Starting phenix.real_space_refine on Tue Aug 4 17:19:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lou_63260/08_2026/9lou_63260.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lou_63260/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9lou_63260/08_2026/9lou_63260.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lou_63260/08_2026/9lou_63260.map" model { file = "/net/cci-nas-00/data/ceres_data/9lou_63260/08_2026/9lou_63260.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lou_63260/08_2026/9lou_63260.cif" } 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): 0.00s 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: 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: 1.18, per 1000 atoms: 0.22 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: 0.40 Conformation dependent library (CDL) restraints added in 179.5 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: 0.41 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: 0.66 Time building geometry restraints manager: 0.54 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=" C1' G Y 6 " pdb=" N9 G Y 6 " ideal model delta sigma weight residual 1.483 1.472 0.011 1.50e-02 4.44e+03 5.09e-01 bond pdb=" C1' G X 9 " pdb=" N9 G X 9 " ideal model delta sigma weight residual 1.483 1.473 0.010 1.50e-02 4.44e+03 4.60e-01 ... (remaining 5419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 7325 1.79 - 3.59: 118 3.59 - 5.38: 10 5.38 - 7.18: 3 7.18 - 8.97: 1 Bond angle restraints: 7457 Sorted by residual: angle pdb=" O5' G Y 10 " pdb=" C5' G Y 10 " pdb=" C4' G Y 10 " ideal model delta sigma weight residual 109.40 112.07 -2.67 8.00e-01 1.56e+00 1.12e+01 angle pdb=" O5' U X 4 " pdb=" C5' U X 4 " pdb=" C4' U X 4 " ideal model delta sigma weight residual 109.40 112.00 -2.60 8.00e-01 1.56e+00 1.05e+01 angle pdb=" O5' C Y 2 " pdb=" C5' C Y 2 " pdb=" C4' C Y 2 " ideal model delta sigma weight residual 109.40 111.98 -2.58 8.00e-01 1.56e+00 1.04e+01 angle pdb=" O5' C Y 8 " pdb=" C5' C Y 8 " pdb=" C4' C Y 8 " ideal model delta sigma weight residual 109.40 111.85 -2.45 8.00e-01 1.56e+00 9.40e+00 angle pdb=" O5' U Y 7 " pdb=" C5' U Y 7 " pdb=" C4' U Y 7 " ideal model delta sigma weight residual 109.40 111.83 -2.43 8.00e-01 1.56e+00 9.26e+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: 622 0.033 - 0.066: 149 0.066 - 0.099: 44 0.099 - 0.132: 27 0.132 - 0.165: 20 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=" C2' U Y 7 " pdb=" C3' U Y 7 " pdb=" O2' U Y 7 " pdb=" C1' U Y 7 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" C2' C X 7 " pdb=" C3' C X 7 " pdb=" O2' C X 7 " pdb=" C1' C X 7 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 5.14e-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: 1.330 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.550 Find NCS groups from input model: 0.030 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: 9.210 ------------------------------------------------------------------------------- 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= 0.112 Angle : 0.506 8.972 7457 Z= 0.287 Chirality : 0.043 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 0.00199 / 0.11 ( 5424) covalent geometry : angle 0.50612 / 0.29 ( 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 : 0.170 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: 0.0753 time to fit residues: 13.1450 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 : 0.108 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4043 r_free = 0.4043 target = 0.169099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.142069 restraints weight = 6713.714| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.28 r_work: 0.3607 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5427 Z= 0.174 Angle : 0.624 7.747 7457 Z= 0.327 Chirality : 0.043 0.191 862 Planarity : 0.005 0.052 870 Dihedral : 13.440 91.352 1017 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.94 % Allowed : 12.62 % Favored : 85.44 % 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: 0.68 (0.34), residues: 586 helix: 1.69 (0.30), residues: 273 sheet: -1.15 (0.55), residues: 94 loop : -0.29 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 285 TYR 0.036 0.003 TYR A 588 PHE 0.020 0.002 PHE A 664 TRP 0.009 0.001 TRP A 652 HIS 0.007 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 ( 5424) covalent geometry : angle 0.62359 / 0.33 ( 7457) hydrogen bonds : bond 0.07444 / 4.92 ( 261) hydrogen bonds : angle 5.24314 / 3.74 ( 726) metal coordination : bond 0.00271 / 0.13 ( 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 93 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 109 MET cc_start: 0.7701 (mtp) cc_final: 0.7488 (mtp) REVERT: A 139 ASP cc_start: 0.8408 (m-30) cc_final: 0.7836 (t0) REVERT: A 255 THR cc_start: 0.8159 (m) cc_final: 0.7782 (p) REVERT: A 264 LYS cc_start: 0.6617 (mptt) cc_final: 0.6083 (ttmt) REVERT: A 287 TYR cc_start: 0.8035 (m-80) cc_final: 0.7834 (m-80) REVERT: A 303 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.7004 (tp) REVERT: A 321 LEU cc_start: 0.6865 (mt) cc_final: 0.6649 (mp) REVERT: A 353 MET cc_start: 0.7928 (ttm) cc_final: 0.7077 (mmt) REVERT: A 512 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7258 (mmmt) outliers start: 10 outliers final: 2 residues processed: 89 average time/residue: 0.0615 time to fit residues: 7.3898 Evaluate side-chains 77 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.154 ------------------------------------------------------------------------------- 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: 4.9990 chunk 15 optimal weight: 0.0370 chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 53 optimal weight: 0.0000 chunk 31 optimal weight: 0.8980 overall best weight: 0.4662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 GLN A 201 GLN A 260 GLN A 314 HIS A 414 HIS A 511 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.170411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.142939 restraints weight = 6652.249| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.32 r_work: 0.3633 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5427 Z= 0.122 Angle : 0.552 7.010 7457 Z= 0.277 Chirality : 0.039 0.147 862 Planarity : 0.003 0.027 870 Dihedral : 13.313 86.938 1016 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.50 % Allowed : 13.40 % Favored : 83.11 % 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: 0.78 (0.34), residues: 586 helix: 1.91 (0.30), residues: 280 sheet: -1.25 (0.50), residues: 104 loop : -0.39 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 285 TYR 0.023 0.003 TYR A 518 PHE 0.014 0.002 PHE A 664 TRP 0.007 0.001 TRP A 652 HIS 0.011 0.001 HIS A 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 5424) covalent geometry : angle 0.55151 / 0.28 ( 7457) hydrogen bonds : bond 0.05248 / 3.44 ( 261) hydrogen bonds : angle 4.72642 / 3.38 ( 726) metal coordination : bond 0.00101 / 0.05 ( 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 94 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.195 Fit side-chains REVERT: A 139 ASP cc_start: 0.8415 (m-30) cc_final: 0.7774 (t0) REVERT: A 179 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.7090 (m-30) REVERT: A 238 ASP cc_start: 0.6880 (m-30) cc_final: 0.6635 (m-30) REVERT: A 255 THR cc_start: 0.8101 (m) cc_final: 0.7693 (p) REVERT: A 257 MET cc_start: 0.7150 (tpt) cc_final: 0.6684 (tpt) REVERT: A 264 LYS cc_start: 0.6503 (mptt) cc_final: 0.5995 (ttmt) REVERT: A 303 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7094 (tp) REVERT: A 326 ARG cc_start: 0.7054 (ptp-170) cc_final: 0.5978 (ttp80) REVERT: A 353 MET cc_start: 0.7893 (ttm) cc_final: 0.7043 (mmt) REVERT: A 626 LYS cc_start: 0.7246 (ttmt) cc_final: 0.6903 (ttmt) outliers start: 18 outliers final: 4 residues processed: 89 average time/residue: 0.0622 time to fit residues: 7.7549 Evaluate side-chains 70 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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: 0.0770 chunk 30 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.168852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.141531 restraints weight = 6705.408| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.32 r_work: 0.3622 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3322 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= 0.124 Angle : 0.534 7.150 7457 Z= 0.267 Chirality : 0.039 0.146 862 Planarity : 0.004 0.040 870 Dihedral : 13.312 86.394 1016 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.72 % Allowed : 16.12 % 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: 0.85 (0.34), residues: 586 helix: 2.00 (0.30), residues: 279 sheet: -1.34 (0.51), residues: 104 loop : -0.30 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 285 TYR 0.019 0.002 TYR A 518 PHE 0.010 0.001 PHE A 309 TRP 0.010 0.001 TRP A 386 HIS 0.005 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 5424) covalent geometry : angle 0.53390 / 0.27 ( 7457) hydrogen bonds : bond 0.04451 / 2.93 ( 261) hydrogen bonds : angle 4.57813 / 3.27 ( 726) metal coordination : bond 0.00111 / 0.06 ( 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 87 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8385 (m-30) cc_final: 0.7735 (t0) REVERT: A 179 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7159 (m-30) REVERT: A 238 ASP cc_start: 0.6911 (m-30) cc_final: 0.6709 (m-30) REVERT: A 255 THR cc_start: 0.8070 (m) cc_final: 0.7718 (p) REVERT: A 257 MET cc_start: 0.7146 (tpt) cc_final: 0.6696 (tpt) REVERT: A 264 LYS cc_start: 0.6540 (mptt) cc_final: 0.6013 (ttmt) REVERT: A 353 MET cc_start: 0.7875 (ttm) cc_final: 0.7057 (mmt) REVERT: A 623 MET cc_start: 0.7728 (ttp) cc_final: 0.7365 (mtp) outliers start: 14 outliers final: 9 residues processed: 85 average time/residue: 0.0679 time to fit residues: 7.8608 Evaluate side-chains 75 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 633 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 0.5980 chunk 44 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.171503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.145403 restraints weight = 7065.288| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.25 r_work: 0.3654 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 5427 Z= 0.117 Angle : 0.521 7.220 7457 Z= 0.259 Chirality : 0.039 0.194 862 Planarity : 0.003 0.025 870 Dihedral : 13.366 85.183 1016 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.72 % Allowed : 16.12 % 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: 0.86 (0.34), residues: 586 helix: 2.02 (0.30), residues: 280 sheet: -1.34 (0.51), residues: 104 loop : -0.34 (0.41), residues: 202 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 0.008 0.001 PHE A 309 TRP 0.009 0.001 TRP A 386 HIS 0.005 0.001 HIS A 381 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 5424) covalent geometry : angle 0.52086 / 0.26 ( 7457) hydrogen bonds : bond 0.04078 / 2.68 ( 261) hydrogen bonds : angle 4.48000 / 3.20 ( 726) metal coordination : bond 0.00092 / 0.05 ( 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 82 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8469 (m-30) cc_final: 0.7937 (t0) REVERT: A 179 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7292 (m-30) REVERT: A 255 THR cc_start: 0.8043 (m) cc_final: 0.7728 (p) REVERT: A 264 LYS cc_start: 0.6507 (mptt) cc_final: 0.6056 (ttmt) REVERT: A 353 MET cc_start: 0.7838 (ttm) cc_final: 0.7116 (mmt) REVERT: A 422 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7233 (mt-10) REVERT: A 455 ARG cc_start: 0.6811 (mmm-85) cc_final: 0.6280 (ptt-90) REVERT: A 626 LYS cc_start: 0.7463 (ttpt) cc_final: 0.6990 (ptmt) outliers start: 14 outliers final: 11 residues processed: 80 average time/residue: 0.0679 time to fit residues: 7.3240 Evaluate side-chains 76 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 633 LEU 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: 2.9990 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 16 optimal weight: 0.0060 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- 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 = 0.170151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.144044 restraints weight = 7042.282| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.25 r_work: 0.3642 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3646 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= 0.125 Angle : 0.529 7.159 7457 Z= 0.262 Chirality : 0.040 0.149 862 Planarity : 0.003 0.025 870 Dihedral : 13.421 84.608 1016 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.30 % Allowed : 16.70 % 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: 0.87 (0.34), residues: 586 helix: 2.00 (0.30), residues: 281 sheet: -1.48 (0.54), residues: 86 loop : -0.36 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 285 TYR 0.017 0.002 TYR A 588 PHE 0.009 0.001 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 0.00275 / 0.13 ( 5424) covalent geometry : angle 0.52899 / 0.26 ( 7457) hydrogen bonds : bond 0.03969 / 2.64 ( 261) hydrogen bonds : angle 4.41714 / 3.15 ( 726) metal coordination : bond 0.00139 / 0.07 ( 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 85 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8501 (m-30) cc_final: 0.7975 (t0) REVERT: A 179 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7310 (m-30) REVERT: A 264 LYS cc_start: 0.6521 (mptt) cc_final: 0.6059 (ttmt) REVERT: A 353 MET cc_start: 0.7872 (ttm) cc_final: 0.7121 (mmt) REVERT: A 422 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7312 (mt-10) REVERT: A 455 ARG cc_start: 0.6786 (mmm-85) cc_final: 0.6259 (ptt-90) REVERT: A 626 LYS cc_start: 0.7561 (ttpt) cc_final: 0.7180 (ptmt) outliers start: 17 outliers final: 14 residues processed: 83 average time/residue: 0.0717 time to fit residues: 8.0361 Evaluate side-chains 77 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.189 ------------------------------------------------------------------------------- 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 315 VAL 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 Chi-restraints excluded: chain A residue 633 LEU 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: 0.0070 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.8004 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.170170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.144248 restraints weight = 6968.292| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.22 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: 0.7799 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5427 Z= 0.123 Angle : 0.525 7.419 7457 Z= 0.257 Chirality : 0.039 0.149 862 Planarity : 0.003 0.025 870 Dihedral : 13.487 83.096 1016 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.30 % Allowed : 16.50 % 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 (0.34), residues: 586 helix: 2.02 (0.30), residues: 281 sheet: -1.44 (0.52), residues: 94 loop : -0.39 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 285 TYR 0.022 0.002 TYR A 518 PHE 0.007 0.001 PHE A 309 TRP 0.011 0.001 TRP A 386 HIS 0.005 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 5424) covalent geometry : angle 0.52480 / 0.26 ( 7457) hydrogen bonds : bond 0.03868 / 2.56 ( 261) hydrogen bonds : angle 4.40142 / 3.14 ( 726) metal coordination : bond 0.00117 / 0.06 ( 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 83 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8494 (m-30) cc_final: 0.7973 (t0) REVERT: A 179 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7307 (m-30) REVERT: A 246 MET cc_start: 0.7512 (tpp) cc_final: 0.7309 (tpp) REVERT: A 264 LYS cc_start: 0.6505 (mptt) cc_final: 0.6074 (ttmt) REVERT: A 353 MET cc_start: 0.7838 (ttm) cc_final: 0.7098 (mmt) REVERT: A 383 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7646 (tt) REVERT: A 422 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7305 (mt-10) REVERT: A 455 ARG cc_start: 0.6784 (mmm-85) cc_final: 0.6259 (ptt-90) REVERT: A 626 LYS cc_start: 0.7514 (ttpt) cc_final: 0.7227 (ttmt) outliers start: 17 outliers final: 13 residues processed: 80 average time/residue: 0.0692 time to fit residues: 7.5272 Evaluate side-chains 78 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.189 ------------------------------------------------------------------------------- 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 303 LEU Chi-restraints excluded: chain A residue 351 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 Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 633 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 3 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.170057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.144306 restraints weight = 6887.341| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.20 r_work: 0.3653 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3861 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= 0.123 Angle : 0.520 7.363 7457 Z= 0.256 Chirality : 0.040 0.151 862 Planarity : 0.003 0.026 870 Dihedral : 13.520 82.435 1016 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.72 % Allowed : 17.28 % 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: 0.86 (0.35), residues: 586 helix: 1.98 (0.30), residues: 287 sheet: -1.53 (0.51), residues: 94 loop : -0.33 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 285 TYR 0.030 0.002 TYR A 36 PHE 0.007 0.001 PHE A 309 TRP 0.014 0.001 TRP A 8 HIS 0.006 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 5424) covalent geometry : angle 0.52009 / 0.26 ( 7457) hydrogen bonds : bond 0.03761 / 2.51 ( 261) hydrogen bonds : angle 4.34332 / 3.10 ( 726) metal coordination : bond 0.00129 / 0.06 ( 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 80 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8490 (m-30) cc_final: 0.7978 (t0) REVERT: A 264 LYS cc_start: 0.6587 (mptt) cc_final: 0.6145 (ttmt) REVERT: A 383 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7686 (tt) REVERT: A 422 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7358 (mt-10) REVERT: A 455 ARG cc_start: 0.6819 (mmm-85) cc_final: 0.6276 (ptt-90) REVERT: A 518 TYR cc_start: 0.6745 (t80) cc_final: 0.6511 (t80) REVERT: A 626 LYS cc_start: 0.7481 (ttpt) cc_final: 0.7191 (ttmt) outliers start: 14 outliers final: 10 residues processed: 78 average time/residue: 0.0693 time to fit residues: 7.3619 Evaluate side-chains 73 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 315 VAL 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 Chi-restraints excluded: chain A residue 633 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 44 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.170181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.144309 restraints weight = 6991.305| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.22 r_work: 0.3650 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3927 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= 0.121 Angle : 0.538 8.395 7457 Z= 0.261 Chirality : 0.040 0.151 862 Planarity : 0.003 0.026 870 Dihedral : 13.554 81.620 1016 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.72 % Allowed : 17.48 % Favored : 79.81 % 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: 0.89 (0.35), residues: 586 helix: 2.03 (0.30), residues: 287 sheet: -1.55 (0.51), residues: 94 loop : -0.33 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 285 TYR 0.018 0.002 TYR A 518 PHE 0.007 0.001 PHE A 309 TRP 0.011 0.001 TRP A 386 HIS 0.007 0.001 HIS A 667 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 5424) covalent geometry : angle 0.53843 / 0.26 ( 7457) hydrogen bonds : bond 0.03720 / 2.48 ( 261) hydrogen bonds : angle 4.33721 / 3.11 ( 726) metal coordination : bond 0.00124 / 0.06 ( 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: 14 poor density : 65 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 139 ASP cc_start: 0.8488 (m-30) cc_final: 0.7974 (t0) REVERT: A 264 LYS cc_start: 0.6541 (mptt) cc_final: 0.6112 (ttmt) REVERT: A 353 MET cc_start: 0.7863 (ttm) cc_final: 0.7027 (mmt) REVERT: A 413 THR cc_start: 0.6327 (OUTLIER) cc_final: 0.5813 (m) REVERT: A 455 ARG cc_start: 0.6791 (mmm-85) cc_final: 0.6279 (ptt-90) REVERT: A 518 TYR cc_start: 0.6767 (t80) cc_final: 0.6512 (t80) REVERT: A 626 LYS cc_start: 0.7532 (ttpt) cc_final: 0.7257 (ttmt) outliers start: 14 outliers final: 10 residues processed: 77 average time/residue: 0.0707 time to fit residues: 7.3572 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 : 0.221 ------------------------------------------------------------------------------- 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 303 LEU Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 413 THR 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 633 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 60 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4078 r_free = 0.4078 target = 0.169661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.143724 restraints weight = 6953.779| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.22 r_work: 0.3672 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3988 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= 0.126 Angle : 0.558 10.379 7457 Z= 0.268 Chirality : 0.040 0.157 862 Planarity : 0.003 0.026 870 Dihedral : 13.591 81.013 1016 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.14 % Allowed : 18.83 % 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: 0.85 (0.35), residues: 586 helix: 2.00 (0.30), residues: 287 sheet: -1.59 (0.52), residues: 94 loop : -0.34 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 326 TYR 0.021 0.002 TYR A 36 PHE 0.007 0.001 PHE A 309 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 0.00285 / 0.13 ( 5424) covalent geometry : angle 0.55802 / 0.27 ( 7457) hydrogen bonds : bond 0.03716 / 2.50 ( 261) hydrogen bonds : angle 4.31818 / 3.10 ( 726) metal coordination : bond 0.00133 / 0.06 ( 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 77 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.188 Fit side-chains REVERT: A 139 ASP cc_start: 0.8485 (m-30) cc_final: 0.7959 (t0) REVERT: A 264 LYS cc_start: 0.6593 (mptt) cc_final: 0.6150 (ttmt) REVERT: A 347 GLU cc_start: 0.6972 (pm20) cc_final: 0.6712 (mp0) REVERT: A 353 MET cc_start: 0.7860 (ttm) cc_final: 0.6984 (mmt) REVERT: A 389 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7294 (mp10) REVERT: A 626 LYS cc_start: 0.7492 (ttpt) cc_final: 0.7218 (ttmt) outliers start: 11 outliers final: 9 residues processed: 75 average time/residue: 0.0753 time to fit residues: 7.5315 Evaluate side-chains 73 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 303 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 633 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 17 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 0.0040 chunk 6 optimal weight: 0.2980 overall best weight: 0.4792 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.173311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.148251 restraints weight = 6866.664| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.15 r_work: 0.3675 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5427 Z= 0.102 Angle : 0.539 10.578 7457 Z= 0.259 Chirality : 0.039 0.180 862 Planarity : 0.003 0.026 870 Dihedral : 13.614 81.811 1016 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.55 % Allowed : 19.61 % Favored : 78.83 % 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: 0.97 (0.35), residues: 586 helix: 2.12 (0.30), residues: 287 sheet: -1.52 (0.52), residues: 94 loop : -0.33 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 285 TYR 0.020 0.002 TYR A 625 PHE 0.007 0.001 PHE A 664 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 0.00218 / 0.10 ( 5424) covalent geometry : angle 0.53922 / 0.26 ( 7457) hydrogen bonds : bond 0.03489 / 2.33 ( 261) hydrogen bonds : angle 4.23889 / 3.04 ( 726) metal coordination : bond 0.00070 / 0.03 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1312.32 seconds wall clock time: 23 minutes 19.29 seconds (1399.29 seconds total)