Starting phenix.real_space_refine on Sun Dec 29 19:43:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsg_32757/12_2024/7wsg_32757.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsg_32757/12_2024/7wsg_32757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wsg_32757/12_2024/7wsg_32757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsg_32757/12_2024/7wsg_32757.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsg_32757/12_2024/7wsg_32757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsg_32757/12_2024/7wsg_32757.cif" } resolution = 3.03 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= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5903 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4102 2.51 5 N 1067 2.21 5 O 1206 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 6413 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4885 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 567} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1527 Classifications: {'peptide': 190} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 177} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.16, per 1000 atoms: 0.80 Number of scatterers: 6413 At special positions: 0 Unit cell: (80.949, 83.625, 120.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1206 8.00 N 1067 7.00 C 4102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " 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 Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 945.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1486 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 4 sheets defined 53.2% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 20 through 27 Processing helix chain 'A' and resid 27 through 53 removed outlier: 4.091A pdb=" N ASN A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 82 removed outlier: 3.611A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.647A pdb=" N LYS A 94 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.777A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 removed outlier: 3.653A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 154 removed outlier: 4.081A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 171 removed outlier: 3.585A pdb=" N TRP A 163 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 194 Proline residue: A 178 - end of helix removed outlier: 3.620A pdb=" N ASN A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 218 through 252 removed outlier: 4.097A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.935A pdb=" N ASP A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 304 through 318 removed outlier: 3.806A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.838A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 386 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.866A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.628A pdb=" N ASN A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 450 removed outlier: 3.532A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLY A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 464 removed outlier: 4.478A pdb=" N GLU A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 474 removed outlier: 3.530A pdb=" N TRP A 473 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N MET A 474 " --> pdb=" O GLU A 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 470 through 474' Processing helix chain 'A' and resid 475 through 485 removed outlier: 3.523A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 531 removed outlier: 4.600A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 560 removed outlier: 3.694A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET A 557 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 560 " --> pdb=" O GLN A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.711A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 371 through 375 removed outlier: 3.573A pdb=" N LEU B 374 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 371 through 375' Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 488 through 491 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.401A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA3, first strand: chain 'B' and resid 341 through 343 removed outlier: 3.539A pdb=" N ALA B 384 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 495 " --> pdb=" O TRP B 423 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP B 423 " --> pdb=" O ARG B 495 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 439 through 441 263 hydrogen bonds defined for protein. 759 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: 1.66 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2060 1.34 - 1.46: 1669 1.46 - 1.58: 2813 1.58 - 1.70: 0 1.70 - 1.81: 59 Bond restraints: 6601 Sorted by residual: bond pdb=" CA VAL B 507 " pdb=" CB VAL B 507 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 9.20e-01 bond pdb=" CB THR A 453 " pdb=" CG2 THR A 453 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.20e-01 bond pdb=" CG1 ILE A 379 " pdb=" CD1 ILE A 379 " ideal model delta sigma weight residual 1.513 1.488 0.025 3.90e-02 6.57e+02 4.06e-01 bond pdb=" CB PRO B 470 " pdb=" CG PRO B 470 " ideal model delta sigma weight residual 1.506 1.482 0.024 3.90e-02 6.57e+02 3.64e-01 bond pdb=" N THR B 468 " pdb=" CA THR B 468 " ideal model delta sigma weight residual 1.460 1.453 0.007 1.29e-02 6.01e+03 3.15e-01 ... (remaining 6596 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 8820 1.64 - 3.28: 125 3.28 - 4.92: 22 4.92 - 6.56: 3 6.56 - 8.19: 2 Bond angle restraints: 8972 Sorted by residual: angle pdb=" N ALA A 304 " pdb=" CA ALA A 304 " pdb=" C ALA A 304 " ideal model delta sigma weight residual 114.62 110.96 3.66 1.14e+00 7.69e-01 1.03e+01 angle pdb=" CA ALA A 304 " pdb=" C ALA A 304 " pdb=" N ARG A 305 " ideal model delta sigma weight residual 119.71 116.33 3.38 1.17e+00 7.31e-01 8.34e+00 angle pdb=" CA LEU A 266 " pdb=" CB LEU A 266 " pdb=" CG LEU A 266 " ideal model delta sigma weight residual 116.30 124.49 -8.19 3.50e+00 8.16e-02 5.48e+00 angle pdb=" CA LEU B 421 " pdb=" CB LEU B 421 " pdb=" CG LEU B 421 " ideal model delta sigma weight residual 116.30 124.30 -8.00 3.50e+00 8.16e-02 5.23e+00 angle pdb=" CA TYR A 385 " pdb=" CB TYR A 385 " pdb=" CG TYR A 385 " ideal model delta sigma weight residual 113.90 117.91 -4.01 1.80e+00 3.09e-01 4.95e+00 ... (remaining 8967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 3563 16.40 - 32.80: 252 32.80 - 49.20: 54 49.20 - 65.60: 24 65.60 - 82.00: 5 Dihedral angle restraints: 3898 sinusoidal: 1582 harmonic: 2316 Sorted by residual: dihedral pdb=" CA ALA A 396 " pdb=" C ALA A 396 " pdb=" N ASN A 397 " pdb=" CA ASN A 397 " ideal model delta harmonic sigma weight residual 180.00 162.19 17.81 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA LYS A 475 " pdb=" C LYS A 475 " pdb=" N LYS A 476 " pdb=" CA LYS A 476 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ASP A 499 " pdb=" CB ASP A 499 " pdb=" CG ASP A 499 " pdb=" OD1 ASP A 499 " ideal model delta sinusoidal sigma weight residual -30.00 -85.77 55.77 1 2.00e+01 2.50e-03 1.05e+01 ... (remaining 3895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 485 0.026 - 0.052: 283 0.052 - 0.078: 100 0.078 - 0.103: 47 0.103 - 0.129: 11 Chirality restraints: 926 Sorted by residual: chirality pdb=" CG LEU A 266 " pdb=" CB LEU A 266 " pdb=" CD1 LEU A 266 " pdb=" CD2 LEU A 266 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA VAL B 420 " pdb=" N VAL B 420 " pdb=" C VAL B 420 " pdb=" CB VAL B 420 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.18e-01 chirality pdb=" CA PRO B 477 " pdb=" N PRO B 477 " pdb=" C PRO B 477 " pdb=" CB PRO B 477 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.04e-01 ... (remaining 923 not shown) Planarity restraints: 1163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 145 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 146 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 489 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO A 490 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 490 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 490 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 291 " -0.006 2.00e-02 2.50e+03 1.25e-02 1.57e+00 pdb=" C ILE A 291 " 0.022 2.00e-02 2.50e+03 pdb=" O ILE A 291 " -0.008 2.00e-02 2.50e+03 pdb=" N ASP A 292 " -0.007 2.00e-02 2.50e+03 ... (remaining 1160 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 81 2.63 - 3.19: 5785 3.19 - 3.76: 10416 3.76 - 4.33: 14655 4.33 - 4.90: 23875 Nonbonded interactions: 54812 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 2.058 2.230 nonbonded pdb=" O THR A 125 " pdb=" OG1 THR A 129 " model vdw 2.207 3.040 nonbonded pdb=" O THR A 449 " pdb=" OG1 THR A 453 " model vdw 2.226 3.040 nonbonded pdb=" NH1 ARG A 245 " pdb=" O PRO A 258 " model vdw 2.235 3.120 nonbonded pdb=" OG1 THR A 276 " pdb=" OG1 THR A 445 " model vdw 2.245 3.040 ... (remaining 54807 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.290 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: 19.920 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6601 Z= 0.167 Angle : 0.524 8.195 8972 Z= 0.275 Chirality : 0.039 0.129 926 Planarity : 0.003 0.039 1163 Dihedral : 12.816 81.998 2394 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.60 % Allowed : 11.08 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.05 (0.29), residues: 783 helix: -0.44 (0.27), residues: 344 sheet: -1.89 (1.09), residues: 23 loop : -0.76 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 328 HIS 0.006 0.001 HIS A 241 PHE 0.009 0.001 PHE A 369 TYR 0.020 0.001 TYR A 385 ARG 0.004 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6266 (mp) REVERT: A 480 MET cc_start: 0.6049 (OUTLIER) cc_final: 0.5717 (mtp) REVERT: A 552 GLN cc_start: 0.7338 (mt0) cc_final: 0.7028 (pt0) REVERT: A 597 GLU cc_start: 0.8382 (tt0) cc_final: 0.7917 (tm-30) REVERT: B 365 LYS cc_start: 0.7484 (ttmt) cc_final: 0.7103 (mtpp) REVERT: B 396 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.6632 (mt0) REVERT: B 498 VAL cc_start: 0.7580 (t) cc_final: 0.7343 (m) outliers start: 32 outliers final: 14 residues processed: 159 average time/residue: 0.2135 time to fit residues: 43.6458 Evaluate side-chains 120 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.0050 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 546 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6601 Z= 0.201 Angle : 0.596 8.053 8972 Z= 0.308 Chirality : 0.042 0.195 926 Planarity : 0.004 0.037 1163 Dihedral : 7.546 63.904 891 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.60 % Allowed : 14.96 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.28), residues: 783 helix: -0.29 (0.26), residues: 354 sheet: -1.40 (1.17), residues: 23 loop : -0.90 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 594 HIS 0.006 0.001 HIS A 241 PHE 0.020 0.002 PHE A 369 TYR 0.024 0.002 TYR A 385 ARG 0.004 0.001 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.6745 (OUTLIER) cc_final: 0.6027 (t70) REVERT: A 485 VAL cc_start: 0.6919 (OUTLIER) cc_final: 0.6623 (t) REVERT: A 552 GLN cc_start: 0.7115 (mt0) cc_final: 0.6867 (pt0) REVERT: A 597 GLU cc_start: 0.8175 (tt0) cc_final: 0.7731 (tm-30) REVERT: B 396 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6620 (mt0) outliers start: 25 outliers final: 16 residues processed: 133 average time/residue: 0.1703 time to fit residues: 30.8175 Evaluate side-chains 113 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 58 optimal weight: 0.0770 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 373 HIS ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6601 Z= 0.219 Angle : 0.568 7.689 8972 Z= 0.294 Chirality : 0.042 0.141 926 Planarity : 0.004 0.040 1163 Dihedral : 7.106 57.047 884 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.74 % Allowed : 16.12 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.92 (0.28), residues: 783 helix: -0.24 (0.26), residues: 363 sheet: -1.53 (1.24), residues: 23 loop : -0.82 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 163 HIS 0.007 0.001 HIS A 241 PHE 0.020 0.002 PHE B 364 TYR 0.028 0.002 TYR A 237 ARG 0.004 0.000 ARG B 495 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 VAL cc_start: 0.7033 (OUTLIER) cc_final: 0.6718 (t) REVERT: A 552 GLN cc_start: 0.7100 (mt0) cc_final: 0.6866 (pt0) REVERT: A 597 GLU cc_start: 0.8207 (tt0) cc_final: 0.7754 (tm-30) REVERT: B 396 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6745 (mt0) outliers start: 26 outliers final: 19 residues processed: 122 average time/residue: 0.1859 time to fit residues: 30.4737 Evaluate side-chains 111 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 396 GLN Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 37 optimal weight: 0.0060 chunk 67 optimal weight: 0.2980 chunk 20 optimal weight: 0.0060 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.2612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6601 Z= 0.139 Angle : 0.523 10.074 8972 Z= 0.263 Chirality : 0.040 0.195 926 Planarity : 0.004 0.037 1163 Dihedral : 6.755 56.143 883 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.03 % Allowed : 16.69 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.49 (0.29), residues: 783 helix: 0.26 (0.27), residues: 354 sheet: -0.89 (1.30), residues: 23 loop : -0.76 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.004 0.001 HIS A 374 PHE 0.015 0.001 PHE B 364 TYR 0.021 0.001 TYR A 237 ARG 0.003 0.000 ARG B 495 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.6722 (OUTLIER) cc_final: 0.5869 (t70) REVERT: A 148 LEU cc_start: 0.4861 (OUTLIER) cc_final: 0.4338 (mp) REVERT: A 485 VAL cc_start: 0.6987 (OUTLIER) cc_final: 0.6629 (t) REVERT: A 597 GLU cc_start: 0.8183 (tt0) cc_final: 0.7764 (tm-30) outliers start: 28 outliers final: 15 residues processed: 127 average time/residue: 0.1624 time to fit residues: 28.4111 Evaluate side-chains 106 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 64 optimal weight: 0.0970 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 552 GLN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6601 Z= 0.203 Angle : 0.549 7.215 8972 Z= 0.281 Chirality : 0.042 0.181 926 Planarity : 0.004 0.039 1163 Dihedral : 6.141 56.092 878 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.74 % Allowed : 17.70 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.61 (0.29), residues: 783 helix: 0.09 (0.27), residues: 364 sheet: -0.98 (1.28), residues: 23 loop : -0.77 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 163 HIS 0.007 0.001 HIS A 241 PHE 0.016 0.001 PHE A 523 TYR 0.022 0.002 TYR A 385 ARG 0.004 0.000 ARG B 495 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.6828 (OUTLIER) cc_final: 0.5961 (t70) REVERT: A 148 LEU cc_start: 0.4868 (OUTLIER) cc_final: 0.4148 (mp) REVERT: A 485 VAL cc_start: 0.7002 (OUTLIER) cc_final: 0.6749 (t) REVERT: A 597 GLU cc_start: 0.8221 (tt0) cc_final: 0.7783 (tm-30) outliers start: 26 outliers final: 21 residues processed: 111 average time/residue: 0.1635 time to fit residues: 25.1185 Evaluate side-chains 108 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6601 Z= 0.223 Angle : 0.561 7.161 8972 Z= 0.290 Chirality : 0.042 0.157 926 Planarity : 0.004 0.041 1163 Dihedral : 6.225 55.394 878 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.88 % Allowed : 18.13 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.68 (0.29), residues: 783 helix: 0.02 (0.27), residues: 362 sheet: -1.07 (1.26), residues: 23 loop : -0.78 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.008 0.001 HIS A 241 PHE 0.017 0.002 PHE A 523 TYR 0.023 0.002 TYR A 385 ARG 0.003 0.000 ARG B 495 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 485 VAL cc_start: 0.7060 (OUTLIER) cc_final: 0.6860 (t) REVERT: A 597 GLU cc_start: 0.8234 (tt0) cc_final: 0.7783 (tm-30) outliers start: 27 outliers final: 24 residues processed: 114 average time/residue: 0.1662 time to fit residues: 26.9722 Evaluate side-chains 113 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 474 CYS Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 0.0570 chunk 44 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6601 Z= 0.181 Angle : 0.545 7.276 8972 Z= 0.279 Chirality : 0.042 0.267 926 Planarity : 0.004 0.039 1163 Dihedral : 6.087 56.894 876 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.88 % Allowed : 18.99 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.58 (0.29), residues: 783 helix: 0.14 (0.27), residues: 362 sheet: -1.05 (1.26), residues: 23 loop : -0.76 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.015 0.001 PHE A 523 TYR 0.020 0.001 TYR A 385 ARG 0.003 0.000 ARG B 495 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 485 VAL cc_start: 0.6974 (OUTLIER) cc_final: 0.6710 (t) REVERT: A 597 GLU cc_start: 0.8226 (tt0) cc_final: 0.7791 (tm-30) outliers start: 27 outliers final: 22 residues processed: 114 average time/residue: 0.1498 time to fit residues: 24.2735 Evaluate side-chains 110 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6601 Z= 0.198 Angle : 0.550 7.255 8972 Z= 0.282 Chirality : 0.042 0.253 926 Planarity : 0.004 0.040 1163 Dihedral : 6.114 58.954 876 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.03 % Allowed : 18.99 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.60 (0.29), residues: 783 helix: 0.11 (0.27), residues: 365 sheet: -1.05 (1.24), residues: 23 loop : -0.77 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 163 HIS 0.007 0.001 HIS A 241 PHE 0.016 0.001 PHE A 523 TYR 0.022 0.002 TYR A 385 ARG 0.003 0.000 ARG B 495 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 485 VAL cc_start: 0.6939 (OUTLIER) cc_final: 0.6689 (t) REVERT: A 597 GLU cc_start: 0.8237 (tt0) cc_final: 0.7808 (tm-30) outliers start: 28 outliers final: 24 residues processed: 113 average time/residue: 0.1597 time to fit residues: 25.5228 Evaluate side-chains 112 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 63 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6601 Z= 0.190 Angle : 0.544 7.292 8972 Z= 0.278 Chirality : 0.042 0.243 926 Planarity : 0.004 0.040 1163 Dihedral : 6.061 58.285 876 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.88 % Allowed : 18.99 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.56 (0.29), residues: 783 helix: 0.17 (0.27), residues: 368 sheet: -1.08 (1.24), residues: 23 loop : -0.78 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 163 HIS 0.007 0.001 HIS A 241 PHE 0.015 0.001 PHE A 523 TYR 0.021 0.001 TYR A 385 ARG 0.003 0.000 ARG B 495 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 VAL cc_start: 0.6901 (OUTLIER) cc_final: 0.6648 (t) REVERT: A 597 GLU cc_start: 0.8217 (tt0) cc_final: 0.7773 (tm-30) REVERT: B 508 LEU cc_start: 0.3039 (OUTLIER) cc_final: 0.2664 (tm) outliers start: 27 outliers final: 22 residues processed: 110 average time/residue: 0.1498 time to fit residues: 23.3470 Evaluate side-chains 113 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 47 optimal weight: 0.0270 chunk 37 optimal weight: 0.0980 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN ** A 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6601 Z= 0.154 Angle : 0.524 7.314 8972 Z= 0.268 Chirality : 0.041 0.234 926 Planarity : 0.004 0.039 1163 Dihedral : 5.767 53.053 874 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.88 % Allowed : 19.28 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.39 (0.29), residues: 783 helix: 0.32 (0.27), residues: 369 sheet: -0.96 (1.27), residues: 23 loop : -0.70 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.014 0.001 PHE A 523 TYR 0.018 0.001 TYR A 385 ARG 0.003 0.000 ARG B 495 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LEU cc_start: 0.4833 (OUTLIER) cc_final: 0.4401 (mp) REVERT: A 473 TRP cc_start: 0.5370 (OUTLIER) cc_final: 0.4652 (t60) REVERT: A 485 VAL cc_start: 0.6878 (OUTLIER) cc_final: 0.6607 (t) REVERT: A 597 GLU cc_start: 0.8200 (tt0) cc_final: 0.7765 (tm-30) REVERT: B 508 LEU cc_start: 0.3068 (OUTLIER) cc_final: 0.2692 (tm) outliers start: 27 outliers final: 18 residues processed: 115 average time/residue: 0.1515 time to fit residues: 24.7078 Evaluate side-chains 115 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 473 TRP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 508 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 54 optimal weight: 0.0970 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.0020 chunk 41 optimal weight: 0.8980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.184875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.163132 restraints weight = 9261.899| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 2.16 r_work: 0.4016 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3896 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6601 Z= 0.184 Angle : 0.542 7.212 8972 Z= 0.277 Chirality : 0.041 0.236 926 Planarity : 0.004 0.040 1163 Dihedral : 5.805 52.608 874 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.45 % Allowed : 20.29 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.43 (0.29), residues: 783 helix: 0.24 (0.27), residues: 375 sheet: -1.00 (1.26), residues: 23 loop : -0.69 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 163 HIS 0.007 0.001 HIS A 241 PHE 0.016 0.001 PHE A 523 TYR 0.020 0.002 TYR A 385 ARG 0.004 0.000 ARG B 495 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1883.23 seconds wall clock time: 35 minutes 34.60 seconds (2134.60 seconds total)