7659 (t0) REVERT: D 500 SER cc_start: 0.8430 (t) cc_final: 0.7911 (p) REVERT: E 393 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8440 (pp) REVERT: F 88 SER cc_start: 0.8780 (t) cc_final: 0.8468 (t) REVERT: F 191 ASP cc_start: 0.8649 (t70) cc_final: 0.8350 (t0) REVERT: F 194 GLU cc_start: 0.7837 (tt0) cc_final: 0.7102 (tm-30) outliers start: 23 outliers final: 20 residues processed: 116 average time/residue: 0.1766 time to fit residues: 25.4191 Evaluate side-chains 121 residues out of total 504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 362 ARG Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 421 GLN Chi-restraints excluded: chain D residue 455 ASP Chi-restraints excluded: chain D residue 497 LEU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 365 LEU Chi-restraints excluded: chain E residue 391 ILE Chi-restraints excluded: chain E residue 393 LEU Chi-restraints excluded: chain E residue 398 GLU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 443 PHE Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 464 SER Chi-restraints excluded: chain E residue 521 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain F residue 178 GLU Chi-restraints excluded: chain F residue 180 PHE Chi-restraints excluded: chain F residue 203 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 7 optimal weight: 0.0770 chunk 27 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 499 ASN E 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.121569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.100324 restraints weight = 16607.514| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.79 r_work: 0.2905 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 4586 Z= 0.119 Angle : 0.528 10.302 6187 Z= 0.267 Chirality : 0.039 0.124 697 Planarity : 0.004 0.056 794 Dihedral : 7.395 61.431 603 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 5.36 % Allowed : 24.01 % Favored : 70.63 % 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: -0.72 (0.39), residues: 535 helix: 0.48 (0.35), residues: 259 sheet: -1.53 (0.81), residues: 42 loop : -1.32 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 414 TYR 0.007 0.001 TYR F 117 PHE 0.005 0.001 PHE F 147 TRP 0.007 0.001 TRP F 185 HIS 0.003 0.001 HIS F 54 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4582) covalent geometry : angle 0.52150 ( 6181) hydrogen bonds : bond 0.02533 ( 162) hydrogen bonds : angle 4.34788 ( 441) metal coordination : bond 0.00622 ( 4) metal coordination : angle 2.79549 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2606.94 seconds wall clock time: 44 minutes 48.53 seconds (2688.53 seconds total)