Starting phenix.real_space_refine on Wed Feb 4 15:01:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ga9_29894/02_2026/8ga9_29894.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ga9_29894/02_2026/8ga9_29894.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ga9_29894/02_2026/8ga9_29894.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ga9_29894/02_2026/8ga9_29894.map" model { file = "/net/cci-nas-00/data/ceres_data/8ga9_29894/02_2026/8ga9_29894.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ga9_29894/02_2026/8ga9_29894.cif" } resolution = 3.71 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= 0.013 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 36 5.16 5 C 3840 2.51 5 N 836 2.21 5 O 976 1.98 5 H 5864 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s 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: 11552 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2888 Classifications: {'peptide': 165} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 152} Chain: "C" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2888 Classifications: {'peptide': 165} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 152} Chain: "E" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2888 Classifications: {'peptide': 165} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 152} Chain: "G" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2888 Classifications: {'peptide': 165} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 152} Time building chain proxies: 2.24, per 1000 atoms: 0.19 Number of scatterers: 11552 At special positions: 0 Unit cell: (89.385, 88.5, 61.95, 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 36 16.00 O 976 8.00 N 836 7.00 C 3840 6.00 H 5864 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: 1.13 Conformation dependent library (CDL) restraints added in 502.6 milliseconds 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1296 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 92.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 1 through 10 removed outlier: 4.236A pdb=" N LEU A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR A 6 " --> pdb=" O LYS A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 24 removed outlier: 3.534A pdb=" N GLN A 16 " --> pdb=" O PRO A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 40 removed outlier: 3.981A pdb=" N GLU A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 53 removed outlier: 3.509A pdb=" N LEU A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 69 removed outlier: 3.911A pdb=" N GLU A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 83 removed outlier: 3.511A pdb=" N PHE A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 95 removed outlier: 3.899A pdb=" N ASN A 93 " --> pdb=" O GLN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 111 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.679A pdb=" N LYS A 124 " --> pdb=" O PHE A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.718A pdb=" N PHE A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 153 Processing helix chain 'A' and resid 155 through 164 Processing helix chain 'C' and resid 168 through 176 Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'C' and resid 192 through 206 removed outlier: 4.122A pdb=" N GLU C 198 " --> pdb=" O GLU C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 219 removed outlier: 3.531A pdb=" N LEU C 212 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 219 " --> pdb=" O ARG C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 235 removed outlier: 3.786A pdb=" N GLU C 234 " --> pdb=" O GLU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 248 removed outlier: 4.476A pdb=" N LEU C 241 " --> pdb=" O GLU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 264 through 277 Processing helix chain 'C' and resid 278 through 292 removed outlier: 3.672A pdb=" N TYR C 288 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 289 " --> pdb=" O PHE C 285 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS C 290 " --> pdb=" O PHE C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 305 Processing helix chain 'C' and resid 307 through 319 Processing helix chain 'C' and resid 321 through 330 Processing helix chain 'E' and resid 334 through 342 Processing helix chain 'E' and resid 344 through 356 Processing helix chain 'E' and resid 358 through 372 removed outlier: 4.255A pdb=" N GLU E 364 " --> pdb=" O GLU E 360 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU E 372 " --> pdb=" O ARG E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 385 removed outlier: 3.602A pdb=" N LEU E 378 " --> pdb=" O GLY E 374 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU E 385 " --> pdb=" O ARG E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 401 removed outlier: 3.535A pdb=" N GLN E 391 " --> pdb=" O HIS E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 415 removed outlier: 3.572A pdb=" N PHE E 405 " --> pdb=" O ASN E 401 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS E 406 " --> pdb=" O PRO E 402 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU E 407 " --> pdb=" O GLU E 403 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 412 " --> pdb=" O PHE E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 427 Processing helix chain 'E' and resid 430 through 443 removed outlier: 3.748A pdb=" N GLN E 434 " --> pdb=" O HIS E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 458 removed outlier: 3.683A pdb=" N LYS E 456 " --> pdb=" O PHE E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 472 removed outlier: 4.611A pdb=" N LEU E 464 " --> pdb=" O GLY E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 485 Processing helix chain 'E' and resid 487 through 497 Processing helix chain 'G' and resid 500 through 509 Processing helix chain 'G' and resid 510 through 523 removed outlier: 3.517A pdb=" N GLN G 514 " --> pdb=" O PRO G 510 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 538 removed outlier: 4.151A pdb=" N GLU G 530 " --> pdb=" O GLU G 526 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU G 538 " --> pdb=" O ARG G 534 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 551 removed outlier: 3.849A pdb=" N LEU G 544 " --> pdb=" O GLY G 540 " (cutoff:3.500A) Processing helix chain 'G' and resid 553 through 566 removed outlier: 3.610A pdb=" N GLU G 566 " --> pdb=" O GLU G 562 " (cutoff:3.500A) Processing helix chain 'G' and resid 570 through 581 removed outlier: 3.736A pdb=" N GLU G 576 " --> pdb=" O LYS G 572 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU G 578 " --> pdb=" O PHE G 574 " (cutoff:3.500A) Processing helix chain 'G' and resid 583 through 593 Processing helix chain 'G' and resid 596 through 609 Processing helix chain 'G' and resid 610 through 624 removed outlier: 3.670A pdb=" N LYS G 622 " --> pdb=" O PHE G 618 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 637 Processing helix chain 'G' and resid 639 through 651 Processing helix chain 'G' and resid 653 through 662 380 hydrogen bonds defined for protein. 1140 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: 2.21 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 5856 1.13 - 1.31: 988 1.31 - 1.48: 2108 1.48 - 1.66: 2688 1.66 - 1.83: 64 Bond restraints: 11704 Sorted by residual: bond pdb=" CD2 PHE G 531 " pdb=" HD2 PHE G 531 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NE2 HIS G 553 " pdb=" HE2 HIS G 553 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N VAL E 497 " pdb=" H VAL E 497 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CE1 HIS E 387 " pdb=" HE1 HIS E 387 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLN C 225 " pdb=" H GLN C 225 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 11699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 17454 2.61 - 5.22: 3284 5.22 - 7.83: 613 7.83 - 10.44: 54 10.44 - 13.05: 7 Bond angle restraints: 21412 Sorted by residual: angle pdb=" CA ASN E 358 " pdb=" CB ASN E 358 " pdb=" CG ASN E 358 " ideal model delta sigma weight residual 112.60 118.38 -5.78 1.00e+00 1.00e+00 3.34e+01 angle pdb=" C MET E 343 " pdb=" N PRO E 344 " pdb=" CA PRO E 344 " ideal model delta sigma weight residual 119.66 123.82 -4.16 7.30e-01 1.88e+00 3.25e+01 angle pdb=" CB HIS C 264 " pdb=" CG HIS C 264 " pdb=" CD2 HIS C 264 " ideal model delta sigma weight residual 131.20 124.15 7.05 1.30e+00 5.92e-01 2.94e+01 angle pdb=" CA PHE C 200 " pdb=" CB PHE C 200 " pdb=" CG PHE C 200 " ideal model delta sigma weight residual 113.80 108.44 5.36 1.00e+00 1.00e+00 2.88e+01 angle pdb=" C ASN E 401 " pdb=" N PRO E 402 " pdb=" CA PRO E 402 " ideal model delta sigma weight residual 119.82 125.06 -5.24 9.80e-01 1.04e+00 2.86e+01 ... (remaining 21407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 5032 17.71 - 35.41: 283 35.41 - 53.11: 93 53.11 - 70.82: 43 70.82 - 88.52: 9 Dihedral angle restraints: 5460 sinusoidal: 2984 harmonic: 2476 Sorted by residual: dihedral pdb=" CA PHE A 77 " pdb=" C PHE A 77 " pdb=" N GLU A 78 " pdb=" CA GLU A 78 " ideal model delta harmonic sigma weight residual 180.00 150.02 29.98 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA ARG E 457 " pdb=" C ARG E 457 " pdb=" N CYS E 458 " pdb=" CA CYS E 458 " ideal model delta harmonic sigma weight residual 180.00 150.67 29.33 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA ASN G 567 " pdb=" C ASN G 567 " pdb=" N PRO G 568 " pdb=" CA PRO G 568 " ideal model delta harmonic sigma weight residual 180.00 -151.35 -28.65 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 5457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 527 0.087 - 0.175: 249 0.175 - 0.262: 51 0.262 - 0.349: 15 0.349 - 0.436: 2 Chirality restraints: 844 Sorted by residual: chirality pdb=" CA PHE A 77 " pdb=" N PHE A 77 " pdb=" C PHE A 77 " pdb=" CB PHE A 77 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA PRO E 431 " pdb=" N PRO E 431 " pdb=" C PRO E 431 " pdb=" CB PRO E 431 " both_signs ideal model delta sigma weight residual False 2.72 2.35 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA MET C 167 " pdb=" N MET C 167 " pdb=" C MET C 167 " pdb=" CB MET C 167 " both_signs ideal model delta sigma weight residual False 2.57 2.24 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 841 not shown) Planarity restraints: 1604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 155 " 0.096 2.00e-02 2.50e+03 8.84e-02 1.17e+02 pdb=" CG ASN A 155 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 155 " -0.062 2.00e-02 2.50e+03 pdb=" ND2 ASN A 155 " -0.076 2.00e-02 2.50e+03 pdb="HD21 ASN A 155 " -0.070 2.00e-02 2.50e+03 pdb="HD22 ASN A 155 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 550 " -0.129 2.00e-02 2.50e+03 5.87e-02 1.03e+02 pdb=" CG TYR G 550 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR G 550 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR G 550 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR G 550 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR G 550 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR G 550 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR G 550 " -0.118 2.00e-02 2.50e+03 pdb=" HD1 TYR G 550 " 0.056 2.00e-02 2.50e+03 pdb=" HD2 TYR G 550 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR G 550 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR G 550 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 25 " -0.088 2.00e-02 2.50e+03 8.19e-02 1.01e+02 pdb=" CG ASN A 25 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A 25 " 0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN A 25 " 0.082 2.00e-02 2.50e+03 pdb="HD21 ASN A 25 " 0.060 2.00e-02 2.50e+03 pdb="HD22 ASN A 25 " -0.137 2.00e-02 2.50e+03 ... (remaining 1601 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.91: 92 1.91 - 2.59: 10184 2.59 - 3.26: 35690 3.26 - 3.93: 44115 3.93 - 4.60: 65969 Nonbonded interactions: 156050 Sorted by model distance: nonbonded pdb="HD12 LEU C 260 " pdb="HD11 LEU C 263 " model vdw 1.242 2.440 nonbonded pdb=" HE2 PHE A 116 " pdb="HD23 LEU A 161 " model vdw 1.568 2.270 nonbonded pdb="HD22 LEU A 106 " pdb="HD21 LEU A 148 " model vdw 1.614 2.440 nonbonded pdb=" O GLN A 102 " pdb="HD13 LEU A 106 " model vdw 1.636 2.620 nonbonded pdb=" OE2 GLU A 78 " pdb=" HH TYR A 122 " model vdw 1.652 2.450 ... (remaining 156045 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.320 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: 0.080 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.030 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 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 : 0.014 0.051 5840 Z= 0.819 Angle : 1.814 8.192 7864 Z= 1.212 Chirality : 0.103 0.436 844 Planarity : 0.015 0.100 996 Dihedral : 13.583 88.525 2304 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Cbeta Deviations : 0.31 % 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: -2.78 (0.27), residues: 652 helix: -1.92 (0.16), residues: 584 sheet: None (None), residues: 0 loop : 1.59 (0.83), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.003 ARG G 547 TYR 0.115 0.023 TYR G 550 PHE 0.100 0.015 PHE E 452 HIS 0.013 0.005 HIS G 596 Details of bonding type rmsd covalent geometry : bond 0.01449 ( 5840) covalent geometry : angle 1.81358 ( 7864) hydrogen bonds : bond 0.20216 ( 380) hydrogen bonds : angle 7.82187 ( 1140) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.7176 (mmtt) cc_final: 0.6636 (ttpt) REVERT: C 282 PHE cc_start: 0.8393 (t80) cc_final: 0.8061 (t80) REVERT: C 312 LYS cc_start: 0.8259 (ptmt) cc_final: 0.7999 (mppt) REVERT: E 432 MET cc_start: 0.7676 (mpp) cc_final: 0.7465 (mpp) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1456 time to fit residues: 35.5768 Evaluate side-chains 141 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 524 ASN G 587 GLN G 600 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.176548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.153514 restraints weight = 23947.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.160669 restraints weight = 11734.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.165238 restraints weight = 6782.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.168205 restraints weight = 4369.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.170196 restraints weight = 3026.875| |-----------------------------------------------------------------------------| r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 5840 Z= 0.219 Angle : 0.789 8.711 7864 Z= 0.404 Chirality : 0.041 0.162 844 Planarity : 0.005 0.041 996 Dihedral : 5.906 28.665 708 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.58 % Allowed : 9.18 % Favored : 89.24 % 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: -0.98 (0.29), residues: 652 helix: -0.68 (0.18), residues: 598 sheet: None (None), residues: 0 loop : 2.18 (0.98), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 547 TYR 0.015 0.002 TYR C 227 PHE 0.022 0.002 PHE E 452 HIS 0.004 0.002 HIS C 264 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 5840) covalent geometry : angle 0.78892 ( 7864) hydrogen bonds : bond 0.07276 ( 380) hydrogen bonds : angle 5.40238 ( 1140) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 312 LYS cc_start: 0.8221 (ptmt) cc_final: 0.7994 (mppt) REVERT: G 657 LYS cc_start: 0.7825 (mmmt) cc_final: 0.7614 (tppt) outliers start: 10 outliers final: 6 residues processed: 148 average time/residue: 0.1112 time to fit residues: 23.1114 Evaluate side-chains 133 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 558 ILE Chi-restraints excluded: chain G residue 620 TYR Chi-restraints excluded: chain G residue 641 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 1 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN E 444 ASN G 587 GLN G 610 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.179808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.159535 restraints weight = 24176.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.165790 restraints weight = 11597.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.169782 restraints weight = 6777.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.172384 restraints weight = 4397.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.174071 restraints weight = 3099.322| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5840 Z= 0.188 Angle : 0.680 8.494 7864 Z= 0.346 Chirality : 0.038 0.155 844 Planarity : 0.005 0.036 996 Dihedral : 5.435 26.711 708 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.74 % Allowed : 10.60 % Favored : 87.66 % 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: -0.26 (0.30), residues: 652 helix: -0.13 (0.19), residues: 596 sheet: None (None), residues: 0 loop : 1.24 (0.94), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 457 TYR 0.011 0.002 TYR G 593 PHE 0.016 0.002 PHE A 120 HIS 0.004 0.001 HIS G 596 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 5840) covalent geometry : angle 0.67982 ( 7864) hydrogen bonds : bond 0.05644 ( 380) hydrogen bonds : angle 5.01468 ( 1140) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.6899 (m-40) cc_final: 0.6681 (m-40) REVERT: C 211 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7471 (mm-30) REVERT: C 270 GLU cc_start: 0.6919 (tp30) cc_final: 0.6680 (tp30) REVERT: E 424 LEU cc_start: 0.8644 (mm) cc_final: 0.8405 (mm) REVERT: G 586 GLU cc_start: 0.6111 (mp0) cc_final: 0.5797 (mp0) outliers start: 11 outliers final: 6 residues processed: 138 average time/residue: 0.1297 time to fit residues: 24.7167 Evaluate side-chains 128 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 620 TYR Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 41 optimal weight: 0.9980 chunk 31 optimal weight: 0.0470 chunk 2 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN G 587 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.174283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.151733 restraints weight = 23368.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.158638 restraints weight = 11279.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.163173 restraints weight = 6471.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.166150 restraints weight = 4141.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.168083 restraints weight = 2841.340| |-----------------------------------------------------------------------------| r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5840 Z= 0.155 Angle : 0.619 7.508 7864 Z= 0.310 Chirality : 0.036 0.142 844 Planarity : 0.005 0.054 996 Dihedral : 5.055 25.810 708 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.58 % Allowed : 11.23 % Favored : 87.18 % 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: 0.37 (0.31), residues: 652 helix: 0.35 (0.20), residues: 598 sheet: None (None), residues: 0 loop : 0.64 (0.97), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 291 TYR 0.011 0.001 TYR C 172 PHE 0.012 0.001 PHE G 571 HIS 0.003 0.001 HIS E 387 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 5840) covalent geometry : angle 0.61871 ( 7864) hydrogen bonds : bond 0.04876 ( 380) hydrogen bonds : angle 4.60207 ( 1140) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ASN cc_start: 0.7063 (m-40) cc_final: 0.6766 (m-40) REVERT: C 211 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7538 (mm-30) REVERT: E 424 LEU cc_start: 0.8462 (mm) cc_final: 0.8227 (mm) outliers start: 10 outliers final: 6 residues processed: 131 average time/residue: 0.1255 time to fit residues: 22.6012 Evaluate side-chains 125 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 620 TYR Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 GLN ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 587 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.171577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.149276 restraints weight = 23456.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.156113 restraints weight = 11169.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.160583 restraints weight = 6370.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.163481 restraints weight = 4069.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.165415 restraints weight = 2809.494| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5840 Z= 0.189 Angle : 0.627 7.931 7864 Z= 0.315 Chirality : 0.037 0.166 844 Planarity : 0.005 0.033 996 Dihedral : 4.955 25.016 708 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.06 % Allowed : 12.34 % Favored : 85.60 % 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: 0.51 (0.31), residues: 652 helix: 0.47 (0.20), residues: 601 sheet: None (None), residues: 0 loop : 0.36 (1.01), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 291 TYR 0.014 0.002 TYR E 384 PHE 0.013 0.002 PHE A 120 HIS 0.003 0.001 HIS E 387 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 5840) covalent geometry : angle 0.62659 ( 7864) hydrogen bonds : bond 0.04766 ( 380) hydrogen bonds : angle 4.61565 ( 1140) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 211 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7573 (mm-30) REVERT: G 586 GLU cc_start: 0.6159 (mp0) cc_final: 0.5510 (mt-10) outliers start: 13 outliers final: 9 residues processed: 135 average time/residue: 0.1239 time to fit residues: 23.4008 Evaluate side-chains 129 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 122 TYR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 620 TYR Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 0.4980 chunk 18 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 ASN G 587 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.172033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.149254 restraints weight = 23528.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.156076 restraints weight = 11385.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.160573 restraints weight = 6576.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.163507 restraints weight = 4250.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.165510 restraints weight = 2969.075| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5840 Z= 0.155 Angle : 0.596 7.223 7864 Z= 0.297 Chirality : 0.036 0.142 844 Planarity : 0.004 0.033 996 Dihedral : 4.799 24.678 708 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.90 % Allowed : 14.08 % Favored : 84.02 % 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: 0.79 (0.32), residues: 652 helix: 0.67 (0.20), residues: 602 sheet: None (None), residues: 0 loop : 0.12 (1.03), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 381 TYR 0.010 0.001 TYR C 172 PHE 0.011 0.001 PHE E 366 HIS 0.003 0.001 HIS E 387 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 5840) covalent geometry : angle 0.59567 ( 7864) hydrogen bonds : bond 0.04460 ( 380) hydrogen bonds : angle 4.41336 ( 1140) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 211 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7472 (mm-30) REVERT: G 586 GLU cc_start: 0.6208 (mp0) cc_final: 0.5569 (mt-10) outliers start: 12 outliers final: 8 residues processed: 134 average time/residue: 0.1132 time to fit residues: 21.5018 Evaluate side-chains 133 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 620 TYR Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 587 GLN G 643 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.170948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.148387 restraints weight = 23610.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.155146 restraints weight = 11383.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.159553 restraints weight = 6570.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.162551 restraints weight = 4243.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.164558 restraints weight = 2934.087| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5840 Z= 0.175 Angle : 0.599 7.605 7864 Z= 0.299 Chirality : 0.037 0.162 844 Planarity : 0.004 0.034 996 Dihedral : 4.749 24.691 708 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.58 % Allowed : 15.03 % Favored : 83.39 % 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: 0.78 (0.32), residues: 652 helix: 0.70 (0.20), residues: 606 sheet: None (None), residues: 0 loop : -0.51 (1.07), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 291 TYR 0.011 0.001 TYR C 172 PHE 0.013 0.001 PHE A 120 HIS 0.003 0.001 HIS E 387 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 5840) covalent geometry : angle 0.59865 ( 7864) hydrogen bonds : bond 0.04449 ( 380) hydrogen bonds : angle 4.46242 ( 1140) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 211 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7474 (mm-30) REVERT: G 586 GLU cc_start: 0.6252 (mp0) cc_final: 0.5527 (mt-10) outliers start: 10 outliers final: 7 residues processed: 135 average time/residue: 0.1143 time to fit residues: 21.5068 Evaluate side-chains 134 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 57 optimal weight: 0.0770 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.171247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.148590 restraints weight = 23976.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.155518 restraints weight = 11592.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.159980 restraints weight = 6657.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.162962 restraints weight = 4278.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.164960 restraints weight = 2949.348| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5840 Z= 0.155 Angle : 0.581 7.107 7864 Z= 0.288 Chirality : 0.036 0.143 844 Planarity : 0.004 0.038 996 Dihedral : 4.664 24.386 708 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.58 % Allowed : 15.19 % Favored : 83.23 % 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: 0.95 (0.32), residues: 652 helix: 0.82 (0.20), residues: 607 sheet: None (None), residues: 0 loop : -0.68 (1.10), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 49 TYR 0.009 0.001 TYR C 172 PHE 0.012 0.001 PHE A 120 HIS 0.002 0.001 HIS E 387 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 5840) covalent geometry : angle 0.58103 ( 7864) hydrogen bonds : bond 0.04265 ( 380) hydrogen bonds : angle 4.33117 ( 1140) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 586 GLU cc_start: 0.6353 (mp0) cc_final: 0.5633 (mt-10) outliers start: 10 outliers final: 7 residues processed: 135 average time/residue: 0.1240 time to fit residues: 23.5053 Evaluate side-chains 134 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 9 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.170592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.148150 restraints weight = 23667.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.154942 restraints weight = 11450.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.159396 restraints weight = 6597.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.162278 restraints weight = 4247.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.164264 restraints weight = 2958.424| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5840 Z= 0.149 Angle : 0.584 6.829 7864 Z= 0.288 Chirality : 0.036 0.141 844 Planarity : 0.004 0.038 996 Dihedral : 4.589 24.051 708 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.74 % Allowed : 15.19 % Favored : 83.07 % 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: 1.14 (0.32), residues: 652 helix: 0.95 (0.20), residues: 607 sheet: None (None), residues: 0 loop : -0.78 (1.12), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 534 TYR 0.010 0.001 TYR C 172 PHE 0.011 0.001 PHE A 120 HIS 0.002 0.001 HIS E 387 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 5840) covalent geometry : angle 0.58363 ( 7864) hydrogen bonds : bond 0.04153 ( 380) hydrogen bonds : angle 4.24334 ( 1140) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 0.197 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: A 52 TYR cc_start: 0.7775 (m-10) cc_final: 0.7558 (m-10) REVERT: G 586 GLU cc_start: 0.6341 (mp0) cc_final: 0.5577 (mt-10) REVERT: G 587 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6438 (tm130) outliers start: 11 outliers final: 8 residues processed: 134 average time/residue: 0.1119 time to fit residues: 21.0918 Evaluate side-chains 138 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 443 GLU Chi-restraints excluded: chain E residue 480 LEU Chi-restraints excluded: chain G residue 561 LEU Chi-restraints excluded: chain G residue 587 GLN Chi-restraints excluded: chain G residue 646 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 0.0030 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 0.0170 chunk 6 optimal weight: 0.9990 chunk 43 optimal weight: 0.0070 chunk 60 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 44 optimal weight: 0.0980 overall best weight: 0.0646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 268 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.175511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.152891 restraints weight = 23438.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.159977 restraints weight = 11191.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.164518 restraints weight = 6363.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.167453 restraints weight = 4050.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.169325 restraints weight = 2789.659| |-----------------------------------------------------------------------------| r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 5840 Z= 0.117 Angle : 0.570 5.988 7864 Z= 0.280 Chirality : 0.035 0.125 844 Planarity : 0.004 0.041 996 Dihedral : 4.315 23.867 708 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.79 % Allowed : 16.14 % Favored : 83.07 % 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: 1.73 (0.33), residues: 652 helix: 1.31 (0.20), residues: 607 sheet: None (None), residues: 0 loop : -0.24 (1.16), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.014 0.001 TYR A 79 PHE 0.018 0.001 PHE A 34 HIS 0.003 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 5840) covalent geometry : angle 0.57024 ( 7864) hydrogen bonds : bond 0.03672 ( 380) hydrogen bonds : angle 3.84350 ( 1140) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1304 Ramachandran restraints generated. 652 Oldfield, 0 Emsley, 652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 135 time to evaluate : 0.303 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: E 491 LYS cc_start: 0.8282 (ttpp) cc_final: 0.7865 (tppt) REVERT: G 586 GLU cc_start: 0.6326 (mp0) cc_final: 0.5573 (mt-10) REVERT: G 587 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6257 (tm130) outliers start: 5 outliers final: 2 residues processed: 136 average time/residue: 0.1271 time to fit residues: 23.8699 Evaluate side-chains 131 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain G residue 587 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 56 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 16 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.171385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.148840 restraints weight = 23763.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.155732 restraints weight = 11458.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.160227 restraints weight = 6579.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.163131 restraints weight = 4220.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.165012 restraints weight = 2931.400| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.5522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5840 Z= 0.174 Angle : 0.606 7.285 7864 Z= 0.299 Chirality : 0.037 0.164 844 Planarity : 0.005 0.041 996 Dihedral : 4.422 23.613 708 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.47 % Allowed : 17.25 % Favored : 82.28 % 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: 1.48 (0.33), residues: 652 helix: 1.18 (0.20), residues: 608 sheet: None (None), residues: 0 loop : -0.94 (1.16), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 117 TYR 0.012 0.001 TYR A 79 PHE 0.012 0.001 PHE C 243 HIS 0.004 0.002 HIS E 430 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 5840) covalent geometry : angle 0.60572 ( 7864) hydrogen bonds : bond 0.04003 ( 380) hydrogen bonds : angle 4.24916 ( 1140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1927.41 seconds wall clock time: 33 minutes 26.08 seconds (2006.08 seconds total)