Starting phenix.real_space_refine on Wed Aug 5 03:10:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fti_29433/08_2026/8fti_29433.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fti_29433/08_2026/8fti_29433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fti_29433/08_2026/8fti_29433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fti_29433/08_2026/8fti_29433.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8fti_29433/08_2026/8fti_29433.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fti_29433/08_2026/8fti_29433.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fti_29433/08_2026/8fti_29433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fti_29433/08_2026/8fti_29433.map" } resolution = 3.5 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 97 5.49 5 S 24 5.16 5 C 4792 2.51 5 N 1443 2.21 5 O 1770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 8126 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 6062 Classifications: {'peptide': 737} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 725} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2064 Classifications: {'RNAv2': 97} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 9, 'rna3p_pur': 45, 'rna3p_pyr': 38} Link IDs: {'rna2p': 13, 'rna3p': 83} Chain breaks: 1 Time building chain proxies: 1.43, per 1000 atoms: 0.18 Number of scatterers: 8126 At special positions: 0 Unit cell: (77.43, 81.78, 137.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 97 15.00 O 1770 8.00 N 1443 7.00 C 4792 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: 0.77 Conformation dependent library (CDL) restraints added in 203.7 milliseconds 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1380 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 3 sheets defined 61.9% alpha, 3.7% beta 33 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 20 through 24 removed outlier: 3.639A pdb=" N ARG A 23 " --> pdb=" O GLN A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 41 removed outlier: 3.980A pdb=" N ILE A 29 " --> pdb=" O TRP A 25 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A 30 " --> pdb=" O CYS A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'A' and resid 62 through 72 Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.641A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 123 removed outlier: 3.509A pdb=" N THR A 107 " --> pdb=" O ASP A 103 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 151 removed outlier: 4.133A pdb=" N PHE A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 Processing helix chain 'A' and resid 166 through 170 removed outlier: 3.676A pdb=" N LYS A 170 " --> pdb=" O GLY A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 184 Processing helix chain 'A' and resid 197 through 211 removed outlier: 3.616A pdb=" N ASP A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.751A pdb=" N TYR A 220 " --> pdb=" O GLU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 258 removed outlier: 3.707A pdb=" N PHE A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 338 removed outlier: 3.624A pdb=" N TYR A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 360 removed outlier: 3.652A pdb=" N ALA A 343 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLN A 352 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 373 through 380 removed outlier: 3.741A pdb=" N LEU A 377 " --> pdb=" O PRO A 373 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N HIS A 380 " --> pdb=" O VAL A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 408 Processing helix chain 'A' and resid 413 through 429 removed outlier: 3.777A pdb=" N TYR A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 447 removed outlier: 3.992A pdb=" N ASN A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 463 removed outlier: 3.624A pdb=" N PHE A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 476 removed outlier: 3.844A pdb=" N TYR A 471 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLN A 476 " --> pdb=" O SER A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 497 Processing helix chain 'A' and resid 500 through 508 Processing helix chain 'A' and resid 516 through 527 removed outlier: 3.691A pdb=" N LYS A 520 " --> pdb=" O ASP A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 540 removed outlier: 3.723A pdb=" N LYS A 537 " --> pdb=" O GLY A 533 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 558 removed outlier: 3.592A pdb=" N HIS A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 606 removed outlier: 3.758A pdb=" N LEU A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU A 588 " --> pdb=" O PRO A 584 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 591 " --> pdb=" O TYR A 587 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 606 " --> pdb=" O TYR A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 644 Processing helix chain 'A' and resid 652 through 662 removed outlier: 3.628A pdb=" N GLY A 656 " --> pdb=" O ALA A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 706 removed outlier: 3.970A pdb=" N PHE A 680 " --> pdb=" O TYR A 676 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARG A 681 " --> pdb=" O GLU A 677 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 682 " --> pdb=" O LYS A 678 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A 706 " --> pdb=" O VAL A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 728 through 744 Processing helix chain 'A' and resid 750 through 764 removed outlier: 4.374A pdb=" N PHE A 754 " --> pdb=" O VAL A 750 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY A 755 " --> pdb=" O ILE A 751 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR A 764 " --> pdb=" O VAL A 760 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 289 through 291 removed outlier: 3.831A pdb=" N VAL A 289 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS A 267 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER A 300 " --> pdb=" O ARG A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 307 through 314 removed outlier: 4.226A pdb=" N LYS A 314 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 317 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 616 through 618 290 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 0.92 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: 1843 1.33 - 1.45: 2318 1.45 - 1.57: 4105 1.57 - 1.69: 192 1.69 - 1.81: 34 Bond restraints: 8492 Sorted by residual: bond pdb=" C TRP A 770 " pdb=" N LYS A 771 " ideal model delta sigma weight residual 1.328 1.339 -0.011 1.30e-02 5.92e+03 6.93e-01 bond pdb=" C1' G B 23 " pdb=" N9 G B 23 " ideal model delta sigma weight residual 1.478 1.462 0.016 2.00e-02 2.50e+03 6.57e-01 bond pdb=" CA GLN A 74 " pdb=" CB GLN A 74 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.55e-01 bond pdb=" C1' A B 31 " pdb=" N9 A B 31 " ideal model delta sigma weight residual 1.478 1.462 0.016 2.00e-02 2.50e+03 6.24e-01 bond pdb=" N LYS A 771 " pdb=" CA LYS A 771 " ideal model delta sigma weight residual 1.460 1.471 -0.011 1.42e-02 4.96e+03 6.01e-01 ... (remaining 8487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 11219 1.37 - 2.75: 474 2.75 - 4.12: 157 4.12 - 5.50: 33 5.50 - 6.87: 2 Bond angle restraints: 11885 Sorted by residual: angle pdb=" C THR A 73 " pdb=" N GLN A 74 " pdb=" CA GLN A 74 " ideal model delta sigma weight residual 121.54 128.41 -6.87 1.91e+00 2.74e-01 1.29e+01 angle pdb=" C3' G B 23 " pdb=" C2' G B 23 " pdb=" O2' G B 23 " ideal model delta sigma weight residual 109.80 115.30 -5.50 2.00e+00 2.50e-01 7.57e+00 angle pdb=" C ALA A 463 " pdb=" N GLU A 464 " pdb=" CA GLU A 464 " ideal model delta sigma weight residual 122.74 126.45 -3.71 1.44e+00 4.82e-01 6.65e+00 angle pdb=" C3' G B -67 " pdb=" C2' G B -67 " pdb=" O2' G B -67 " ideal model delta sigma weight residual 109.80 114.89 -5.09 2.00e+00 2.50e-01 6.47e+00 angle pdb=" C3' G B -40 " pdb=" C2' G B -40 " pdb=" O2' G B -40 " ideal model delta sigma weight residual 109.80 114.65 -4.85 2.00e+00 2.50e-01 5.88e+00 ... (remaining 11880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 4627 34.54 - 69.07: 230 69.07 - 103.61: 19 103.61 - 138.15: 0 138.15 - 172.68: 1 Dihedral angle restraints: 4877 sinusoidal: 2727 harmonic: 2150 Sorted by residual: dihedral pdb=" C4' U B -56 " pdb=" C3' U B -56 " pdb=" C2' U B -56 " pdb=" C1' U B -56 " ideal model delta sinusoidal sigma weight residual 36.34 -37.10 73.45 1 3.10e+00 1.04e-01 7.14e+02 dihedral pdb=" C4' U B 17 " pdb=" C3' U B 17 " pdb=" C2' U B 17 " pdb=" C1' U B 17 " ideal model delta sinusoidal sigma weight residual 36.34 -36.70 73.04 1 3.10e+00 1.04e-01 7.08e+02 dihedral pdb=" C4' A B 28 " pdb=" C3' A B 28 " pdb=" C2' A B 28 " pdb=" C1' A B 28 " ideal model delta sinusoidal sigma weight residual 36.35 -36.53 72.87 1 3.10e+00 1.04e-01 7.05e+02 ... (remaining 4874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1141 0.061 - 0.123: 83 0.123 - 0.184: 5 0.184 - 0.245: 102 0.245 - 0.306: 23 Chirality restraints: 1354 Sorted by residual: chirality pdb=" C2' U B -56 " pdb=" C3' U B -56 " pdb=" O2' U B -56 " pdb=" C1' U B -56 " both_signs ideal model delta sigma weight residual False -2.79 -2.48 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C2' G B 23 " pdb=" C3' G B 23 " pdb=" O2' G B 23 " pdb=" C1' G B 23 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C2' G B -67 " pdb=" C3' G B -67 " pdb=" O2' G B -67 " pdb=" C1' G B -67 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 1351 not shown) Planarity restraints: 1162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 583 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO A 584 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 584 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 584 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G B 4 " 0.018 2.00e-02 2.50e+03 9.03e-03 2.44e+00 pdb=" N9 G B 4 " -0.025 2.00e-02 2.50e+03 pdb=" C8 G B 4 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G B 4 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G B 4 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G B 4 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G B 4 " 0.002 2.00e-02 2.50e+03 pdb=" N1 G B 4 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G B 4 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 4 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G B 4 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G B 4 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B -24 " -0.019 2.00e-02 2.50e+03 8.87e-03 2.16e+00 pdb=" N9 A B -24 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A B -24 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B -24 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A B -24 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A B -24 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A B -24 " -0.005 2.00e-02 2.50e+03 pdb=" N1 A B -24 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A B -24 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A B -24 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A B -24 " -0.000 2.00e-02 2.50e+03 ... (remaining 1159 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1653 2.77 - 3.30: 7856 3.30 - 3.83: 13459 3.83 - 4.37: 15275 4.37 - 4.90: 23661 Nonbonded interactions: 61904 Sorted by model distance: nonbonded pdb=" OH TYR A 253 " pdb=" OG SER A 335 " model vdw 2.237 3.040 nonbonded pdb=" OE1 GLN A 257 " pdb=" OH TYR A 602 " model vdw 2.250 3.040 nonbonded pdb=" O GLU A 104 " pdb=" OG1 THR A 107 " model vdw 2.255 3.040 nonbonded pdb=" O PHE A 147 " pdb=" OG SER A 150 " model vdw 2.277 3.040 nonbonded pdb=" OE1 GLU A 552 " pdb=" NE ARG A 594 " model vdw 2.303 3.120 ... (remaining 61899 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 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: 0.010 Set scattering table: 0.020 Process input model: 8.720 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8492 Z= 0.142 Angle : 0.729 6.869 11885 Z= 0.357 Chirality : 0.079 0.306 1354 Planarity : 0.003 0.047 1162 Dihedral : 16.987 172.685 3497 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.55 % Allowed : 10.34 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.31), residues: 729 helix: 1.10 (0.25), residues: 419 sheet: -0.24 (1.17), residues: 27 loop : -1.24 (0.34), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 51 TYR 0.013 0.001 TYR A 321 PHE 0.017 0.001 PHE A 638 TRP 0.010 0.001 TRP A 402 HIS 0.003 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 ( 8492) covalent geometry : angle 0.72936 / 0.36 (11885) hydrogen bonds : bond 0.18413 / 11.87 ( 371) hydrogen bonds : angle 5.79611 / 4.24 ( 1014) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.5421 (mtt-85) REVERT: A 518 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7689 (mmmt) REVERT: A 761 MET cc_start: 0.7806 (tpt) cc_final: 0.7345 (tpp) REVERT: A 770 TRP cc_start: 0.5377 (OUTLIER) cc_final: 0.3557 (m-90) outliers start: 29 outliers final: 12 residues processed: 112 average time/residue: 0.1031 time to fit residues: 14.9192 Evaluate side-chains 73 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 518 LYS Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 770 TRP Chi-restraints excluded: chain A residue 771 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 397 HIS A 476 GLN A 561 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.161077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.120825 restraints weight = 15483.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.124719 restraints weight = 8513.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.127192 restraints weight = 6016.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.128487 restraints weight = 4899.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.129431 restraints weight = 4378.344| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8492 Z= 0.143 Angle : 0.854 12.606 11885 Z= 0.363 Chirality : 0.064 0.451 1354 Planarity : 0.004 0.045 1162 Dihedral : 15.662 164.621 2021 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.76 % Allowed : 14.58 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.31), residues: 729 helix: 1.49 (0.25), residues: 431 sheet: -0.16 (1.18), residues: 27 loop : -1.33 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 459 TYR 0.012 0.001 TYR A 321 PHE 0.020 0.001 PHE A 638 TRP 0.010 0.001 TRP A 60 HIS 0.003 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 8492) covalent geometry : angle 0.85393 / 0.36 (11885) hydrogen bonds : bond 0.05649 / 3.72 ( 371) hydrogen bonds : angle 4.07888 / 2.97 ( 1014) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 118 PHE cc_start: 0.7870 (t80) cc_final: 0.7555 (t80) REVERT: A 191 ARG cc_start: 0.6211 (OUTLIER) cc_final: 0.4931 (mtt-85) REVERT: A 608 ARG cc_start: 0.5627 (tpt-90) cc_final: 0.5298 (ttt-90) REVERT: A 657 ARG cc_start: 0.7896 (tpp80) cc_final: 0.7633 (tpp80) REVERT: A 663 MET cc_start: 0.6975 (tpt) cc_final: 0.6675 (tpt) REVERT: A 770 TRP cc_start: 0.5511 (OUTLIER) cc_final: 0.3506 (m-90) outliers start: 24 outliers final: 18 residues processed: 91 average time/residue: 0.0949 time to fit residues: 11.4116 Evaluate side-chains 83 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 770 TRP Chi-restraints excluded: chain A residue 771 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 16 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 0.1980 chunk 47 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 HIS A 353 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.162237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.128022 restraints weight = 15154.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.126590 restraints weight = 9091.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.127917 restraints weight = 7428.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.129395 restraints weight = 6190.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.129462 restraints weight = 5305.982| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8492 Z= 0.124 Angle : 0.774 12.671 11885 Z= 0.331 Chirality : 0.055 0.337 1354 Planarity : 0.003 0.042 1162 Dihedral : 15.227 163.252 2015 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.92 % Allowed : 15.99 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.31), residues: 729 helix: 1.77 (0.25), residues: 422 sheet: -0.22 (1.13), residues: 29 loop : -1.43 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 459 TYR 0.012 0.001 TYR A 321 PHE 0.020 0.001 PHE A 638 TRP 0.009 0.001 TRP A 60 HIS 0.003 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 8492) covalent geometry : angle 0.77435 / 0.33 (11885) hydrogen bonds : bond 0.04714 / 3.03 ( 371) hydrogen bonds : angle 3.74983 / 2.71 ( 1014) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7936 (tm-30) REVERT: A 191 ARG cc_start: 0.6195 (OUTLIER) cc_final: 0.4246 (mtt-85) REVERT: A 334 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7995 (tt) REVERT: A 608 ARG cc_start: 0.5729 (tpt-90) cc_final: 0.5479 (ttt-90) REVERT: A 657 ARG cc_start: 0.7865 (tpp80) cc_final: 0.7368 (tpp80) REVERT: A 698 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7617 (mm-30) REVERT: A 770 TRP cc_start: 0.5535 (OUTLIER) cc_final: 0.3680 (m-90) outliers start: 25 outliers final: 13 residues processed: 84 average time/residue: 0.0862 time to fit residues: 9.7642 Evaluate side-chains 77 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 770 TRP Chi-restraints excluded: chain A residue 771 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 4 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 673 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.155258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.114185 restraints weight = 15487.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.117757 restraints weight = 8738.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.119977 restraints weight = 6266.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.121267 restraints weight = 5158.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.122076 restraints weight = 4609.697| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8492 Z= 0.268 Angle : 0.955 13.097 11885 Z= 0.416 Chirality : 0.069 0.782 1354 Planarity : 0.005 0.048 1162 Dihedral : 15.467 166.725 2007 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 6.11 % Allowed : 17.08 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.30), residues: 729 helix: 1.25 (0.25), residues: 419 sheet: -0.52 (1.05), residues: 31 loop : -1.76 (0.32), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 191 TYR 0.023 0.002 TYR A 321 PHE 0.025 0.002 PHE A 638 TRP 0.014 0.002 TRP A 60 HIS 0.007 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.27 ( 8492) covalent geometry : angle 0.95464 / 0.42 (11885) hydrogen bonds : bond 0.07237 / 4.73 ( 371) hydrogen bonds : angle 4.43476 / 3.19 ( 1014) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 56 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.7967 (ttt-90) REVERT: A 191 ARG cc_start: 0.6340 (OUTLIER) cc_final: 0.5148 (mtt-85) REVERT: A 247 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7819 (mt) REVERT: A 518 LYS cc_start: 0.7513 (mmmt) cc_final: 0.7083 (tptp) REVERT: A 770 TRP cc_start: 0.5591 (OUTLIER) cc_final: 0.3325 (m-90) outliers start: 39 outliers final: 29 residues processed: 89 average time/residue: 0.0899 time to fit residues: 10.6666 Evaluate side-chains 88 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 55 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 770 TRP Chi-restraints excluded: chain A residue 771 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 0.0770 chunk 46 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 26 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.4294 r_free = 0.4294 target = 0.160378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.120126 restraints weight = 15552.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.124005 restraints weight = 8622.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.126450 restraints weight = 6091.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.127841 restraints weight = 4959.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.128765 restraints weight = 4401.228| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8492 Z= 0.118 Angle : 0.785 12.448 11885 Z= 0.336 Chirality : 0.056 0.300 1354 Planarity : 0.003 0.048 1162 Dihedral : 15.158 162.224 2006 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.55 % Allowed : 18.97 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.30), residues: 729 helix: 1.57 (0.25), residues: 422 sheet: -0.28 (1.11), residues: 29 loop : -1.66 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 681 TYR 0.020 0.001 TYR A 471 PHE 0.019 0.001 PHE A 638 TRP 0.011 0.001 TRP A 402 HIS 0.002 0.001 HIS A 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 ( 8492) covalent geometry : angle 0.78537 / 0.34 (11885) hydrogen bonds : bond 0.04812 / 3.03 ( 371) hydrogen bonds : angle 3.73937 / 2.70 ( 1014) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7880 (tm-30) REVERT: A 191 ARG cc_start: 0.6289 (OUTLIER) cc_final: 0.5335 (mtt-85) REVERT: A 334 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7973 (tt) REVERT: A 608 ARG cc_start: 0.5347 (tpt170) cc_final: 0.4673 (tpt-90) REVERT: A 657 ARG cc_start: 0.7869 (tpp80) cc_final: 0.7437 (tpp80) REVERT: A 747 LEU cc_start: 0.8911 (pt) cc_final: 0.8620 (pp) outliers start: 29 outliers final: 20 residues processed: 91 average time/residue: 0.0956 time to fit residues: 11.4936 Evaluate side-chains 82 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 771 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 40 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 0.0040 chunk 9 optimal weight: 0.9980 overall best weight: 1.1396 ------------------------------------------------------------------------------- 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 = 0.4289 r_free = 0.4289 target = 0.160033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.119744 restraints weight = 15177.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.123548 restraints weight = 8489.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.125865 restraints weight = 6019.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.127306 restraints weight = 4917.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.128097 restraints weight = 4359.525| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8492 Z= 0.133 Angle : 0.790 12.260 11885 Z= 0.338 Chirality : 0.056 0.340 1354 Planarity : 0.004 0.048 1162 Dihedral : 15.051 162.334 2004 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.86 % Allowed : 18.65 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.31), residues: 729 helix: 1.68 (0.25), residues: 422 sheet: -0.29 (1.11), residues: 29 loop : -1.68 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 681 TYR 0.013 0.001 TYR A 321 PHE 0.022 0.001 PHE A 638 TRP 0.010 0.001 TRP A 402 HIS 0.003 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 8492) covalent geometry : angle 0.78977 / 0.34 (11885) hydrogen bonds : bond 0.04974 / 3.17 ( 371) hydrogen bonds : angle 3.71159 / 2.69 ( 1014) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 65 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7933 (tm-30) REVERT: A 191 ARG cc_start: 0.6188 (OUTLIER) cc_final: 0.5203 (mtt-85) REVERT: A 247 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7686 (mt) REVERT: A 334 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7965 (tt) REVERT: A 657 ARG cc_start: 0.7825 (tpp80) cc_final: 0.7376 (tpp80) outliers start: 31 outliers final: 22 residues processed: 92 average time/residue: 0.0884 time to fit residues: 11.1273 Evaluate side-chains 87 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 771 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 32 optimal weight: 0.0770 chunk 23 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.2544 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.159303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.118701 restraints weight = 15756.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.122477 restraints weight = 8949.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.124796 restraints weight = 6418.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.126216 restraints weight = 5276.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.126962 restraints weight = 4699.147| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8492 Z= 0.136 Angle : 0.789 12.240 11885 Z= 0.338 Chirality : 0.057 0.355 1354 Planarity : 0.004 0.048 1162 Dihedral : 15.040 162.174 2004 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 4.55 % Allowed : 19.12 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.31), residues: 729 helix: 1.73 (0.25), residues: 422 sheet: -0.38 (1.10), residues: 29 loop : -1.63 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 681 TYR 0.024 0.001 TYR A 471 PHE 0.023 0.001 PHE A 638 TRP 0.010 0.001 TRP A 60 HIS 0.003 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 8492) covalent geometry : angle 0.78904 / 0.34 (11885) hydrogen bonds : bond 0.05058 / 3.23 ( 371) hydrogen bonds : angle 3.76639 / 2.73 ( 1014) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 63 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7942 (tm-30) REVERT: A 191 ARG cc_start: 0.6228 (OUTLIER) cc_final: 0.5212 (mtt-85) REVERT: A 247 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7672 (mt) REVERT: A 334 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7960 (tt) REVERT: A 657 ARG cc_start: 0.7805 (tpp80) cc_final: 0.7367 (tpp80) REVERT: A 740 ARG cc_start: 0.7811 (ptt90) cc_final: 0.7348 (mmp-170) REVERT: A 770 TRP cc_start: 0.5607 (OUTLIER) cc_final: 0.3499 (m-90) outliers start: 29 outliers final: 20 residues processed: 88 average time/residue: 0.0886 time to fit residues: 10.6887 Evaluate side-chains 84 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 770 TRP Chi-restraints excluded: chain A residue 771 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 70 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.4292 r_free = 0.4292 target = 0.160171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.119759 restraints weight = 15620.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.123534 restraints weight = 8943.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.125862 restraints weight = 6421.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.127087 restraints weight = 5283.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.128018 restraints weight = 4743.968| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8492 Z= 0.127 Angle : 0.777 12.369 11885 Z= 0.333 Chirality : 0.056 0.322 1354 Planarity : 0.003 0.047 1162 Dihedral : 14.991 161.764 2003 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.39 % Allowed : 19.44 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.31), residues: 729 helix: 1.76 (0.25), residues: 422 sheet: -0.29 (1.10), residues: 29 loop : -1.63 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 681 TYR 0.024 0.001 TYR A 175 PHE 0.021 0.001 PHE A 638 TRP 0.010 0.001 TRP A 60 HIS 0.003 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 ( 8492) covalent geometry : angle 0.77683 / 0.33 (11885) hydrogen bonds : bond 0.04842 / 3.08 ( 371) hydrogen bonds : angle 3.69111 / 2.67 ( 1014) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7966 (tm-30) REVERT: A 191 ARG cc_start: 0.6332 (OUTLIER) cc_final: 0.5083 (mtt-85) REVERT: A 247 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7666 (mt) REVERT: A 334 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7955 (tt) REVERT: A 357 ILE cc_start: 0.8365 (mm) cc_final: 0.8137 (tt) REVERT: A 608 ARG cc_start: 0.5560 (tpt-90) cc_final: 0.5299 (tpt-90) REVERT: A 657 ARG cc_start: 0.7870 (tpp80) cc_final: 0.7427 (tpp80) REVERT: A 740 ARG cc_start: 0.7812 (ptt90) cc_final: 0.7427 (mmp-170) outliers start: 28 outliers final: 23 residues processed: 88 average time/residue: 0.0932 time to fit residues: 10.9885 Evaluate side-chains 86 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 771 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 = 0.4283 r_free = 0.4283 target = 0.159355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.118759 restraints weight = 15675.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.122467 restraints weight = 8992.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.124822 restraints weight = 6468.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.126215 restraints weight = 5323.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.126833 restraints weight = 4742.943| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8492 Z= 0.145 Angle : 0.799 12.285 11885 Z= 0.345 Chirality : 0.057 0.359 1354 Planarity : 0.004 0.048 1162 Dihedral : 14.997 161.915 2003 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.55 % Allowed : 19.59 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.31), residues: 729 helix: 1.71 (0.25), residues: 422 sheet: -0.36 (1.10), residues: 29 loop : -1.68 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 681 TYR 0.013 0.001 TYR A 321 PHE 0.024 0.002 PHE A 638 TRP 0.010 0.001 TRP A 60 HIS 0.003 0.001 HIS A 554 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 8492) covalent geometry : angle 0.79919 / 0.34 (11885) hydrogen bonds : bond 0.05057 / 3.24 ( 371) hydrogen bonds : angle 3.73875 / 2.71 ( 1014) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7941 (tm-30) REVERT: A 191 ARG cc_start: 0.6335 (OUTLIER) cc_final: 0.5068 (mtt-85) REVERT: A 247 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7729 (mt) REVERT: A 334 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7967 (tt) REVERT: A 657 ARG cc_start: 0.7833 (tpp80) cc_final: 0.7393 (tpp80) REVERT: A 740 ARG cc_start: 0.7797 (ptt90) cc_final: 0.7443 (mmp-170) outliers start: 29 outliers final: 21 residues processed: 88 average time/residue: 0.0812 time to fit residues: 9.6849 Evaluate side-chains 82 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 771 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 0.0040 chunk 60 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.162874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.127910 restraints weight = 15905.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.129810 restraints weight = 9669.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.130715 restraints weight = 7248.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.131069 restraints weight = 6356.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.131704 restraints weight = 6041.462| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8492 Z= 0.113 Angle : 0.763 12.664 11885 Z= 0.328 Chirality : 0.054 0.282 1354 Planarity : 0.003 0.043 1162 Dihedral : 14.880 160.842 2003 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.13 % Allowed : 21.32 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.31), residues: 729 helix: 1.85 (0.25), residues: 422 sheet: -0.24 (1.08), residues: 29 loop : -1.64 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 681 TYR 0.021 0.001 TYR A 471 PHE 0.017 0.001 PHE A 638 TRP 0.011 0.001 TRP A 60 HIS 0.002 0.001 HIS A 353 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 8492) covalent geometry : angle 0.76321 / 0.33 (11885) hydrogen bonds : bond 0.04320 / 2.72 ( 371) hydrogen bonds : angle 3.57266 / 2.59 ( 1014) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1458 Ramachandran restraints generated. 729 Oldfield, 0 Emsley, 729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7968 (tm-30) REVERT: A 191 ARG cc_start: 0.6359 (OUTLIER) cc_final: 0.4975 (mtt-85) REVERT: A 334 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7882 (tt) REVERT: A 657 ARG cc_start: 0.7918 (tpp80) cc_final: 0.7494 (tpp80) REVERT: A 698 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7529 (mm-30) REVERT: A 740 ARG cc_start: 0.7650 (ptt90) cc_final: 0.7410 (mmp-170) outliers start: 20 outliers final: 17 residues processed: 86 average time/residue: 0.0955 time to fit residues: 11.0795 Evaluate side-chains 78 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 98 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 191 ARG Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 433 PHE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 771 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 6 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 64 optimal weight: 0.1980 chunk 48 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 58 optimal weight: 0.0030 overall best weight: 2.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.156427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.115314 restraints weight = 15936.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.118955 restraints weight = 9197.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.121234 restraints weight = 6640.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.122610 restraints weight = 5471.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.123396 restraints weight = 4879.415| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8492 Z= 0.214 Angle : 0.883 12.024 11885 Z= 0.386 Chirality : 0.063 0.573 1354 Planarity : 0.004 0.048 1162 Dihedral : 15.070 162.614 2001 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.92 % Allowed : 20.85 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.31), residues: 729 helix: 1.52 (0.25), residues: 422 sheet: -0.50 (1.10), residues: 29 loop : -1.78 (0.33), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 681 TYR 0.018 0.002 TYR A 321 PHE 0.025 0.002 PHE A 638 TRP 0.010 0.002 TRP A 60 HIS 0.004 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.21 ( 8492) covalent geometry : angle 0.88321 / 0.39 (11885) hydrogen bonds : bond 0.06145 / 4.01 ( 371) hydrogen bonds : angle 3.99793 / 2.88 ( 1014) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1434.64 seconds wall clock time: 25 minutes 24.31 seconds (1524.31 seconds total)