Starting phenix.real_space_refine on Wed Aug 5 16:41:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k30_62002/08_2026/9k30_62002.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k30_62002/08_2026/9k30_62002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k30_62002/08_2026/9k30_62002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k30_62002/08_2026/9k30_62002.map" model { file = "/net/cci-nas-00/data/ceres_data/9k30_62002/08_2026/9k30_62002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k30_62002/08_2026/9k30_62002.cif" } resolution = 3.17 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= 0.001 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 334 5.49 5 Mg 1 5.21 5 S 19 5.16 5 C 5431 2.51 5 N 1929 2.21 5 O 2909 1.98 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10624 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3551 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 422} Chain breaks: 3 Chain: "B" Number of atoms: 6261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 6261 Classifications: {'RNA': 294} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 13, 'rna3p_pur': 144, 'rna3p_pyr': 122} Link IDs: {'rna2p': 27, 'rna3p': 266} Chain breaks: 2 Chain: "C" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 583 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 227 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1020 SG CYS A 125 31.529 83.927 77.087 1.00 90.03 S ATOM 1040 SG CYS A 128 27.886 84.496 76.209 1.00 91.19 S ATOM 1112 SG CYS A 139 30.618 86.444 74.477 1.00 91.01 S Time building chain proxies: 2.06, per 1000 atoms: 0.19 Number of scatterers: 10624 At special positions: 0 Unit cell: (83, 109.56, 152.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 19 16.00 P 334 15.00 Mg 1 11.99 O 2909 8.00 N 1929 7.00 C 5431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 90.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 142 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 139 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 125 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 128 " Number of angles added : 3 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 842 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 7 sheets defined 25.4% alpha, 27.7% beta 123 base pairs and 222 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 17 through 27 Processing helix chain 'A' and resid 91 through 109 removed outlier: 3.732A pdb=" N ARG A 109 " --> pdb=" O CYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 176 removed outlier: 3.657A pdb=" N ARG A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 211 through 225 removed outlier: 3.588A pdb=" N ILE A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.717A pdb=" N LEU A 313 " --> pdb=" O TYR A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 Processing helix chain 'A' and resid 336 through 347 removed outlier: 3.524A pdb=" N THR A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 removed outlier: 3.555A pdb=" N VAL A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 removed outlier: 6.422A pdb=" N PHE A 4 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LEU A 42 " --> pdb=" O PHE A 4 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL A 6 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL A 39 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 332 through 333 removed outlier: 6.858A pdb=" N ILE A 184 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 54 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE A 185 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL A 56 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 68 " --> pdb=" O GLY A 57 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 82 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 71 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL A 80 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 333 removed outlier: 6.858A pdb=" N ILE A 184 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL A 54 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE A 185 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL A 56 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 68 " --> pdb=" O GLY A 57 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A 82 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 71 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL A 80 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N TYR A 381 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS A 83 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE A 383 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLN A 85 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ASP A 87 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 394 through 399 removed outlier: 5.013A pdb=" N ALA A 432 " --> pdb=" O THR A 395 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N THR A 397 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE A 430 " --> pdb=" O THR A 397 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 405 through 408 Processing sheet with id=AA6, first strand: chain 'A' and resid 448 through 455 removed outlier: 3.565A pdb=" N ALA A 439 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET A 466 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 503 through 507 removed outlier: 3.504A pdb=" N ALA A 507 " --> pdb=" O ILE A 496 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LYS A 497 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A 486 " --> pdb=" O ASN A 499 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR A 516 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N GLU A 475 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU A 514 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ASN A 477 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR A 512 " --> pdb=" O ASN A 477 " (cutoff:3.500A) 126 hydrogen bonds defined for protein. 354 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 298 hydrogen bonds 548 hydrogen bond angles 0 basepair planarities 123 basepair parallelities 222 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1652 1.34 - 1.46: 4642 1.46 - 1.58: 4508 1.58 - 1.70: 684 1.70 - 1.82: 27 Bond restraints: 11513 Sorted by residual: bond pdb=" C LEU A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 1.331 1.371 -0.039 8.70e-03 1.32e+04 2.06e+01 bond pdb=" C ILE A 179 " pdb=" N PRO A 180 " ideal model delta sigma weight residual 1.335 1.372 -0.037 8.70e-03 1.32e+04 1.82e+01 bond pdb=" C ILE A 349 " pdb=" N PRO A 350 " ideal model delta sigma weight residual 1.330 1.376 -0.046 1.22e-02 6.72e+03 1.41e+01 bond pdb=" C LYS A 370 " pdb=" N PRO A 371 " ideal model delta sigma weight residual 1.329 1.370 -0.041 1.20e-02 6.94e+03 1.19e+01 bond pdb=" O5' A B 338 " pdb=" C5' A B 338 " ideal model delta sigma weight residual 1.424 1.478 -0.054 1.60e-02 3.91e+03 1.12e+01 ... (remaining 11508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 15279 2.14 - 4.28: 1710 4.28 - 6.42: 127 6.42 - 8.56: 14 8.56 - 10.70: 2 Bond angle restraints: 17132 Sorted by residual: angle pdb=" O4' DG D 1 " pdb=" C1' DG D 1 " pdb=" N9 DG D 1 " ideal model delta sigma weight residual 108.00 112.32 -4.32 7.00e-01 2.04e+00 3.82e+01 angle pdb=" C3' DC C 18 " pdb=" O3' DC C 18 " pdb=" P DC C 19 " ideal model delta sigma weight residual 119.70 127.05 -7.35 1.20e+00 6.94e-01 3.75e+01 angle pdb=" C2' G B 274 " pdb=" C1' G B 274 " pdb=" N9 G B 274 " ideal model delta sigma weight residual 112.00 118.26 -6.26 1.10e+00 8.26e-01 3.24e+01 angle pdb=" CA ASP A 366 " pdb=" CB ASP A 366 " pdb=" CG ASP A 366 " ideal model delta sigma weight residual 112.60 118.04 -5.44 1.00e+00 1.00e+00 2.96e+01 angle pdb=" C TYR A 365 " pdb=" CA TYR A 365 " pdb=" CB TYR A 365 " ideal model delta sigma weight residual 110.42 121.12 -10.70 1.99e+00 2.53e-01 2.89e+01 ... (remaining 17127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.31: 6324 30.31 - 60.62: 596 60.62 - 90.93: 211 90.93 - 121.25: 1 121.25 - 151.56: 1 Dihedral angle restraints: 7133 sinusoidal: 5836 harmonic: 1297 Sorted by residual: dihedral pdb=" C5' G B 168 " pdb=" C4' G B 168 " pdb=" C3' G B 168 " pdb=" O3' G B 168 " ideal model delta sinusoidal sigma weight residual 147.00 98.22 48.78 1 8.00e+00 1.56e-02 5.12e+01 dihedral pdb=" O4' U B -9 " pdb=" C2' U B -9 " pdb=" C1' U B -9 " pdb=" C3' U B -9 " ideal model delta sinusoidal sigma weight residual 25.00 -22.22 47.22 1 8.00e+00 1.56e-02 4.81e+01 dihedral pdb=" C5' U B 299 " pdb=" C4' U B 299 " pdb=" C3' U B 299 " pdb=" O3' U B 299 " ideal model delta sinusoidal sigma weight residual 147.00 101.55 45.45 1 8.00e+00 1.56e-02 4.48e+01 ... (remaining 7130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 1860 0.130 - 0.261: 309 0.261 - 0.391: 0 0.391 - 0.521: 0 0.521 - 0.651: 5 Chirality restraints: 2174 Sorted by residual: chirality pdb=" P DC C -9 " pdb=" OP1 DC C -9 " pdb=" OP2 DC C -9 " pdb=" O5' DC C -9 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" P DC D -1 " pdb=" OP1 DC D -1 " pdb=" OP2 DC D -1 " pdb=" O5' DC D -1 " both_signs ideal model delta sigma weight residual True 2.34 2.99 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" P C B 144 " pdb=" OP1 C B 144 " pdb=" OP2 C B 144 " pdb=" O5' C B 144 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.26e+00 ... (remaining 2171 not shown) Planarity restraints: 949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 34 " -0.155 9.50e-02 1.11e+02 7.01e-02 3.72e+00 pdb=" NE ARG A 34 " 0.005 2.00e-02 2.50e+03 pdb=" CZ ARG A 34 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG A 34 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 34 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 414 " -0.120 9.50e-02 1.11e+02 5.41e-02 2.30e+00 pdb=" NE ARG A 414 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 414 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 414 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 414 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG D 1 " -0.014 2.00e-02 2.50e+03 6.17e-03 1.14e+00 pdb=" N9 DG D 1 " 0.015 2.00e-02 2.50e+03 pdb=" C8 DG D 1 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG D 1 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG D 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG D 1 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG D 1 " -0.002 2.00e-02 2.50e+03 pdb=" N1 DG D 1 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DG D 1 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG D 1 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DG D 1 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG D 1 " 0.000 2.00e-02 2.50e+03 ... (remaining 946 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 20 2.55 - 3.14: 6649 3.14 - 3.72: 18518 3.72 - 4.31: 27549 4.31 - 4.90: 36921 Nonbonded interactions: 89657 Sorted by model distance: nonbonded pdb=" OP1 G B 275 " pdb="MG MG B 501 " model vdw 1.959 2.170 nonbonded pdb=" OP1 A B 276 " pdb="MG MG B 501 " model vdw 2.265 2.170 nonbonded pdb=" O TYR A 309 " pdb=" N GLN A 312 " model vdw 2.431 3.120 nonbonded pdb=" O2' U B 236 " pdb=" O2' C B 355 " model vdw 2.464 3.040 nonbonded pdb=" OE1 GLN A 52 " pdb=" O2' A B 411 " model vdw 2.468 3.040 ... (remaining 89652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.200 Find NCS groups from input model: 0.160 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: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.083 11517 Z= 0.783 Angle : 1.327 10.703 17135 Z= 0.957 Chirality : 0.086 0.651 2174 Planarity : 0.004 0.070 949 Dihedral : 21.380 151.557 6291 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 0.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.02 % Allowed : 9.85 % Favored : 88.13 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 5.56 % 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: -3.07 (0.34), residues: 433 helix: -2.05 (0.40), residues: 102 sheet: -1.39 (0.50), residues: 104 loop : -2.35 (0.34), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 34 TYR 0.012 0.002 TYR A 336 PHE 0.005 0.001 PHE A 331 TRP 0.011 0.002 TRP A 342 HIS 0.001 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.01113 / 0.78 (11513) covalent geometry : angle 1.32606 / 0.96 (17132) hydrogen bonds : bond 0.19264 / 12.40 ( 416) hydrogen bonds : angle 7.49832 / 5.08 ( 902) metal coordination : bond 0.04212 / 2.11 ( 4) metal coordination : angle 3.83734 / 2.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.9048 (ttpt) cc_final: 0.8832 (ttpp) REVERT: A 340 THR cc_start: 0.8632 (m) cc_final: 0.8393 (p) REVERT: A 347 PHE cc_start: 0.8343 (m-80) cc_final: 0.8054 (m-80) REVERT: A 366 ASP cc_start: 0.6222 (OUTLIER) cc_final: 0.1057 (t0) outliers start: 8 outliers final: 0 residues processed: 105 average time/residue: 0.0998 time to fit residues: 13.9991 Evaluate side-chains 56 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 10 ASN A 133 GLN A 198 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 GLN A 343 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.075599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.057234 restraints weight = 33650.049| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.03 r_work: 0.2892 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 11517 Z= 0.312 Angle : 0.746 6.528 17135 Z= 0.426 Chirality : 0.053 0.325 2174 Planarity : 0.006 0.029 949 Dihedral : 21.991 140.590 5350 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.04 % Allowed : 16.41 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.82 (0.37), residues: 433 helix: 0.09 (0.47), residues: 107 sheet: -1.27 (0.46), residues: 117 loop : -1.84 (0.37), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 104 TYR 0.016 0.003 TYR A 212 PHE 0.024 0.003 PHE A 331 TRP 0.009 0.003 TRP A 156 HIS 0.004 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.31 (11513) covalent geometry : angle 0.74588 / 0.43 (17132) hydrogen bonds : bond 0.09271 / 6.02 ( 416) hydrogen bonds : angle 4.45478 / 3.08 ( 902) metal coordination : bond 0.01513 / 0.76 ( 4) metal coordination : angle 1.40829 / 0.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.8826 (OUTLIER) cc_final: 0.8275 (m-40) REVERT: A 14 MET cc_start: 0.8876 (mmm) cc_final: 0.8637 (mmt) REVERT: A 182 ASN cc_start: 0.8750 (m-40) cc_final: 0.8533 (m-40) outliers start: 16 outliers final: 11 residues processed: 66 average time/residue: 0.0791 time to fit residues: 7.4776 Evaluate side-chains 60 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASN Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 522 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 47 optimal weight: 30.0000 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 0.4980 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 ASN A 183 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.073330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.055283 restraints weight = 34757.320| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.00 r_work: 0.2872 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 11517 Z= 0.302 Angle : 0.686 8.450 17135 Z= 0.389 Chirality : 0.047 0.210 2174 Planarity : 0.005 0.037 949 Dihedral : 22.370 138.407 5348 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.55 % Allowed : 16.67 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.61 (0.38), residues: 433 helix: 0.60 (0.50), residues: 108 sheet: -1.34 (0.47), residues: 116 loop : -1.78 (0.38), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 344 TYR 0.019 0.002 TYR A 212 PHE 0.023 0.003 PHE A 347 TRP 0.011 0.003 TRP A 342 HIS 0.005 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.30 (11513) covalent geometry : angle 0.68534 / 0.39 (17132) hydrogen bonds : bond 0.08274 / 5.18 ( 416) hydrogen bonds : angle 4.18629 / 2.89 ( 902) metal coordination : bond 0.02232 / 1.12 ( 4) metal coordination : angle 2.35628 / 1.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 ASN cc_start: 0.8728 (m-40) cc_final: 0.8496 (m-40) REVERT: A 326 ASP cc_start: 0.8451 (m-30) cc_final: 0.8171 (m-30) outliers start: 18 outliers final: 13 residues processed: 66 average time/residue: 0.0815 time to fit residues: 7.7994 Evaluate side-chains 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 522 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 45 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.074479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.056448 restraints weight = 34342.458| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.97 r_work: 0.2897 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11517 Z= 0.200 Angle : 0.546 7.131 17135 Z= 0.327 Chirality : 0.039 0.184 2174 Planarity : 0.004 0.024 949 Dihedral : 22.345 138.889 5348 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.28 % Allowed : 19.19 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.46 (0.38), residues: 433 helix: 0.80 (0.50), residues: 108 sheet: -1.24 (0.46), residues: 119 loop : -1.74 (0.38), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 22 TYR 0.014 0.002 TYR A 212 PHE 0.020 0.002 PHE A 347 TRP 0.009 0.002 TRP A 342 HIS 0.007 0.002 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.20 (11513) covalent geometry : angle 0.54557 / 0.33 (17132) hydrogen bonds : bond 0.07110 / 4.40 ( 416) hydrogen bonds : angle 3.82012 / 2.63 ( 902) metal coordination : bond 0.01632 / 0.82 ( 4) metal coordination : angle 1.62432 / 0.84 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8719 (m-30) cc_final: 0.7685 (t0) REVERT: A 326 ASP cc_start: 0.8478 (m-30) cc_final: 0.8075 (m-30) REVERT: A 456 MET cc_start: 0.8604 (mmm) cc_final: 0.8334 (mmm) outliers start: 13 outliers final: 11 residues processed: 58 average time/residue: 0.0813 time to fit residues: 6.8718 Evaluate side-chains 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 522 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 43 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 15 optimal weight: 0.3980 chunk 35 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.074796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.056627 restraints weight = 34531.992| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.01 r_work: 0.2896 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11517 Z= 0.181 Angle : 0.512 7.574 17135 Z= 0.307 Chirality : 0.037 0.176 2174 Planarity : 0.004 0.029 949 Dihedral : 22.320 138.251 5348 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.29 % Allowed : 17.93 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.28 (0.38), residues: 433 helix: 0.93 (0.50), residues: 109 sheet: -1.04 (0.47), residues: 115 loop : -1.70 (0.38), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 22 TYR 0.012 0.002 TYR A 212 PHE 0.017 0.002 PHE A 347 TRP 0.008 0.002 TRP A 342 HIS 0.002 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.18 (11513) covalent geometry : angle 0.51213 / 0.31 (17132) hydrogen bonds : bond 0.06762 / 4.21 ( 416) hydrogen bonds : angle 3.63354 / 2.50 ( 902) metal coordination : bond 0.01550 / 0.78 ( 4) metal coordination : angle 1.45909 / 0.74 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 200 ASP cc_start: 0.8536 (m-30) cc_final: 0.7634 (t0) REVERT: A 326 ASP cc_start: 0.8411 (m-30) cc_final: 0.7954 (m-30) REVERT: A 456 MET cc_start: 0.8567 (mmm) cc_final: 0.8307 (mmm) outliers start: 17 outliers final: 11 residues processed: 59 average time/residue: 0.0807 time to fit residues: 6.9058 Evaluate side-chains 57 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 522 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 49 optimal weight: 10.9990 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 70 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 44 optimal weight: 30.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.073491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.055299 restraints weight = 35168.496| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.02 r_work: 0.2868 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11517 Z= 0.267 Angle : 0.604 7.264 17135 Z= 0.343 Chirality : 0.042 0.197 2174 Planarity : 0.005 0.029 949 Dihedral : 22.345 137.670 5348 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.80 % Allowed : 18.94 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.56 (0.38), residues: 433 helix: 0.72 (0.50), residues: 109 sheet: -1.27 (0.47), residues: 114 loop : -1.85 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 22 TYR 0.016 0.002 TYR A 309 PHE 0.025 0.002 PHE A 347 TRP 0.006 0.002 TRP A 342 HIS 0.003 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.27 (11513) covalent geometry : angle 0.60372 / 0.34 (17132) hydrogen bonds : bond 0.07602 / 4.76 ( 416) hydrogen bonds : angle 3.73294 / 2.55 ( 902) metal coordination : bond 0.02308 / 1.15 ( 4) metal coordination : angle 2.17957 / 1.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 14 MET cc_start: 0.8932 (mmt) cc_final: 0.8726 (tpp) REVERT: A 98 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8414 (mp0) REVERT: A 200 ASP cc_start: 0.8454 (m-30) cc_final: 0.7471 (t0) REVERT: A 326 ASP cc_start: 0.8489 (m-30) cc_final: 0.8030 (m-30) REVERT: A 456 MET cc_start: 0.8595 (mmm) cc_final: 0.8323 (mmm) outliers start: 19 outliers final: 13 residues processed: 57 average time/residue: 0.1010 time to fit residues: 8.4480 Evaluate side-chains 53 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 522 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 67 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 28 optimal weight: 0.0470 chunk 59 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 overall best weight: 2.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 182 ASN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.074322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.056169 restraints weight = 34830.023| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.99 r_work: 0.2895 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11517 Z= 0.186 Angle : 0.514 6.934 17135 Z= 0.307 Chirality : 0.037 0.180 2174 Planarity : 0.004 0.028 949 Dihedral : 22.303 137.770 5348 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.04 % Allowed : 20.20 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.41 (0.38), residues: 433 helix: 0.91 (0.49), residues: 109 sheet: -1.15 (0.48), residues: 114 loop : -1.82 (0.38), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 22 TYR 0.011 0.001 TYR A 212 PHE 0.020 0.002 PHE A 347 TRP 0.006 0.002 TRP A 342 HIS 0.002 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.19 (11513) covalent geometry : angle 0.51307 / 0.31 (17132) hydrogen bonds : bond 0.06784 / 4.20 ( 416) hydrogen bonds : angle 3.56408 / 2.43 ( 902) metal coordination : bond 0.01794 / 0.90 ( 4) metal coordination : angle 1.68346 / 0.87 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 98 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8373 (mp0) REVERT: A 200 ASP cc_start: 0.8479 (m-30) cc_final: 0.7469 (t0) REVERT: A 326 ASP cc_start: 0.8476 (m-30) cc_final: 0.7966 (m-30) REVERT: A 353 HIS cc_start: 0.9036 (t-90) cc_final: 0.8661 (t-90) REVERT: A 456 MET cc_start: 0.8569 (mmm) cc_final: 0.8312 (mmm) outliers start: 16 outliers final: 12 residues processed: 54 average time/residue: 0.0744 time to fit residues: 6.0402 Evaluate side-chains 51 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 522 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 44 optimal weight: 30.0000 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 20.0000 chunk 60 optimal weight: 10.9990 chunk 48 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.074797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.056667 restraints weight = 34640.292| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.98 r_work: 0.2907 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11517 Z= 0.161 Angle : 0.495 8.007 17135 Z= 0.299 Chirality : 0.035 0.173 2174 Planarity : 0.004 0.030 949 Dihedral : 22.254 138.151 5348 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.28 % Allowed : 21.46 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.32 (0.39), residues: 433 helix: 0.79 (0.50), residues: 110 sheet: -0.99 (0.50), residues: 114 loop : -1.72 (0.38), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 22 TYR 0.010 0.001 TYR A 212 PHE 0.032 0.002 PHE A 347 TRP 0.006 0.001 TRP A 342 HIS 0.002 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.16 (11513) covalent geometry : angle 0.49472 / 0.30 (17132) hydrogen bonds : bond 0.06508 / 4.06 ( 416) hydrogen bonds : angle 3.46029 / 2.35 ( 902) metal coordination : bond 0.01534 / 0.77 ( 4) metal coordination : angle 1.51713 / 0.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 98 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8370 (mp0) REVERT: A 200 ASP cc_start: 0.8412 (m-30) cc_final: 0.7454 (t0) REVERT: A 326 ASP cc_start: 0.8469 (m-30) cc_final: 0.7951 (m-30) REVERT: A 456 MET cc_start: 0.8568 (mmm) cc_final: 0.8312 (mmm) outliers start: 13 outliers final: 11 residues processed: 50 average time/residue: 0.0809 time to fit residues: 5.9972 Evaluate side-chains 51 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 522 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 43 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 59 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 chunk 71 optimal weight: 30.0000 chunk 49 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.073771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.055647 restraints weight = 34675.554| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.97 r_work: 0.2882 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11517 Z= 0.233 Angle : 0.567 7.101 17135 Z= 0.325 Chirality : 0.040 0.182 2174 Planarity : 0.004 0.029 949 Dihedral : 22.254 137.877 5348 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.28 % Allowed : 22.47 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.47 (0.39), residues: 433 helix: 0.71 (0.50), residues: 112 sheet: -1.12 (0.49), residues: 114 loop : -1.84 (0.38), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 22 TYR 0.012 0.002 TYR A 212 PHE 0.028 0.002 PHE A 347 TRP 0.009 0.002 TRP A 342 HIS 0.003 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.23 (11513) covalent geometry : angle 0.56616 / 0.32 (17132) hydrogen bonds : bond 0.07127 / 4.47 ( 416) hydrogen bonds : angle 3.57742 / 2.43 ( 902) metal coordination : bond 0.02038 / 1.02 ( 4) metal coordination : angle 1.94723 / 0.99 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 98 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8405 (mp0) REVERT: A 200 ASP cc_start: 0.8459 (m-30) cc_final: 0.8233 (m-30) REVERT: A 326 ASP cc_start: 0.8498 (m-30) cc_final: 0.8020 (m-30) REVERT: A 456 MET cc_start: 0.8567 (mmm) cc_final: 0.8351 (mmm) outliers start: 13 outliers final: 12 residues processed: 48 average time/residue: 0.0914 time to fit residues: 6.6238 Evaluate side-chains 51 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 522 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 47 optimal weight: 30.0000 chunk 48 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.073989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.055895 restraints weight = 34555.598| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.95 r_work: 0.2889 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11517 Z= 0.211 Angle : 0.541 8.547 17135 Z= 0.316 Chirality : 0.038 0.177 2174 Planarity : 0.004 0.032 949 Dihedral : 22.271 137.675 5348 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.28 % Allowed : 22.22 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.36 (0.39), residues: 433 helix: 1.14 (0.50), residues: 104 sheet: -1.09 (0.50), residues: 114 loop : -1.86 (0.37), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 22 TYR 0.011 0.001 TYR A 212 PHE 0.036 0.003 PHE A 347 TRP 0.008 0.002 TRP A 342 HIS 0.002 0.001 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.21 (11513) covalent geometry : angle 0.54054 / 0.32 (17132) hydrogen bonds : bond 0.06927 / 4.32 ( 416) hydrogen bonds : angle 3.54737 / 2.40 ( 902) metal coordination : bond 0.02055 / 1.03 ( 4) metal coordination : angle 1.85293 / 0.95 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 866 Ramachandran restraints generated. 433 Oldfield, 0 Emsley, 433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 98 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8428 (mp0) REVERT: A 200 ASP cc_start: 0.8462 (m-30) cc_final: 0.8237 (m-30) REVERT: A 326 ASP cc_start: 0.8490 (m-30) cc_final: 0.8009 (m-30) REVERT: A 456 MET cc_start: 0.8549 (mmm) cc_final: 0.8324 (mmm) outliers start: 13 outliers final: 12 residues processed: 47 average time/residue: 0.0895 time to fit residues: 6.1086 Evaluate side-chains 49 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 490 CYS Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 522 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 44 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 47 optimal weight: 30.0000 chunk 55 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 71 optimal weight: 30.0000 chunk 9 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 overall best weight: 7.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.070894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.053026 restraints weight = 35023.653| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.15 r_work: 0.2815 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 11517 Z= 0.461 Angle : 0.830 8.962 17135 Z= 0.437 Chirality : 0.056 0.267 2174 Planarity : 0.007 0.057 949 Dihedral : 22.469 136.352 5348 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 3.28 % Allowed : 21.97 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.02 (0.37), residues: 433 helix: 0.70 (0.50), residues: 103 sheet: -1.65 (0.46), residues: 114 loop : -2.21 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 22 TYR 0.017 0.002 TYR A 319 PHE 0.029 0.003 PHE A 347 TRP 0.013 0.004 TRP A 342 HIS 0.006 0.002 HIS A 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00835 / 0.46 (11513) covalent geometry : angle 0.82899 / 0.44 (17132) hydrogen bonds : bond 0.09724 / 6.17 ( 416) hydrogen bonds : angle 4.09331 / 2.78 ( 902) metal coordination : bond 0.04000 / 2.00 ( 4) metal coordination : angle 3.80550 / 1.93 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2031.60 seconds wall clock time: 35 minutes 33.76 seconds (2133.76 seconds total)