Starting phenix.real_space_refine on Fri Dec 27 19:23:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fdk_31546/12_2024/7fdk_31546.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fdk_31546/12_2024/7fdk_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_31546/12_2024/7fdk_31546.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fdk_31546/12_2024/7fdk_31546.map" model { file = "/net/cci-nas-00/data/ceres_data/7fdk_31546/12_2024/7fdk_31546.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fdk_31546/12_2024/7fdk_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-5532/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: 6.16, per 1000 atoms: 0.96 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: 1.47 Conformation dependent library (CDL) restraints added in 1.4 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: 0.54 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: 1.61 Time building geometry restraints manager: 1.75 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: 3.910 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 20.470 Find NCS groups from input model: 0.060 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.440 ------------------------------------------------------------------------------- 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 : 0.778 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: 0.2364 time to fit residues: 29.4982 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 : 0.704 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 : 0.709 Fit side-chains revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6530 (mm-40) cc_final: 0.6142 (pp30) REVERT: A 152 MET cc_start: 0.6753 (mtp) cc_final: 0.6498 (ttm) REVERT: A 265 HIS cc_start: 0.8021 (p-80) cc_final: 0.7608 (p90) REVERT: A 383 MET cc_start: 0.8693 (ttt) cc_final: 0.8392 (ttt) REVERT: A 557 MET cc_start: 0.8816 (tmm) cc_final: 0.8610 (tmm) REVERT: E 347 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6346 (m-80) REVERT: E 357 ARG cc_start: 0.8546 (ttt90) cc_final: 0.6548 (mtt180) REVERT: E 424 LYS cc_start: 0.8749 (tptp) cc_final: 0.8427 (tttp) REVERT: E 451 TYR cc_start: 0.7848 (m-80) cc_final: 0.6967 (m-80) REVERT: E 462 LYS cc_start: 0.8601 (mtpt) cc_final: 0.8367 (mtpp) REVERT: E 467 ASP cc_start: 0.7871 (t0) cc_final: 0.7481 (t70) REVERT: E 495 TYR cc_start: 0.8342 (OUTLIER) cc_final: 0.8103 (p90) REVERT: E 508 TYR cc_start: 0.8393 (m-80) cc_final: 0.8083 (m-80) outliers start: 9 outliers final: 5 residues processed: 101 average time/residue: 0.2175 time to fit residues: 28.3982 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 : 0.799 ------------------------------------------------------------------------------- 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 39 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 0.0770 chunk 70 optimal weight: 0.0570 chunk 76 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2545 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= 0.177 Angle : 0.614 7.141 9010 Z= 0.312 Chirality : 0.042 0.201 944 Planarity : 0.005 0.059 1167 Dihedral : 6.196 56.056 932 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.01 % Favored : 91.87 % Rotamer: Outliers : 1.60 % Allowed : 12.79 % Favored : 85.61 % 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: -1.93 (0.29), residues: 788 helix: 0.10 (0.27), residues: 370 sheet: -2.16 (0.66), residues: 46 loop : -2.70 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 163 HIS 0.004 0.001 HIS A 378 PHE 0.015 0.002 PHE A 525 TYR 0.021 0.001 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 119 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6597 (mm-40) cc_final: 0.6311 (pp30) REVERT: A 265 HIS cc_start: 0.7900 (p-80) cc_final: 0.7499 (p90) REVERT: A 376 MET cc_start: 0.8364 (ttp) cc_final: 0.8117 (ttp) REVERT: A 402 GLU cc_start: 0.6846 (tp30) cc_final: 0.6072 (mp0) REVERT: A 518 ARG cc_start: 0.8144 (ptt-90) cc_final: 0.7857 (ttp-170) REVERT: E 356 LYS cc_start: 0.8585 (tttt) cc_final: 0.7739 (mmtt) REVERT: E 357 ARG cc_start: 0.8558 (ttt90) cc_final: 0.6428 (mtt180) REVERT: E 424 LYS cc_start: 0.8614 (tptp) cc_final: 0.8290 (tttm) REVERT: E 451 TYR cc_start: 0.7761 (m-80) cc_final: 0.6859 (m-80) REVERT: E 462 LYS cc_start: 0.8470 (mtpt) cc_final: 0.8243 (mtpp) REVERT: E 467 ASP cc_start: 0.7730 (t0) cc_final: 0.7413 (t70) REVERT: E 508 TYR cc_start: 0.8362 (m-80) cc_final: 0.8084 (m-80) outliers start: 10 outliers final: 6 residues processed: 115 average time/residue: 0.2226 time to fit residues: 34.2574 Evaluate side-chains 94 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 468 ILE 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 36 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 0.0170 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2890 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= 0.198 Angle : 0.633 7.277 9010 Z= 0.314 Chirality : 0.042 0.195 944 Planarity : 0.005 0.056 1167 Dihedral : 5.684 56.155 932 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.77 % Favored : 91.11 % Rotamer: Outliers : 1.89 % Allowed : 14.68 % Favored : 83.43 % 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 (0.29), residues: 788 helix: 0.25 (0.27), residues: 379 sheet: -1.94 (0.67), residues: 46 loop : -2.47 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.004 0.001 HIS A 378 PHE 0.014 0.002 PHE A 512 TYR 0.018 0.001 TYR A 587 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 106 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6528 (mm-40) cc_final: 0.6299 (pp30) REVERT: A 265 HIS cc_start: 0.7882 (p-80) cc_final: 0.7482 (p90) REVERT: A 402 GLU cc_start: 0.7011 (tp30) cc_final: 0.6697 (mp0) REVERT: A 591 LEU cc_start: 0.8230 (tt) cc_final: 0.7925 (tt) REVERT: E 347 PHE cc_start: 0.6802 (OUTLIER) cc_final: 0.6167 (m-80) REVERT: E 356 LYS cc_start: 0.8609 (tttt) cc_final: 0.7809 (mmtt) REVERT: E 357 ARG cc_start: 0.8560 (ttt90) cc_final: 0.6396 (mtt180) REVERT: E 424 LYS cc_start: 0.8638 (tptp) cc_final: 0.8389 (tttm) REVERT: E 451 TYR cc_start: 0.7807 (m-80) cc_final: 0.6962 (m-80) REVERT: E 462 LYS cc_start: 0.8438 (mtpt) cc_final: 0.8234 (mtpp) REVERT: E 495 TYR cc_start: 0.8300 (OUTLIER) cc_final: 0.8099 (p90) REVERT: E 508 TYR cc_start: 0.8366 (m-80) cc_final: 0.8113 (m-80) outliers start: 12 outliers final: 8 residues processed: 101 average time/residue: 0.2298 time to fit residues: 29.6583 Evaluate side-chains 98 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 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 1 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6631 Z= 0.329 Angle : 0.690 8.534 9010 Z= 0.346 Chirality : 0.045 0.203 944 Planarity : 0.005 0.054 1167 Dihedral : 5.946 56.836 932 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.28 % Favored : 90.60 % Rotamer: Outliers : 2.76 % Allowed : 15.55 % Favored : 81.69 % 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: -1.65 (0.29), residues: 788 helix: 0.19 (0.27), residues: 380 sheet: -1.73 (0.72), residues: 46 loop : -2.50 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 163 HIS 0.007 0.001 HIS A 378 PHE 0.022 0.002 PHE A 390 TYR 0.021 0.002 TYR E 453 ARG 0.005 0.001 ARG A 465 *********************** 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 104 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6558 (mm-40) cc_final: 0.6307 (pp30) REVERT: A 265 HIS cc_start: 0.7958 (p-80) cc_final: 0.7640 (p90) REVERT: A 267 LEU cc_start: 0.8326 (mt) cc_final: 0.7841 (mt) REVERT: A 402 GLU cc_start: 0.6942 (tp30) cc_final: 0.6716 (mp0) REVERT: E 347 PHE cc_start: 0.7138 (OUTLIER) cc_final: 0.6250 (m-80) REVERT: E 356 LYS cc_start: 0.8558 (tttt) cc_final: 0.7645 (mmtt) REVERT: E 357 ARG cc_start: 0.8621 (ttt90) cc_final: 0.6591 (mtt180) REVERT: E 424 LYS cc_start: 0.8825 (tptp) cc_final: 0.8532 (tttp) REVERT: E 451 TYR cc_start: 0.7919 (m-80) cc_final: 0.7104 (m-80) REVERT: E 462 LYS cc_start: 0.8625 (mtpt) cc_final: 0.8400 (mtpp) REVERT: E 495 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.8217 (p90) REVERT: E 508 TYR cc_start: 0.8419 (m-80) cc_final: 0.8161 (m-80) outliers start: 18 outliers final: 10 residues processed: 99 average time/residue: 0.2205 time to fit residues: 28.4238 Evaluate side-chains 91 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 266 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.0770 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6631 Z= 0.175 Angle : 0.628 7.768 9010 Z= 0.310 Chirality : 0.041 0.196 944 Planarity : 0.005 0.053 1167 Dihedral : 5.351 55.299 932 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.37 % Favored : 92.50 % Rotamer: Outliers : 1.74 % Allowed : 16.86 % Favored : 81.40 % 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: -1.25 (0.30), residues: 788 helix: 0.49 (0.27), residues: 379 sheet: -1.43 (0.71), residues: 46 loop : -2.25 (0.32), residues: 363 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 0.011 0.001 PHE A 525 TYR 0.017 0.001 TYR A 587 ARG 0.005 0.001 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 108 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.729 Fit side-chains REVERT: A 161 ARG cc_start: 0.7200 (mtp180) cc_final: 0.6583 (ttm170) REVERT: A 249 MET cc_start: 0.8012 (tpp) cc_final: 0.7720 (tpp) REVERT: A 265 HIS cc_start: 0.7893 (p-80) cc_final: 0.7132 (p90) REVERT: A 267 LEU cc_start: 0.8246 (mt) cc_final: 0.7685 (mt) REVERT: A 270 MET cc_start: 0.6076 (tpp) cc_final: 0.5344 (tpp) REVERT: A 402 GLU cc_start: 0.6610 (tp30) cc_final: 0.6347 (mp0) REVERT: A 480 MET cc_start: 0.7724 (mtp) cc_final: 0.7378 (mtm) REVERT: A 557 MET cc_start: 0.8732 (tmm) cc_final: 0.8521 (tmm) REVERT: E 356 LYS cc_start: 0.8507 (tttt) cc_final: 0.7756 (mmtt) REVERT: E 357 ARG cc_start: 0.8571 (ttt90) cc_final: 0.6532 (mtt180) REVERT: E 424 LYS cc_start: 0.8628 (tptp) cc_final: 0.8346 (tttm) REVERT: E 451 TYR cc_start: 0.7653 (m-80) cc_final: 0.6797 (m-80) REVERT: E 462 LYS cc_start: 0.8419 (mtpt) cc_final: 0.8207 (mtpp) REVERT: E 467 ASP cc_start: 0.7721 (t0) cc_final: 0.7425 (t70) REVERT: E 495 TYR cc_start: 0.8340 (OUTLIER) cc_final: 0.8082 (p90) REVERT: E 508 TYR cc_start: 0.8344 (m-80) cc_final: 0.8115 (m-80) REVERT: E 516 GLU cc_start: 0.6870 (pm20) cc_final: 0.6508 (pm20) outliers start: 11 outliers final: 7 residues processed: 104 average time/residue: 0.2325 time to fit residues: 31.1900 Evaluate side-chains 92 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 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 495 TYR Chi-restraints excluded: chain E residue 501 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 55 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 7.9990 chunk 75 optimal weight: 0.2980 chunk 47 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6631 Z= 0.190 Angle : 0.637 7.645 9010 Z= 0.315 Chirality : 0.041 0.190 944 Planarity : 0.005 0.052 1167 Dihedral : 5.124 55.251 930 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 1.31 % Allowed : 18.60 % 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: -1.11 (0.30), residues: 788 helix: 0.60 (0.27), residues: 378 sheet: -1.21 (0.73), residues: 46 loop : -2.20 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 168 HIS 0.006 0.001 HIS E 493 PHE 0.015 0.001 PHE A 390 TYR 0.021 0.002 TYR A 50 ARG 0.005 0.000 ARG E 466 *********************** 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 96 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 161 ARG cc_start: 0.7202 (mtp180) cc_final: 0.6570 (ttt180) REVERT: A 265 HIS cc_start: 0.7865 (p-80) cc_final: 0.7214 (p90) REVERT: A 270 MET cc_start: 0.6005 (tpp) cc_final: 0.5345 (tpp) REVERT: A 402 GLU cc_start: 0.6618 (tp30) cc_final: 0.6351 (mp0) REVERT: A 480 MET cc_start: 0.7699 (mtp) cc_final: 0.7307 (mtm) REVERT: A 591 LEU cc_start: 0.8172 (tt) cc_final: 0.7820 (tt) REVERT: E 356 LYS cc_start: 0.8441 (tttt) cc_final: 0.7695 (mmtt) REVERT: E 357 ARG cc_start: 0.8605 (ttt90) cc_final: 0.6497 (mtt180) REVERT: E 424 LYS cc_start: 0.8669 (tptp) cc_final: 0.8360 (tttm) REVERT: E 451 TYR cc_start: 0.7814 (m-80) cc_final: 0.6976 (m-80) REVERT: E 462 LYS cc_start: 0.8436 (mtpt) cc_final: 0.8208 (mtpp) REVERT: E 495 TYR cc_start: 0.8440 (OUTLIER) cc_final: 0.8090 (p90) REVERT: E 508 TYR cc_start: 0.8355 (m-80) cc_final: 0.8094 (m-80) REVERT: E 516 GLU cc_start: 0.6841 (pm20) cc_final: 0.6557 (pm20) outliers start: 8 outliers final: 7 residues processed: 93 average time/residue: 0.2399 time to fit residues: 29.6051 Evaluate side-chains 90 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 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 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 14 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 59 optimal weight: 0.0170 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.0624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 HIS E 409 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6631 Z= 0.195 Angle : 0.642 7.289 9010 Z= 0.319 Chirality : 0.042 0.190 944 Planarity : 0.005 0.051 1167 Dihedral : 5.081 55.196 930 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 1.74 % Allowed : 18.46 % Favored : 79.80 % 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: -1.04 (0.30), residues: 788 helix: 0.63 (0.27), residues: 378 sheet: -1.10 (0.75), residues: 46 loop : -2.12 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 478 HIS 0.007 0.001 HIS E 493 PHE 0.017 0.001 PHE E 374 TYR 0.021 0.001 TYR A 50 ARG 0.005 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 94 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.784 Fit side-chains REVERT: A 161 ARG cc_start: 0.7178 (mtp180) cc_final: 0.6716 (ttt180) REVERT: A 249 MET cc_start: 0.7703 (tpp) cc_final: 0.7413 (tpp) REVERT: A 265 HIS cc_start: 0.7817 (p-80) cc_final: 0.7136 (p90) REVERT: A 267 LEU cc_start: 0.8175 (mt) cc_final: 0.7490 (mt) REVERT: A 270 MET cc_start: 0.5851 (tpp) cc_final: 0.5576 (tpp) REVERT: A 402 GLU cc_start: 0.6669 (tp30) cc_final: 0.6310 (mp0) REVERT: A 480 MET cc_start: 0.7645 (mtp) cc_final: 0.7261 (mtm) REVERT: A 557 MET cc_start: 0.8813 (tmm) cc_final: 0.8479 (tmm) REVERT: A 591 LEU cc_start: 0.8166 (tt) cc_final: 0.7802 (tt) REVERT: E 355 ARG cc_start: 0.8406 (ttm-80) cc_final: 0.7454 (ttt90) REVERT: E 356 LYS cc_start: 0.8375 (tttt) cc_final: 0.7669 (mmtt) REVERT: E 357 ARG cc_start: 0.8603 (ttt90) cc_final: 0.6526 (mtt180) REVERT: E 424 LYS cc_start: 0.8686 (tptp) cc_final: 0.8385 (tttm) REVERT: E 451 TYR cc_start: 0.7804 (m-80) cc_final: 0.7040 (m-80) REVERT: E 462 LYS cc_start: 0.8409 (mtpt) cc_final: 0.8170 (mtpp) REVERT: E 474 GLN cc_start: 0.7293 (tt0) cc_final: 0.6992 (pm20) REVERT: E 495 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.8078 (p90) REVERT: E 508 TYR cc_start: 0.8375 (m-80) cc_final: 0.8107 (m-80) outliers start: 11 outliers final: 7 residues processed: 89 average time/residue: 0.2254 time to fit residues: 25.9636 Evaluate side-chains 90 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 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 495 TYR Chi-restraints excluded: chain E residue 501 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 30 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 74 optimal weight: 0.2980 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6631 Z= 0.205 Angle : 0.649 7.267 9010 Z= 0.326 Chirality : 0.042 0.193 944 Planarity : 0.005 0.051 1167 Dihedral : 5.080 55.061 930 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 1.89 % Allowed : 19.48 % Favored : 78.63 % 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: -1.02 (0.30), residues: 788 helix: 0.59 (0.27), residues: 379 sheet: -1.02 (0.76), residues: 46 loop : -2.07 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 477 HIS 0.006 0.001 HIS E 493 PHE 0.019 0.002 PHE E 374 TYR 0.017 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 99 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 ARG cc_start: 0.7190 (mtp180) cc_final: 0.6620 (ttm170) REVERT: A 249 MET cc_start: 0.7669 (tpp) cc_final: 0.7390 (tpp) REVERT: A 265 HIS cc_start: 0.7813 (p-80) cc_final: 0.7051 (p90) REVERT: A 298 MET cc_start: 0.7922 (mpp) cc_final: 0.7695 (mpp) REVERT: A 402 GLU cc_start: 0.6837 (tp30) cc_final: 0.6533 (mp0) REVERT: A 480 MET cc_start: 0.7633 (mtp) cc_final: 0.7233 (mtm) REVERT: A 557 MET cc_start: 0.8807 (tmm) cc_final: 0.8492 (tmm) REVERT: A 591 LEU cc_start: 0.8184 (tt) cc_final: 0.7839 (tt) REVERT: E 346 ARG cc_start: 0.6985 (ttm110) cc_final: 0.5618 (ptt180) REVERT: E 347 PHE cc_start: 0.6797 (OUTLIER) cc_final: 0.6043 (m-80) REVERT: E 355 ARG cc_start: 0.8414 (ttm-80) cc_final: 0.7486 (ttt90) REVERT: E 356 LYS cc_start: 0.8331 (tttt) cc_final: 0.7597 (mmtt) REVERT: E 357 ARG cc_start: 0.8599 (ttt90) cc_final: 0.6545 (mtt180) REVERT: E 424 LYS cc_start: 0.8710 (tptp) cc_final: 0.8425 (tttm) REVERT: E 451 TYR cc_start: 0.7828 (m-80) cc_final: 0.7059 (m-80) REVERT: E 462 LYS cc_start: 0.8401 (mtpt) cc_final: 0.8165 (mtpp) REVERT: E 474 GLN cc_start: 0.7279 (tt0) cc_final: 0.6929 (pm20) REVERT: E 495 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.8008 (p90) REVERT: E 508 TYR cc_start: 0.8364 (m-80) cc_final: 0.8086 (m-80) outliers start: 12 outliers final: 8 residues processed: 94 average time/residue: 0.2426 time to fit residues: 29.4639 Evaluate side-chains 95 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 383 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.0870 chunk 71 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 6 optimal weight: 0.3980 chunk 47 optimal weight: 6.9990 chunk 37 optimal weight: 0.1980 chunk 49 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 overall best weight: 0.3358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6631 Z= 0.173 Angle : 0.659 8.038 9010 Z= 0.326 Chirality : 0.042 0.217 944 Planarity : 0.005 0.051 1167 Dihedral : 4.881 54.324 930 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 1.45 % Allowed : 19.77 % 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: -0.86 (0.31), residues: 788 helix: 0.75 (0.28), residues: 373 sheet: -0.94 (0.78), residues: 46 loop : -1.99 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 477 HIS 0.003 0.001 HIS A 378 PHE 0.015 0.001 PHE E 374 TYR 0.026 0.001 TYR A 50 ARG 0.007 0.001 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 105 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 182 GLU cc_start: 0.7881 (tp30) cc_final: 0.7555 (tp30) REVERT: A 249 MET cc_start: 0.7606 (tpp) cc_final: 0.7362 (tpp) REVERT: A 366 MET cc_start: 0.7831 (tpt) cc_final: 0.7613 (tpp) REVERT: A 402 GLU cc_start: 0.6661 (tp30) cc_final: 0.6302 (mp0) REVERT: A 480 MET cc_start: 0.7531 (mtp) cc_final: 0.7250 (mtm) REVERT: A 557 MET cc_start: 0.8771 (tmm) cc_final: 0.8377 (tmm) REVERT: E 355 ARG cc_start: 0.8277 (ttm-80) cc_final: 0.7524 (ttt90) REVERT: E 356 LYS cc_start: 0.8097 (tttt) cc_final: 0.7546 (mptt) REVERT: E 357 ARG cc_start: 0.8563 (ttt90) cc_final: 0.6449 (mtt180) REVERT: E 424 LYS cc_start: 0.8634 (tptp) cc_final: 0.8358 (tttm) REVERT: E 451 TYR cc_start: 0.7660 (m-80) cc_final: 0.6873 (m-80) REVERT: E 462 LYS cc_start: 0.8254 (mtpt) cc_final: 0.8054 (mtpp) REVERT: E 474 GLN cc_start: 0.7356 (tt0) cc_final: 0.6951 (pm20) REVERT: E 495 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7938 (p90) REVERT: E 508 TYR cc_start: 0.8338 (m-80) cc_final: 0.8062 (m-80) outliers start: 9 outliers final: 5 residues processed: 101 average time/residue: 0.2185 time to fit residues: 28.8341 Evaluate side-chains 96 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 17 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 chunk 63 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 54 optimal weight: 0.0980 chunk 3 optimal weight: 10.0000 chunk 44 optimal weight: 0.0870 chunk 70 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4076 r_free = 0.4076 target = 0.153286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.121689 restraints weight = 16556.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.124432 restraints weight = 8664.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.125424 restraints weight = 6644.453| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6631 Z= 0.173 Angle : 0.671 10.348 9010 Z= 0.332 Chirality : 0.042 0.201 944 Planarity : 0.005 0.050 1167 Dihedral : 4.810 54.444 930 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.74 % Allowed : 19.33 % Favored : 78.92 % 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: -0.83 (0.31), residues: 788 helix: 0.73 (0.27), residues: 374 sheet: -0.78 (0.78), residues: 46 loop : -1.94 (0.33), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 477 HIS 0.006 0.001 HIS A 265 PHE 0.015 0.001 PHE E 374 TYR 0.024 0.001 TYR A 50 ARG 0.007 0.000 ARG E 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1677.79 seconds wall clock time: 31 minutes 39.35 seconds (1899.35 seconds total)