Starting phenix.real_space_refine on Thu Jul 2 01:39:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lou_63260/07_2026/9lou_63260.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lou_63260/07_2026/9lou_63260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lou_63260/07_2026/9lou_63260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lou_63260/07_2026/9lou_63260.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lou_63260/07_2026/9lou_63260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lou_63260/07_2026/9lou_63260.map" } resolution = 3.36 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= 0.010 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 28 5.49 5 Mg 1 5.21 5 S 28 5.16 5 C 3212 2.51 5 N 965 2.21 5 O 1045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5280 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4732 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 574} Chain breaks: 4 Chain: "X" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 269 Unusual residues: {'GTP': 1} Classifications: {'RNA': 11, 'undetermined': 1} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 4} Link IDs: {'rna3p': 10, None: 1} Not linked: pdbres="GTP X 1 " pdbres=" A X 2 " Chain: "Y" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 8} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3806 SG CYS A 556 61.626 23.071 57.700 1.00 76.86 S ATOM 3828 SG CYS A 559 63.139 20.116 60.401 1.00 82.01 S ATOM 4267 SG CYS A 615 59.977 20.342 58.642 1.00 82.08 S Time building chain proxies: 1.43, per 1000 atoms: 0.27 Number of scatterers: 5280 At special positions: 0 Unit cell: (88.81, 87.98, 89.64, 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 28 16.00 P 28 15.00 Mg 1 11.99 O 1045 8.00 N 965 7.00 C 3212 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: 0.54 Conformation dependent library (CDL) restraints added in 168.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 702 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 615 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 559 " pdb="ZN ZN A 702 " - pdb=" SG CYS A 556 " 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1126 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 5 sheets defined 55.0% alpha, 11.7% beta 9 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 removed outlier: 3.893A pdb=" N GLU A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL A 10 " --> pdb=" O TYR A 6 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 11 " --> pdb=" O GLN A 7 " (cutoff:3.500A) Proline residue: A 13 - end of helix removed outlier: 4.003A pdb=" N GLU A 16 " --> pdb=" O MET A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 56 through 71 removed outlier: 3.804A pdb=" N VAL A 60 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN A 62 " --> pdb=" O HIS A 58 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 121 through 125 removed outlier: 3.521A pdb=" N PHE A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 136 Processing helix chain 'A' and resid 140 through 156 removed outlier: 3.607A pdb=" N GLN A 148 " --> pdb=" O VAL A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 193 Processing helix chain 'A' and resid 227 through 245 removed outlier: 3.580A pdb=" N GLU A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 273 Processing helix chain 'A' and resid 274 through 297 removed outlier: 3.553A pdb=" N ARG A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.658A pdb=" N ALA A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS A 314 " --> pdb=" O TYR A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 345 removed outlier: 3.503A pdb=" N ASP A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN A 336 " --> pdb=" O ASP A 332 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N HIS A 340 " --> pdb=" O ASN A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 362 Processing helix chain 'A' and resid 377 through 390 removed outlier: 3.618A pdb=" N GLN A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 396 removed outlier: 3.573A pdb=" N THR A 395 " --> pdb=" O GLN A 391 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 430 removed outlier: 3.525A pdb=" N GLU A 422 " --> pdb=" O ARG A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 514 through 544 removed outlier: 3.532A pdb=" N ALA A 520 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 551 Processing helix chain 'A' and resid 581 through 586 Processing helix chain 'A' and resid 651 through 655 removed outlier: 3.805A pdb=" N VAL A 655 " --> pdb=" O TRP A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 672 removed outlier: 3.522A pdb=" N GLU A 670 " --> pdb=" O GLN A 666 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.447A pdb=" N THR A 78 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N THR A 103 " --> pdb=" O THR A 78 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL A 50 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N CYS A 102 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL A 52 " --> pdb=" O CYS A 102 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 21 " --> pdb=" O CYS A 196 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP A 23 " --> pdb=" O MET A 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 434 through 437 removed outlier: 6.991A pdb=" N GLY A 370 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA A 437 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE A 372 " --> pdb=" O ALA A 437 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 454 " --> pdb=" O ILE A 371 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 562 through 565 Processing sheet with id=AA4, first strand: chain 'A' and resid 569 through 572 removed outlier: 3.528A pdb=" N VAL A 578 " --> pdb=" O ARG A 570 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 588 through 590 removed outlier: 5.276A pdb=" N GLN A 622 " --> pdb=" O GLY A 607 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N VAL A 609 " --> pdb=" O GLY A 620 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLY A 620 " --> pdb=" O VAL A 609 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER A 611 " --> pdb=" O VAL A 618 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 618 " --> pdb=" O SER A 611 " (cutoff:3.500A) 240 hydrogen bonds defined for protein. 684 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1495 1.33 - 1.45: 929 1.45 - 1.57: 2904 1.57 - 1.69: 52 1.69 - 1.81: 44 Bond restraints: 5424 Sorted by residual: bond pdb=" C4 ADP A 701 " pdb=" C5 ADP A 701 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.01e+00 bond pdb=" C LEU A 402 " pdb=" N LEU A 403 " ideal model delta sigma weight residual 1.333 1.345 -0.012 1.30e-02 5.92e+03 8.02e-01 bond pdb=" N9 A X 2 " pdb=" C4 A X 2 " ideal model delta sigma weight residual 1.374 1.370 0.004 6.00e-03 2.78e+04 5.22e-01 bond pdb=" C2' GTP X 1 " pdb=" C3' GTP X 1 " ideal model delta sigma weight residual 1.524 1.510 0.014 2.00e-02 2.50e+03 4.58e-01 bond pdb=" N1 C Y 12 " pdb=" C6 C Y 12 " ideal model delta sigma weight residual 1.367 1.363 0.004 6.00e-03 2.78e+04 4.50e-01 ... (remaining 5419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 7393 1.79 - 3.59: 50 3.59 - 5.38: 10 5.38 - 7.18: 3 7.18 - 8.97: 1 Bond angle restraints: 7457 Sorted by residual: angle pdb=" C2' GTP X 1 " pdb=" C3' GTP X 1 " pdb=" C4' GTP X 1 " ideal model delta sigma weight residual 111.00 102.03 8.97 3.00e+00 1.11e-01 8.94e+00 angle pdb=" CA GLY A 171 " pdb=" C GLY A 171 " pdb=" O GLY A 171 " ideal model delta sigma weight residual 122.24 120.58 1.66 8.70e-01 1.32e+00 3.64e+00 angle pdb=" C1' GTP X 1 " pdb=" C2' GTP X 1 " pdb=" C3' GTP X 1 " ideal model delta sigma weight residual 111.00 105.33 5.67 3.00e+00 1.11e-01 3.57e+00 angle pdb=" O1B ADP A 701 " pdb=" PB ADP A 701 " pdb=" O2B ADP A 701 " ideal model delta sigma weight residual 119.90 114.25 5.65 3.00e+00 1.11e-01 3.54e+00 angle pdb=" O1B ADP A 701 " pdb=" PB ADP A 701 " pdb=" O3B ADP A 701 " ideal model delta sigma weight residual 119.90 114.45 5.45 3.00e+00 1.11e-01 3.30e+00 ... (remaining 7452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.37: 2994 18.37 - 36.74: 221 36.74 - 55.11: 49 55.11 - 73.48: 29 73.48 - 91.85: 7 Dihedral angle restraints: 3300 sinusoidal: 1570 harmonic: 1730 Sorted by residual: dihedral pdb=" C8 GTP X 1 " pdb=" C1' GTP X 1 " pdb=" N9 GTP X 1 " pdb=" O4' GTP X 1 " ideal model delta sinusoidal sigma weight residual 104.59 12.74 91.85 1 2.00e+01 2.50e-03 2.48e+01 dihedral pdb=" C4' GTP X 1 " pdb=" C5' GTP X 1 " pdb=" O5' GTP X 1 " pdb=" PA GTP X 1 " ideal model delta sinusoidal sigma weight residual 260.87 174.24 86.63 1 2.00e+01 2.50e-03 2.26e+01 dihedral pdb=" CA ARG A 369 " pdb=" CB ARG A 369 " pdb=" CG ARG A 369 " pdb=" CD ARG A 369 " ideal model delta sinusoidal sigma weight residual -60.00 -117.88 57.88 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 3297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 645 0.033 - 0.066: 149 0.066 - 0.099: 44 0.099 - 0.132: 22 0.132 - 0.165: 2 Chirality restraints: 862 Sorted by residual: chirality pdb=" C2' GTP X 1 " pdb=" C1' GTP X 1 " pdb=" C3' GTP X 1 " pdb=" O2' GTP X 1 " both_signs ideal model delta sigma weight residual False -2.47 -2.64 0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" CA VAL A 120 " pdb=" N VAL A 120 " pdb=" C VAL A 120 " pdb=" CB VAL A 120 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE A 197 " pdb=" N ILE A 197 " pdb=" C ILE A 197 " pdb=" CB ILE A 197 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 859 not shown) Planarity restraints: 870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 348 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO A 349 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 349 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 349 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 642 " -0.016 5.00e-02 4.00e+02 2.46e-02 9.70e-01 pdb=" N PRO A 643 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 643 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 643 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 12 " 0.014 5.00e-02 4.00e+02 2.10e-02 7.09e-01 pdb=" N PRO A 13 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO A 13 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 13 " 0.012 5.00e-02 4.00e+02 ... (remaining 867 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 3 2.15 - 2.84: 1631 2.84 - 3.53: 7355 3.53 - 4.21: 12781 4.21 - 4.90: 21308 Nonbonded interactions: 43078 Sorted by model distance: nonbonded pdb=" O3' GTP X 1 " pdb=" OP1 A X 2 " model vdw 1.465 3.040 nonbonded pdb=" O3' GTP X 1 " pdb=" P A X 2 " model vdw 1.722 3.400 nonbonded pdb=" C3' GTP X 1 " pdb=" P A X 2 " model vdw 2.078 3.830 nonbonded pdb=" OH TYR A 6 " pdb=" O ALA A 28 " model vdw 2.223 3.040 nonbonded pdb=" O THR A 296 " pdb=" OH TYR A 456 " model vdw 2.226 3.040 ... (remaining 43073 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: 2.750 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.660 Find NCS groups from input model: 0.020 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 0.002 0.020 5427 Z= 0.104 Angle : 0.450 8.972 7457 Z= 0.229 Chirality : 0.036 0.165 862 Planarity : 0.003 0.030 870 Dihedral : 15.046 91.850 2174 Min Nonbonded Distance : 1.465 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.78 % Allowed : 9.71 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.44 (0.35), residues: 586 helix: 1.03 (0.31), residues: 265 sheet: -0.80 (0.58), residues: 90 loop : 0.08 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 298 TYR 0.007 0.001 TYR A 588 PHE 0.006 0.001 PHE A 584 TRP 0.006 0.001 TRP A 75 HIS 0.002 0.001 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.10 ( 5424) covalent geometry : angle 0.44969 / 0.23 ( 7457) hydrogen bonds : bond 0.29705 / 19.44 ( 261) hydrogen bonds : angle 8.15580 / 5.74 ( 726) metal coordination : bond 0.00145 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8360 (m-30) cc_final: 0.7936 (t0) REVERT: A 264 LYS cc_start: 0.6643 (mptt) cc_final: 0.6006 (ttmt) REVERT: A 287 TYR cc_start: 0.8241 (m-80) cc_final: 0.8001 (m-80) REVERT: A 311 HIS cc_start: 0.6548 (m-70) cc_final: 0.6255 (m90) REVERT: A 321 LEU cc_start: 0.6902 (mt) cc_final: 0.6681 (mp) REVERT: A 347 GLU cc_start: 0.6714 (pm20) cc_final: 0.5028 (tt0) REVERT: A 378 GLN cc_start: 0.6985 (mt0) cc_final: 0.6581 (mp10) REVERT: A 604 TRP cc_start: 0.8115 (p-90) cc_final: 0.7838 (p-90) REVERT: A 626 LYS cc_start: 0.7271 (mttt) cc_final: 0.7025 (ttmt) outliers start: 4 outliers final: 1 residues processed: 142 average time/residue: 0.0941 time to fit residues: 16.3271 Evaluate side-chains 76 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.1980 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 0.0070 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 ASN A 63 HIS A 119 HIS A 359 GLN A 414 HIS A 505 GLN A 515 GLN A 519 GLN A 551 HIS A 666 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.169754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.142801 restraints weight = 6709.761| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.29 r_work: 0.3616 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5427 Z= 0.164 Angle : 0.626 6.805 7457 Z= 0.327 Chirality : 0.043 0.183 862 Planarity : 0.005 0.052 870 Dihedral : 13.459 91.441 1017 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.94 % Allowed : 12.23 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.70 (0.34), residues: 586 helix: 1.74 (0.29), residues: 273 sheet: -1.14 (0.55), residues: 94 loop : -0.32 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 285 TYR 0.033 0.003 TYR A 588 PHE 0.020 0.002 PHE A 664 TRP 0.008 0.001 TRP A 652 HIS 0.007 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 ( 5424) covalent geometry : angle 0.62584 / 0.33 ( 7457) hydrogen bonds : bond 0.06969 / 4.62 ( 261) hydrogen bonds : angle 5.28695 / 3.77 ( 726) metal coordination : bond 0.00207 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.113 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8374 (m-30) cc_final: 0.7810 (t0) REVERT: A 255 THR cc_start: 0.8161 (m) cc_final: 0.7783 (p) REVERT: A 264 LYS cc_start: 0.6593 (mptt) cc_final: 0.6054 (ttmt) REVERT: A 287 TYR cc_start: 0.8011 (m-80) cc_final: 0.7783 (m-80) REVERT: A 303 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.7016 (tp) REVERT: A 321 LEU cc_start: 0.6862 (mt) cc_final: 0.6649 (mp) REVERT: A 353 MET cc_start: 0.7907 (ttm) cc_final: 0.7050 (mmt) REVERT: A 512 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7273 (mmmt) outliers start: 10 outliers final: 2 residues processed: 91 average time/residue: 0.0607 time to fit residues: 7.4103 Evaluate side-chains 76 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 512 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.7980 chunk 15 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 GLN A 201 GLN A 260 GLN A 414 HIS A 511 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.168855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.141287 restraints weight = 6684.906| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.32 r_work: 0.3594 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5427 Z= 0.137 Angle : 0.559 7.113 7457 Z= 0.283 Chirality : 0.040 0.148 862 Planarity : 0.003 0.027 870 Dihedral : 13.359 87.510 1016 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.50 % Allowed : 13.59 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.75 (0.34), residues: 586 helix: 1.85 (0.30), residues: 279 sheet: -1.24 (0.53), residues: 96 loop : -0.39 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 285 TYR 0.023 0.003 TYR A 518 PHE 0.013 0.002 PHE A 309 TRP 0.008 0.001 TRP A 652 HIS 0.005 0.001 HIS A 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 5424) covalent geometry : angle 0.55906 / 0.28 ( 7457) hydrogen bonds : bond 0.05407 / 3.56 ( 261) hydrogen bonds : angle 4.82424 / 3.44 ( 726) metal coordination : bond 0.00166 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.119 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8449 (m-30) cc_final: 0.7874 (t0) REVERT: A 179 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7155 (m-30) REVERT: A 255 THR cc_start: 0.8211 (m) cc_final: 0.7763 (p) REVERT: A 264 LYS cc_start: 0.6598 (mptt) cc_final: 0.6056 (ttmt) REVERT: A 303 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7105 (tp) REVERT: A 353 MET cc_start: 0.7850 (ttm) cc_final: 0.7019 (mmt) REVERT: A 626 LYS cc_start: 0.7380 (ttmt) cc_final: 0.7132 (ttmt) outliers start: 18 outliers final: 4 residues processed: 89 average time/residue: 0.0552 time to fit residues: 6.7706 Evaluate side-chains 73 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 609 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 35 optimal weight: 0.0060 chunk 30 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 HIS A 511 GLN ** A 667 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.168612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.141298 restraints weight = 6742.939| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.32 r_work: 0.3612 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5427 Z= 0.128 Angle : 0.537 7.273 7457 Z= 0.270 Chirality : 0.040 0.190 862 Planarity : 0.003 0.027 870 Dihedral : 13.376 86.295 1016 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.11 % Allowed : 15.34 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.87 (0.34), residues: 586 helix: 1.96 (0.30), residues: 279 sheet: -1.29 (0.54), residues: 96 loop : -0.31 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 285 TYR 0.020 0.002 TYR A 518 PHE 0.011 0.001 PHE A 309 TRP 0.008 0.001 TRP A 386 HIS 0.005 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 5424) covalent geometry : angle 0.53651 / 0.27 ( 7457) hydrogen bonds : bond 0.04530 / 2.96 ( 261) hydrogen bonds : angle 4.60706 / 3.29 ( 726) metal coordination : bond 0.00108 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8418 (m-30) cc_final: 0.7773 (t0) REVERT: A 179 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7165 (m-30) REVERT: A 238 ASP cc_start: 0.6902 (m-30) cc_final: 0.6701 (m-30) REVERT: A 255 THR cc_start: 0.8084 (m) cc_final: 0.7712 (p) REVERT: A 264 LYS cc_start: 0.6587 (mptt) cc_final: 0.6039 (ttmt) REVERT: A 353 MET cc_start: 0.7869 (ttm) cc_final: 0.7029 (mmt) REVERT: A 422 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7078 (mt-10) outliers start: 16 outliers final: 8 residues processed: 86 average time/residue: 0.0638 time to fit residues: 7.4417 Evaluate side-chains 74 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 609 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 0.0270 chunk 44 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.170992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.144829 restraints weight = 7056.509| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.25 r_work: 0.3650 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5427 Z= 0.117 Angle : 0.524 7.364 7457 Z= 0.262 Chirality : 0.039 0.150 862 Planarity : 0.003 0.025 870 Dihedral : 13.408 85.107 1016 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.11 % Allowed : 15.73 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.87 (0.34), residues: 586 helix: 1.99 (0.30), residues: 280 sheet: -1.52 (0.53), residues: 98 loop : -0.21 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 285 TYR 0.021 0.002 TYR A 518 PHE 0.010 0.001 PHE A 601 TRP 0.008 0.001 TRP A 386 HIS 0.006 0.001 HIS A 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 5424) covalent geometry : angle 0.52433 / 0.26 ( 7457) hydrogen bonds : bond 0.04128 / 2.71 ( 261) hydrogen bonds : angle 4.41329 / 3.14 ( 726) metal coordination : bond 0.00079 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8466 (m-30) cc_final: 0.7963 (t0) REVERT: A 179 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.7292 (m-30) REVERT: A 255 THR cc_start: 0.8031 (m) cc_final: 0.7707 (p) REVERT: A 258 TYR cc_start: 0.8430 (t80) cc_final: 0.8211 (t80) REVERT: A 264 LYS cc_start: 0.6529 (mptt) cc_final: 0.6053 (ttmt) REVERT: A 353 MET cc_start: 0.7871 (ttm) cc_final: 0.7120 (mmt) REVERT: A 422 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7254 (mt-10) REVERT: A 455 ARG cc_start: 0.6804 (mmm-85) cc_final: 0.6262 (ptt-90) REVERT: A 626 LYS cc_start: 0.7477 (ttpt) cc_final: 0.7111 (ptmt) outliers start: 16 outliers final: 12 residues processed: 85 average time/residue: 0.0733 time to fit residues: 8.3770 Evaluate side-chains 82 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 609 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 33 optimal weight: 0.0060 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 576 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.167446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.141341 restraints weight = 6948.225| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.20 r_work: 0.3621 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5427 Z= 0.154 Angle : 0.557 7.084 7457 Z= 0.279 Chirality : 0.041 0.158 862 Planarity : 0.003 0.026 870 Dihedral : 13.478 85.101 1016 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.91 % Allowed : 16.70 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.71 (0.34), residues: 586 helix: 1.84 (0.30), residues: 280 sheet: -1.59 (0.54), residues: 86 loop : -0.35 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 285 TYR 0.011 0.002 TYR A 588 PHE 0.012 0.002 PHE A 362 TRP 0.010 0.001 TRP A 386 HIS 0.006 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 5424) covalent geometry : angle 0.55696 / 0.28 ( 7457) hydrogen bonds : bond 0.04246 / 2.83 ( 261) hydrogen bonds : angle 4.46397 / 3.19 ( 726) metal coordination : bond 0.00198 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8497 (m-30) cc_final: 0.8014 (t0) REVERT: A 179 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7373 (m-30) REVERT: A 264 LYS cc_start: 0.6652 (mptt) cc_final: 0.6121 (ttmt) REVERT: A 353 MET cc_start: 0.7876 (ttm) cc_final: 0.7096 (mmt) REVERT: A 422 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7284 (mt-10) REVERT: A 455 ARG cc_start: 0.6809 (mmm-85) cc_final: 0.6268 (ptt-90) REVERT: A 623 MET cc_start: 0.7601 (ttp) cc_final: 0.7357 (mtp) REVERT: A 626 LYS cc_start: 0.7551 (ttpt) cc_final: 0.7164 (ptmt) outliers start: 15 outliers final: 10 residues processed: 79 average time/residue: 0.0673 time to fit residues: 7.3140 Evaluate side-chains 74 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 591 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 4 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.169993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.144008 restraints weight = 6990.550| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.23 r_work: 0.3649 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5427 Z= 0.121 Angle : 0.526 7.666 7457 Z= 0.260 Chirality : 0.040 0.152 862 Planarity : 0.003 0.026 870 Dihedral : 13.532 82.961 1016 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.52 % Allowed : 17.28 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.85 (0.35), residues: 586 helix: 1.94 (0.30), residues: 280 sheet: -1.55 (0.55), residues: 86 loop : -0.26 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 285 TYR 0.013 0.002 TYR A 6 PHE 0.007 0.001 PHE A 309 TRP 0.009 0.001 TRP A 386 HIS 0.006 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 5424) covalent geometry : angle 0.52586 / 0.26 ( 7457) hydrogen bonds : bond 0.03936 / 2.59 ( 261) hydrogen bonds : angle 4.36612 / 3.13 ( 726) metal coordination : bond 0.00111 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8478 (m-30) cc_final: 0.7961 (t0) REVERT: A 179 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7284 (m-30) REVERT: A 246 MET cc_start: 0.7652 (tpp) cc_final: 0.7445 (tpp) REVERT: A 264 LYS cc_start: 0.6640 (mptt) cc_final: 0.6137 (ttmt) REVERT: A 353 MET cc_start: 0.7854 (ttm) cc_final: 0.7087 (mmt) REVERT: A 383 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7741 (tt) REVERT: A 389 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7372 (mp10) REVERT: A 422 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7306 (mt-10) REVERT: A 455 ARG cc_start: 0.6810 (mmm-85) cc_final: 0.6276 (ptt-90) REVERT: A 518 TYR cc_start: 0.6745 (t80) cc_final: 0.6445 (t80) REVERT: A 623 MET cc_start: 0.7669 (ttp) cc_final: 0.7281 (mtp) REVERT: A 626 LYS cc_start: 0.7482 (ttpt) cc_final: 0.7212 (ttmt) outliers start: 13 outliers final: 8 residues processed: 76 average time/residue: 0.0671 time to fit residues: 6.9095 Evaluate side-chains 76 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 591 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 3 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.168168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.142462 restraints weight = 6808.426| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.17 r_work: 0.3640 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5427 Z= 0.129 Angle : 0.528 7.289 7457 Z= 0.260 Chirality : 0.040 0.154 862 Planarity : 0.003 0.025 870 Dihedral : 13.572 82.701 1016 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.52 % Allowed : 17.48 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.90 (0.34), residues: 586 helix: 2.12 (0.29), residues: 274 sheet: -1.66 (0.54), residues: 86 loop : -0.29 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 285 TYR 0.011 0.002 TYR A 6 PHE 0.008 0.001 PHE A 309 TRP 0.010 0.001 TRP A 386 HIS 0.006 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 5424) covalent geometry : angle 0.52808 / 0.26 ( 7457) hydrogen bonds : bond 0.03865 / 2.57 ( 261) hydrogen bonds : angle 4.32495 / 3.09 ( 726) metal coordination : bond 0.00141 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8458 (m-30) cc_final: 0.7990 (t0) REVERT: A 264 LYS cc_start: 0.6615 (mptt) cc_final: 0.6155 (ttmt) REVERT: A 271 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7953 (mp) REVERT: A 353 MET cc_start: 0.7884 (ttm) cc_final: 0.7086 (mmt) REVERT: A 383 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7783 (tt) REVERT: A 389 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7449 (mp10) REVERT: A 422 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7351 (mt-10) REVERT: A 455 ARG cc_start: 0.6847 (mmm-85) cc_final: 0.6317 (ptt-90) REVERT: A 623 MET cc_start: 0.7678 (ttp) cc_final: 0.7298 (mtp) REVERT: A 626 LYS cc_start: 0.7496 (ttpt) cc_final: 0.7257 (ttmt) outliers start: 13 outliers final: 7 residues processed: 77 average time/residue: 0.0625 time to fit residues: 6.5062 Evaluate side-chains 74 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 591 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 44 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.170388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.144501 restraints weight = 6991.315| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.21 r_work: 0.3651 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5427 Z= 0.112 Angle : 0.517 7.593 7457 Z= 0.254 Chirality : 0.039 0.151 862 Planarity : 0.003 0.025 870 Dihedral : 13.613 81.140 1016 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.33 % Allowed : 18.06 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.02 (0.35), residues: 586 helix: 2.20 (0.30), residues: 275 sheet: -1.62 (0.55), residues: 86 loop : -0.21 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 326 TYR 0.019 0.002 TYR A 625 PHE 0.007 0.001 PHE A 309 TRP 0.010 0.001 TRP A 386 HIS 0.007 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 5424) covalent geometry : angle 0.51723 / 0.25 ( 7457) hydrogen bonds : bond 0.03720 / 2.47 ( 261) hydrogen bonds : angle 4.27626 / 3.06 ( 726) metal coordination : bond 0.00103 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8481 (m-30) cc_final: 0.7978 (t0) REVERT: A 264 LYS cc_start: 0.6607 (mptt) cc_final: 0.6155 (ttmt) REVERT: A 271 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7902 (mp) REVERT: A 353 MET cc_start: 0.7870 (ttm) cc_final: 0.6998 (mmt) REVERT: A 383 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7707 (tt) REVERT: A 389 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7475 (mp10) REVERT: A 455 ARG cc_start: 0.6910 (mmm-85) cc_final: 0.6315 (ptt-90) REVERT: A 626 LYS cc_start: 0.7619 (ttpt) cc_final: 0.7358 (ttmt) outliers start: 12 outliers final: 9 residues processed: 75 average time/residue: 0.0636 time to fit residues: 6.4607 Evaluate side-chains 75 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 591 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 60 optimal weight: 7.9990 chunk 44 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 37 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.170113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.144199 restraints weight = 7003.357| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.21 r_work: 0.3672 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5427 Z= 0.117 Angle : 0.542 8.782 7457 Z= 0.266 Chirality : 0.039 0.150 862 Planarity : 0.003 0.024 870 Dihedral : 13.635 81.260 1016 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.33 % Allowed : 18.64 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.35), residues: 586 helix: 2.08 (0.30), residues: 281 sheet: -1.68 (0.54), residues: 86 loop : -0.22 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 326 TYR 0.018 0.002 TYR A 625 PHE 0.007 0.001 PHE A 362 TRP 0.012 0.001 TRP A 386 HIS 0.008 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 5424) covalent geometry : angle 0.54177 / 0.27 ( 7457) hydrogen bonds : bond 0.03700 / 2.48 ( 261) hydrogen bonds : angle 4.25591 / 3.04 ( 726) metal coordination : bond 0.00108 / 0.05 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8466 (m-30) cc_final: 0.8002 (t0) REVERT: A 264 LYS cc_start: 0.6600 (mptt) cc_final: 0.6148 (ttmt) REVERT: A 271 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7871 (mp) REVERT: A 347 GLU cc_start: 0.7057 (pm20) cc_final: 0.6599 (mt-10) REVERT: A 383 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7676 (tt) REVERT: A 389 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7517 (mp10) REVERT: A 626 LYS cc_start: 0.7573 (ttpt) cc_final: 0.7292 (ptmt) outliers start: 12 outliers final: 8 residues processed: 74 average time/residue: 0.0641 time to fit residues: 6.3766 Evaluate side-chains 75 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 591 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 0.0870 chunk 6 optimal weight: 0.8980 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.169813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.144073 restraints weight = 7006.047| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.21 r_work: 0.3651 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5427 Z= 0.116 Angle : 0.533 10.568 7457 Z= 0.258 Chirality : 0.039 0.150 862 Planarity : 0.003 0.025 870 Dihedral : 13.636 82.528 1016 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.33 % Allowed : 18.25 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.35), residues: 586 helix: 2.08 (0.29), residues: 281 sheet: -1.64 (0.55), residues: 86 loop : -0.25 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 285 TYR 0.011 0.002 TYR A 6 PHE 0.007 0.001 PHE A 309 TRP 0.013 0.001 TRP A 386 HIS 0.009 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 5424) covalent geometry : angle 0.53338 / 0.26 ( 7457) hydrogen bonds : bond 0.03657 / 2.46 ( 261) hydrogen bonds : angle 4.25861 / 3.04 ( 726) metal coordination : bond 0.00114 / 0.06 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1200.17 seconds wall clock time: 21 minutes 18.72 seconds (1278.72 seconds total)