Starting phenix.real_space_refine on Tue Mar 11 18:28:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fdk_31546/03_2025/7fdk_31546.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fdk_31546/03_2025/7fdk_31546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fdk_31546/03_2025/7fdk_31546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fdk_31546/03_2025/7fdk_31546.map" model { file = "/net/cci-nas-00/data/ceres_data/7fdk_31546/03_2025/7fdk_31546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fdk_31546/03_2025/7fdk_31546.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.004 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4113 2.51 5 N 1076 2.21 5 O 1223 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6449 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4867 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4860 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 26, 'TRANS': 570} Conformer: "B" Number of residues, atoms: 597, 4860 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 26, 'TRANS': 570} bond proxies already assigned to first conformer: 4986 Chain: "E" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1540 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.71, per 1000 atoms: 1.04 Number of scatterers: 6449 At special positions: 0 Unit cell: (118.56, 83.2, 80.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1223 8.00 N 1076 7.00 C 4113 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 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 Links applied NAG-ASN " NAG A 701 " - " ASN A 546 " " NAG A 702 " - " ASN A 53 " " NAG E 601 " - " ASN E 343 " Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 1.5 seconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 6 sheets defined 50.8% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.883A pdb=" N ASN A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 79 removed outlier: 4.058A pdb=" N SER A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU A 64 " --> pdb=" O GLN A 60 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 144 through 148 Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.614A pdb=" N THR A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 194 Proline residue: A 178 - end of helix removed outlier: 3.962A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 231 removed outlier: 4.171A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.540A pdb=" N LYS A 247 " --> pdb=" O TYR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.561A pdb=" N THR A 282 " --> pdb=" O TYR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.526A pdb=" N ALA A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.808A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 383 removed outlier: 4.248A pdb=" N ALA A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 411 removed outlier: 4.328A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 465 removed outlier: 4.036A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.549A pdb=" N ARG A 465 " --> pdb=" O TRP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 485 Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.439A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 4.528A pdb=" N LEU A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.529A pdb=" N ALA A 569 " --> pdb=" O PRO A 565 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 383 through 390 Processing helix chain 'E' and resid 403 through 407 removed outlier: 3.638A pdb=" N GLU E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.524A pdb=" N ASP E 442 " --> pdb=" O SER E 438 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.405A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.426A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 355 removed outlier: 4.005A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE E 402 " --> pdb=" O TYR E 508 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 270 hydrogen bonds defined for protein. 788 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2071 1.34 - 1.46: 1721 1.46 - 1.58: 2781 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6631 Sorted by residual: bond pdb=" C LYS A 359 " pdb=" N MET A 360 " ideal model delta sigma weight residual 1.330 1.535 -0.205 1.23e-02 6.61e+03 2.79e+02 bond pdb=" C ILE A 358 " pdb=" N LYS A 359 " ideal model delta sigma weight residual 1.331 1.551 -0.221 1.66e-02 3.63e+03 1.77e+02 bond pdb=" C ALA E 397 " pdb=" N ASP E 398 " ideal model delta sigma weight residual 1.328 1.432 -0.104 1.42e-02 4.96e+03 5.37e+01 bond pdb=" C ASP E 398 " pdb=" N SER E 399 " ideal model delta sigma weight residual 1.332 1.392 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" C SER A 563 " pdb=" N GLU A 564 " ideal model delta sigma weight residual 1.335 1.231 0.104 3.04e-02 1.08e+03 1.16e+01 ... (remaining 6626 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 8756 2.24 - 4.47: 219 4.47 - 6.71: 29 6.71 - 8.95: 2 8.95 - 11.18: 4 Bond angle restraints: 9010 Sorted by residual: angle pdb=" O ILE A 358 " pdb=" C ILE A 358 " pdb=" N LYS A 359 " ideal model delta sigma weight residual 123.26 134.44 -11.18 1.08e+00 8.57e-01 1.07e+02 angle pdb=" CA ILE A 358 " pdb=" C ILE A 358 " pdb=" N LYS A 359 " ideal model delta sigma weight residual 116.31 105.62 10.69 1.14e+00 7.69e-01 8.79e+01 angle pdb=" N GLN A 86 " pdb=" CA GLN A 86 " pdb=" C GLN A 86 " ideal model delta sigma weight residual 114.56 108.10 6.46 1.27e+00 6.20e-01 2.59e+01 angle pdb=" O ALA E 397 " pdb=" C ALA E 397 " pdb=" N ASP E 398 " ideal model delta sigma weight residual 123.27 129.19 -5.92 1.17e+00 7.31e-01 2.56e+01 angle pdb=" CA ALA E 397 " pdb=" C ALA E 397 " pdb=" N ASP E 398 " ideal model delta sigma weight residual 116.45 110.39 6.06 1.23e+00 6.61e-01 2.43e+01 ... (remaining 9005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 3478 17.73 - 35.45: 361 35.45 - 53.18: 74 53.18 - 70.91: 18 70.91 - 88.64: 10 Dihedral angle restraints: 3941 sinusoidal: 1615 harmonic: 2326 Sorted by residual: dihedral pdb=" CA GLU A 145 " pdb=" C GLU A 145 " pdb=" N PRO A 146 " pdb=" CA PRO A 146 " ideal model delta harmonic sigma weight residual -180.00 -130.48 -49.52 0 5.00e+00 4.00e-02 9.81e+01 dihedral pdb=" CA VAL A 581 " pdb=" C VAL A 581 " pdb=" N LYS A 582 " pdb=" CA LYS A 582 " ideal model delta harmonic sigma weight residual 180.00 150.16 29.84 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA CYS E 361 " pdb=" C CYS E 361 " pdb=" N VAL E 362 " pdb=" CA VAL E 362 " ideal model delta harmonic sigma weight residual 180.00 151.67 28.33 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 3938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 523 0.036 - 0.072: 311 0.072 - 0.108: 84 0.108 - 0.144: 22 0.144 - 0.180: 4 Chirality restraints: 944 Sorted by residual: chirality pdb=" C1 NAG E 601 " pdb=" ND2 ASN E 343 " pdb=" C2 NAG E 601 " pdb=" O5 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.11e-01 chirality pdb=" CA PRO E 337 " pdb=" N PRO E 337 " pdb=" C PRO E 337 " pdb=" CB PRO E 337 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.60e-01 chirality pdb=" CA ILE E 434 " pdb=" N ILE E 434 " pdb=" C ILE E 434 " pdb=" CB ILE E 434 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.57e-01 ... (remaining 941 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.64e+00 pdb=" N PRO A 146 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 453 " 0.021 2.00e-02 2.50e+03 1.68e-02 5.68e+00 pdb=" CG TYR E 453 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR E 453 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR E 453 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 453 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR E 453 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR E 453 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 453 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 388 " -0.039 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO A 389 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 389 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 389 " -0.031 5.00e-02 4.00e+02 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 138 2.64 - 3.21: 6520 3.21 - 3.77: 9963 3.77 - 4.34: 13424 4.34 - 4.90: 21531 Nonbonded interactions: 51576 Sorted by model distance: nonbonded pdb=" OH TYR A 41 " pdb=" O THR E 500 " model vdw 2.080 3.040 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.113 3.040 nonbonded pdb=" OH TYR A 535 " pdb=" O SER A 538 " model vdw 2.117 3.040 nonbonded pdb=" O ILE E 418 " pdb=" N ASP E 420 " model vdw 2.122 3.120 nonbonded pdb=" OH TYR A 535 " pdb=" O LYS A 541 " model vdw 2.156 3.040 ... (remaining 51571 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=0.50 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: 0.620 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.460 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 : 0.008 0.221 6631 Z= 0.546 Angle : 0.882 11.185 9010 Z= 0.522 Chirality : 0.048 0.180 944 Planarity : 0.006 0.069 1167 Dihedral : 15.522 88.637 2442 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.21 % Favored : 86.66 % Rotamer: Outliers : 0.29 % Allowed : 6.83 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.24), residues: 788 helix: -2.30 (0.21), residues: 373 sheet: -3.02 (0.68), residues: 44 loop : -3.82 (0.27), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 302 HIS 0.006 0.002 HIS A 378 PHE 0.028 0.003 PHE A 390 TYR 0.041 0.002 TYR E 453 ARG 0.003 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 HIS cc_start: 0.8167 (p-80) cc_final: 0.7876 (p90) REVERT: A 297 MET cc_start: 0.6037 (ptt) cc_final: 0.5796 (ptp) REVERT: A 454 TYR cc_start: 0.7576 (t80) cc_final: 0.7248 (t80) REVERT: E 346 ARG cc_start: 0.7135 (ttm110) cc_final: 0.5726 (ptt180) REVERT: E 356 LYS cc_start: 0.8944 (tttm) cc_final: 0.8680 (ttmt) REVERT: E 357 ARG cc_start: 0.8591 (ttt90) cc_final: 0.6566 (mtt180) REVERT: E 424 LYS cc_start: 0.8907 (tptp) cc_final: 0.8506 (tttp) REVERT: E 451 TYR cc_start: 0.8044 (m-80) cc_final: 0.7096 (m-80) REVERT: E 462 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8407 (mtpp) REVERT: E 465 GLU cc_start: 0.6060 (tp30) cc_final: 0.5740 (tp30) REVERT: E 466 ARG cc_start: 0.8504 (ttm110) cc_final: 0.8212 (ttm110) REVERT: E 467 ASP cc_start: 0.7996 (t0) cc_final: 0.7492 (t70) REVERT: E 508 TYR cc_start: 0.8344 (m-80) cc_final: 0.7998 (m-80) outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.2552 time to fit residues: 32.0267 Evaluate side-chains 77 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 33 ASN A 34 GLN A 134 ASN A 195 ASN A 388 GLN A 522 GLN A 599 ASN E 460 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.141136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.111690 restraints weight = 19853.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.113934 restraints weight = 10495.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.114242 restraints weight = 9184.879| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6631 Z= 0.238 Angle : 0.675 8.228 9010 Z= 0.345 Chirality : 0.044 0.217 944 Planarity : 0.006 0.062 1167 Dihedral : 7.028 58.281 932 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.53 % Favored : 90.34 % Rotamer: Outliers : 1.45 % Allowed : 11.19 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.27), residues: 788 helix: -0.68 (0.25), residues: 370 sheet: -2.75 (0.64), residues: 50 loop : -3.23 (0.28), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 163 HIS 0.004 0.001 HIS A 373 PHE 0.017 0.002 PHE A 390 TYR 0.016 0.002 TYR E 495 ARG 0.006 0.001 ARG E 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6638 (mm-40) cc_final: 0.6171 (pp30) REVERT: A 152 MET cc_start: 0.6774 (mtp) cc_final: 0.6477 (ttm) REVERT: A 265 HIS cc_start: 0.8110 (p-80) cc_final: 0.7661 (p90) REVERT: A 383 MET cc_start: 0.8693 (ttt) cc_final: 0.8384 (ttt) REVERT: A 557 MET cc_start: 0.8861 (tmm) cc_final: 0.8622 (tmm) REVERT: E 347 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.6294 (m-80) REVERT: E 357 ARG cc_start: 0.8546 (ttt90) cc_final: 0.6465 (mtt180) REVERT: E 424 LYS cc_start: 0.8848 (tptp) cc_final: 0.8401 (tttp) REVERT: E 451 TYR cc_start: 0.8006 (m-80) cc_final: 0.6886 (m-80) REVERT: E 462 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8387 (mtpp) REVERT: E 467 ASP cc_start: 0.7803 (t0) cc_final: 0.7312 (t70) REVERT: E 495 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.8115 (p90) REVERT: E 508 TYR cc_start: 0.8363 (m-80) cc_final: 0.7953 (m-80) outliers start: 9 outliers final: 5 residues processed: 101 average time/residue: 0.2220 time to fit residues: 29.0404 Evaluate side-chains 87 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 501 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 28 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.143048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.113821 restraints weight = 20231.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.116757 restraints weight = 13366.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.117282 restraints weight = 9279.358| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6631 Z= 0.215 Angle : 0.635 7.628 9010 Z= 0.323 Chirality : 0.043 0.206 944 Planarity : 0.005 0.058 1167 Dihedral : 6.470 56.614 932 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.89 % Favored : 90.98 % Rotamer: Outliers : 2.18 % Allowed : 12.50 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.29), residues: 788 helix: -0.01 (0.27), residues: 369 sheet: -2.12 (0.68), residues: 48 loop : -2.76 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 163 HIS 0.005 0.001 HIS A 378 PHE 0.017 0.002 PHE A 390 TYR 0.019 0.002 TYR A 252 ARG 0.005 0.001 ARG E 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6569 (mm-40) cc_final: 0.6254 (pp30) REVERT: A 265 HIS cc_start: 0.7943 (p-80) cc_final: 0.7473 (p90) REVERT: A 402 GLU cc_start: 0.6991 (tp30) cc_final: 0.6467 (mp0) REVERT: A 557 MET cc_start: 0.8849 (tmm) cc_final: 0.8642 (tmm) REVERT: A 591 LEU cc_start: 0.8253 (tt) cc_final: 0.7942 (tt) REVERT: E 347 PHE cc_start: 0.7047 (OUTLIER) cc_final: 0.6216 (m-80) REVERT: E 356 LYS cc_start: 0.8726 (tttt) cc_final: 0.7753 (mmtt) REVERT: E 357 ARG cc_start: 0.8574 (ttt90) cc_final: 0.6473 (mtt180) REVERT: E 424 LYS cc_start: 0.8838 (tptp) cc_final: 0.8321 (tttm) REVERT: E 451 TYR cc_start: 0.8005 (m-80) cc_final: 0.6854 (m-80) REVERT: E 462 LYS cc_start: 0.8617 (mtpt) cc_final: 0.8356 (mtpp) REVERT: E 467 ASP cc_start: 0.7709 (t0) cc_final: 0.7171 (t70) REVERT: E 495 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.7978 (p90) REVERT: E 508 TYR cc_start: 0.8222 (m-80) cc_final: 0.7856 (m-80) outliers start: 14 outliers final: 8 residues processed: 111 average time/residue: 0.2109 time to fit residues: 31.1049 Evaluate side-chains 97 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 501 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 59 optimal weight: 0.0870 chunk 58 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 12 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.3164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.144512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.114102 restraints weight = 26554.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.119293 restraints weight = 16601.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.119619 restraints weight = 8675.286| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6631 Z= 0.210 Angle : 0.633 7.164 9010 Z= 0.317 Chirality : 0.043 0.199 944 Planarity : 0.005 0.056 1167 Dihedral : 5.926 56.370 932 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.28 % Favored : 90.60 % Rotamer: Outliers : 2.33 % Allowed : 14.39 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.30), residues: 788 helix: 0.28 (0.27), residues: 378 sheet: -2.00 (0.67), residues: 46 loop : -2.50 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.005 0.001 HIS A 378 PHE 0.016 0.002 PHE A 390 TYR 0.015 0.001 TYR E 495 ARG 0.004 0.000 ARG E 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6579 (mm-40) cc_final: 0.6302 (pp30) REVERT: A 265 HIS cc_start: 0.7916 (p-80) cc_final: 0.7519 (p90) REVERT: A 270 MET cc_start: 0.6027 (tpp) cc_final: 0.5132 (tpp) REVERT: A 402 GLU cc_start: 0.7093 (tp30) cc_final: 0.6579 (mp0) REVERT: A 591 LEU cc_start: 0.8256 (tt) cc_final: 0.7941 (tt) REVERT: E 347 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.6209 (m-80) REVERT: E 356 LYS cc_start: 0.8660 (tttt) cc_final: 0.7746 (mmtt) REVERT: E 357 ARG cc_start: 0.8559 (ttt90) cc_final: 0.6429 (mtt180) REVERT: E 424 LYS cc_start: 0.8852 (tptp) cc_final: 0.8361 (tttm) REVERT: E 451 TYR cc_start: 0.7998 (m-80) cc_final: 0.6948 (m-80) REVERT: E 462 LYS cc_start: 0.8592 (mtpt) cc_final: 0.8320 (mtpp) REVERT: E 495 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.8098 (p90) REVERT: E 508 TYR cc_start: 0.8249 (m-80) cc_final: 0.7883 (m-80) outliers start: 15 outliers final: 7 residues processed: 101 average time/residue: 0.2469 time to fit residues: 32.8664 Evaluate side-chains 92 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 501 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.145013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.115575 restraints weight = 20193.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.119589 restraints weight = 12825.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.120282 restraints weight = 7966.222| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3628 r_free = 0.3628 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6631 Z= 0.206 Angle : 0.630 7.048 9010 Z= 0.315 Chirality : 0.043 0.197 944 Planarity : 0.005 0.055 1167 Dihedral : 5.564 55.905 932 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.39 % Favored : 91.49 % Rotamer: Outliers : 2.33 % Allowed : 15.41 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.30), residues: 788 helix: 0.33 (0.27), residues: 382 sheet: -1.75 (0.70), residues: 46 loop : -2.38 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.005 0.001 HIS A 378 PHE 0.017 0.002 PHE A 512 TYR 0.019 0.001 TYR A 50 ARG 0.005 0.000 ARG E 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6614 (mm-40) cc_final: 0.6376 (pp30) REVERT: A 249 MET cc_start: 0.8050 (tpp) cc_final: 0.7778 (tpp) REVERT: A 265 HIS cc_start: 0.8007 (p-80) cc_final: 0.7757 (p90) REVERT: A 267 LEU cc_start: 0.8411 (mt) cc_final: 0.7781 (mt) REVERT: A 402 GLU cc_start: 0.6724 (tp30) cc_final: 0.6521 (mp0) REVERT: A 591 LEU cc_start: 0.8187 (tt) cc_final: 0.7858 (tt) REVERT: E 347 PHE cc_start: 0.6974 (OUTLIER) cc_final: 0.6168 (m-80) REVERT: E 356 LYS cc_start: 0.8595 (tttt) cc_final: 0.7718 (mmtt) REVERT: E 357 ARG cc_start: 0.8530 (ttt90) cc_final: 0.6470 (mtt180) REVERT: E 424 LYS cc_start: 0.8827 (tptp) cc_final: 0.8323 (tttm) REVERT: E 451 TYR cc_start: 0.7906 (m-80) cc_final: 0.6880 (m-80) REVERT: E 462 LYS cc_start: 0.8530 (mtpt) cc_final: 0.8257 (mtpp) REVERT: E 495 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.8087 (p90) REVERT: E 508 TYR cc_start: 0.8275 (m-80) cc_final: 0.7887 (m-80) REVERT: E 515 PHE cc_start: 0.7003 (m-80) cc_final: 0.6783 (m-80) outliers start: 15 outliers final: 10 residues processed: 103 average time/residue: 0.2208 time to fit residues: 29.9169 Evaluate side-chains 96 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 501 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.143093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.113347 restraints weight = 22162.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.117981 restraints weight = 13473.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.117797 restraints weight = 9835.086| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6631 Z= 0.263 Angle : 0.660 7.661 9010 Z= 0.328 Chirality : 0.043 0.200 944 Planarity : 0.005 0.053 1167 Dihedral : 5.633 56.138 932 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.15 % Favored : 90.72 % Rotamer: Outliers : 2.18 % Allowed : 16.42 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.30), residues: 788 helix: 0.35 (0.27), residues: 379 sheet: -1.52 (0.73), residues: 46 loop : -2.35 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.005 0.001 HIS A 378 PHE 0.019 0.002 PHE A 390 TYR 0.018 0.002 TYR E 495 ARG 0.005 0.000 ARG E 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.704 Fit side-chains REVERT: A 139 GLN cc_start: 0.6672 (mm-40) cc_final: 0.6435 (pp30) REVERT: A 148 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7394 (mt) REVERT: A 161 ARG cc_start: 0.7136 (mtp180) cc_final: 0.6590 (ttm170) REVERT: A 249 MET cc_start: 0.8008 (tpp) cc_final: 0.7591 (tpp) REVERT: A 265 HIS cc_start: 0.8041 (p-80) cc_final: 0.7185 (p90) REVERT: A 267 LEU cc_start: 0.8429 (mt) cc_final: 0.7768 (mt) REVERT: A 298 MET cc_start: 0.8230 (mmm) cc_final: 0.7992 (mpp) REVERT: A 402 GLU cc_start: 0.7187 (tp30) cc_final: 0.6660 (mp0) REVERT: A 474 MET cc_start: 0.6903 (mmp) cc_final: 0.6621 (mmp) REVERT: A 489 GLU cc_start: 0.7397 (pt0) cc_final: 0.6539 (pt0) REVERT: E 347 PHE cc_start: 0.7091 (OUTLIER) cc_final: 0.6186 (m-80) REVERT: E 356 LYS cc_start: 0.8563 (tttt) cc_final: 0.7615 (mmtt) REVERT: E 357 ARG cc_start: 0.8580 (ttt90) cc_final: 0.6532 (mtt180) REVERT: E 424 LYS cc_start: 0.8880 (tptp) cc_final: 0.8365 (tttm) REVERT: E 451 TYR cc_start: 0.7974 (m-80) cc_final: 0.6925 (m-80) REVERT: E 462 LYS cc_start: 0.8600 (mtpt) cc_final: 0.8319 (mtpp) REVERT: E 495 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.8142 (p90) REVERT: E 508 TYR cc_start: 0.8333 (m-80) cc_final: 0.7979 (m-80) REVERT: E 516 GLU cc_start: 0.6800 (pm20) cc_final: 0.6438 (pm20) outliers start: 14 outliers final: 11 residues processed: 98 average time/residue: 0.2227 time to fit residues: 28.0806 Evaluate side-chains 97 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 53 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 28 optimal weight: 0.0470 chunk 3 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.146491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.117463 restraints weight = 26372.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.123410 restraints weight = 16843.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.124150 restraints weight = 6854.063| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6631 Z= 0.184 Angle : 0.624 7.789 9010 Z= 0.310 Chirality : 0.042 0.197 944 Planarity : 0.005 0.052 1167 Dihedral : 5.382 55.452 932 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 2.33 % Allowed : 17.30 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.30), residues: 788 helix: 0.49 (0.27), residues: 380 sheet: -1.33 (0.74), residues: 46 loop : -2.16 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.004 0.001 HIS A 378 PHE 0.012 0.001 PHE A 390 TYR 0.016 0.001 TYR A 50 ARG 0.009 0.001 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 161 ARG cc_start: 0.7258 (mtp180) cc_final: 0.6856 (ttm170) REVERT: A 265 HIS cc_start: 0.7888 (p-80) cc_final: 0.7255 (p90) REVERT: A 267 LEU cc_start: 0.8260 (mt) cc_final: 0.7657 (mt) REVERT: A 402 GLU cc_start: 0.6766 (tp30) cc_final: 0.6308 (mp0) REVERT: A 474 MET cc_start: 0.6734 (mmp) cc_final: 0.6513 (mmp) REVERT: A 480 MET cc_start: 0.8035 (mtp) cc_final: 0.7627 (mtm) REVERT: A 489 GLU cc_start: 0.7267 (pt0) cc_final: 0.6584 (pt0) REVERT: A 557 MET cc_start: 0.8767 (tmm) cc_final: 0.8513 (tmm) REVERT: A 591 LEU cc_start: 0.8213 (tt) cc_final: 0.7875 (tt) REVERT: E 356 LYS cc_start: 0.8462 (tttt) cc_final: 0.7609 (mmtt) REVERT: E 357 ARG cc_start: 0.8553 (ttt90) cc_final: 0.6517 (mtt180) REVERT: E 424 LYS cc_start: 0.8866 (tptp) cc_final: 0.8362 (tttm) REVERT: E 451 TYR cc_start: 0.7888 (m-80) cc_final: 0.6763 (m-80) REVERT: E 462 LYS cc_start: 0.8498 (mtpt) cc_final: 0.8231 (mtpp) REVERT: E 495 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.7980 (p90) REVERT: E 508 TYR cc_start: 0.8330 (m-80) cc_final: 0.7957 (m-80) REVERT: E 516 GLU cc_start: 0.6857 (pm20) cc_final: 0.6581 (pm20) outliers start: 15 outliers final: 10 residues processed: 106 average time/residue: 0.2456 time to fit residues: 33.8996 Evaluate side-chains 96 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 501 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 37 optimal weight: 0.0770 chunk 15 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 66 optimal weight: 0.2980 overall best weight: 1.4140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.146744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.117247 restraints weight = 16939.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.116984 restraints weight = 10167.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.118708 restraints weight = 7724.521| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6631 Z= 0.217 Angle : 0.646 7.919 9010 Z= 0.323 Chirality : 0.042 0.195 944 Planarity : 0.005 0.052 1167 Dihedral : 5.391 55.431 932 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.26 % Favored : 91.61 % Rotamer: Outliers : 2.03 % Allowed : 17.88 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.30), residues: 788 helix: 0.52 (0.27), residues: 379 sheet: -1.16 (0.75), residues: 46 loop : -2.13 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.005 0.001 HIS A 378 PHE 0.017 0.002 PHE A 390 TYR 0.020 0.002 TYR A 50 ARG 0.006 0.000 ARG E 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 ARG cc_start: 0.7085 (mtp180) cc_final: 0.6559 (ttm170) REVERT: A 249 MET cc_start: 0.7919 (tpp) cc_final: 0.7625 (tpp) REVERT: A 265 HIS cc_start: 0.7982 (p-80) cc_final: 0.7191 (p90) REVERT: A 480 MET cc_start: 0.8071 (mtp) cc_final: 0.7613 (mtm) REVERT: A 489 GLU cc_start: 0.7485 (pt0) cc_final: 0.6639 (pt0) REVERT: A 557 MET cc_start: 0.8749 (tmm) cc_final: 0.8535 (tmm) REVERT: A 591 LEU cc_start: 0.8236 (tt) cc_final: 0.7874 (tt) REVERT: E 347 PHE cc_start: 0.6931 (OUTLIER) cc_final: 0.6174 (m-80) REVERT: E 356 LYS cc_start: 0.8444 (tttt) cc_final: 0.7639 (mptt) REVERT: E 357 ARG cc_start: 0.8596 (ttt90) cc_final: 0.6542 (mtt180) REVERT: E 424 LYS cc_start: 0.8858 (tptp) cc_final: 0.8367 (tttm) REVERT: E 451 TYR cc_start: 0.7806 (m-80) cc_final: 0.6924 (m-80) REVERT: E 462 LYS cc_start: 0.8531 (mtpt) cc_final: 0.8275 (mtpp) REVERT: E 495 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.8071 (p90) REVERT: E 508 TYR cc_start: 0.8214 (m-80) cc_final: 0.7858 (m-80) outliers start: 13 outliers final: 9 residues processed: 96 average time/residue: 0.2348 time to fit residues: 29.3050 Evaluate side-chains 94 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 20 optimal weight: 0.0270 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.150816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.119539 restraints weight = 14422.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.122261 restraints weight = 7875.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.122989 restraints weight = 5860.923| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3684 r_free = 0.3684 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6631 Z= 0.178 Angle : 0.629 7.542 9010 Z= 0.314 Chirality : 0.041 0.191 944 Planarity : 0.005 0.051 1167 Dihedral : 5.137 54.786 932 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 1.89 % Allowed : 18.02 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.30), residues: 788 helix: 0.61 (0.27), residues: 382 sheet: -1.00 (0.77), residues: 46 loop : -2.01 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 477 HIS 0.006 0.001 HIS E 493 PHE 0.012 0.001 PHE A 390 TYR 0.021 0.001 TYR A 50 ARG 0.007 0.000 ARG E 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 148 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7322 (mt) REVERT: A 161 ARG cc_start: 0.7156 (mtp180) cc_final: 0.6614 (ttm170) REVERT: A 249 MET cc_start: 0.7677 (tpp) cc_final: 0.7386 (tpp) REVERT: A 265 HIS cc_start: 0.7928 (p-80) cc_final: 0.7161 (p90) REVERT: A 267 LEU cc_start: 0.8201 (mt) cc_final: 0.7581 (mt) REVERT: A 474 MET cc_start: 0.6410 (mmp) cc_final: 0.6018 (mmm) REVERT: A 480 MET cc_start: 0.7926 (mtp) cc_final: 0.7492 (mtm) REVERT: A 557 MET cc_start: 0.8699 (tmm) cc_final: 0.8495 (tmm) REVERT: A 591 LEU cc_start: 0.8136 (tt) cc_final: 0.7799 (tt) REVERT: E 356 LYS cc_start: 0.8215 (tttt) cc_final: 0.7574 (mptt) REVERT: E 357 ARG cc_start: 0.8565 (ttt90) cc_final: 0.6522 (mtt180) REVERT: E 424 LYS cc_start: 0.8676 (tptp) cc_final: 0.8450 (tttm) REVERT: E 451 TYR cc_start: 0.7696 (m-80) cc_final: 0.6853 (m-80) REVERT: E 462 LYS cc_start: 0.8354 (mtpt) cc_final: 0.8109 (mtpp) REVERT: E 474 GLN cc_start: 0.7366 (tt0) cc_final: 0.6891 (pm20) REVERT: E 508 TYR cc_start: 0.8449 (m-80) cc_final: 0.8154 (m-80) outliers start: 12 outliers final: 8 residues processed: 103 average time/residue: 0.2299 time to fit residues: 30.8540 Evaluate side-chains 97 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 501 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 12 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 68 optimal weight: 0.0970 chunk 29 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 GLN E 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.146659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.115442 restraints weight = 14501.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.117499 restraints weight = 8465.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.118281 restraints weight = 6977.897| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6631 Z= 0.269 Angle : 0.691 7.970 9010 Z= 0.345 Chirality : 0.043 0.195 944 Planarity : 0.005 0.051 1167 Dihedral : 5.256 55.280 930 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.39 % Favored : 91.49 % Rotamer: Outliers : 2.03 % Allowed : 19.19 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.31), residues: 788 helix: 0.56 (0.27), residues: 380 sheet: -1.04 (0.76), residues: 46 loop : -1.99 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.009 0.001 HIS E 493 PHE 0.020 0.002 PHE A 390 TYR 0.022 0.002 TYR A 50 ARG 0.007 0.000 ARG E 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7414 (mt) REVERT: A 161 ARG cc_start: 0.7074 (mtp180) cc_final: 0.6609 (ttm170) REVERT: A 249 MET cc_start: 0.7700 (tpp) cc_final: 0.7416 (tpp) REVERT: A 265 HIS cc_start: 0.7890 (p-80) cc_final: 0.7104 (p90) REVERT: A 480 MET cc_start: 0.7903 (mtp) cc_final: 0.7463 (mtm) REVERT: E 347 PHE cc_start: 0.7006 (OUTLIER) cc_final: 0.6178 (m-80) REVERT: E 356 LYS cc_start: 0.8400 (tttt) cc_final: 0.7673 (mptt) REVERT: E 357 ARG cc_start: 0.8694 (ttt90) cc_final: 0.6661 (mtt180) REVERT: E 424 LYS cc_start: 0.8701 (tptp) cc_final: 0.8401 (tttm) REVERT: E 451 TYR cc_start: 0.7816 (m-80) cc_final: 0.7005 (m-80) REVERT: E 462 LYS cc_start: 0.8511 (mtpt) cc_final: 0.8277 (mtpp) REVERT: E 495 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7963 (p90) REVERT: E 508 TYR cc_start: 0.8464 (m-80) cc_final: 0.8210 (m-80) outliers start: 13 outliers final: 9 residues processed: 94 average time/residue: 0.2188 time to fit residues: 27.3658 Evaluate side-chains 95 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain E residue 347 PHE Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 402 ILE Chi-restraints excluded: chain E residue 432 CYS Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 50 optimal weight: 0.3980 chunk 64 optimal weight: 10.0000 chunk 9 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 72 optimal weight: 0.0370 chunk 59 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 0.0070 chunk 24 optimal weight: 0.3980 overall best weight: 0.2676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 409 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.151750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.120734 restraints weight = 16049.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.122951 restraints weight = 8783.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.123742 restraints weight = 6805.998| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 6631 Z= 0.186 Angle : 0.683 9.487 9010 Z= 0.340 Chirality : 0.042 0.210 944 Planarity : 0.005 0.051 1167 Dihedral : 5.032 54.375 930 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.03 % Allowed : 19.91 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.31), residues: 788 helix: 0.68 (0.27), residues: 378 sheet: -1.01 (0.78), residues: 46 loop : -1.94 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 477 HIS 0.005 0.001 HIS E 493 PHE 0.013 0.001 PHE A 390 TYR 0.031 0.001 TYR A 50 ARG 0.008 0.001 ARG E 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2498.20 seconds wall clock time: 44 minutes 7.55 seconds (2647.55 seconds total)