Starting phenix.real_space_refine on Tue Jun 10 03:15:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wsg_32757/06_2025/7wsg_32757.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wsg_32757/06_2025/7wsg_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_32757/06_2025/7wsg_32757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wsg_32757/06_2025/7wsg_32757.map" model { file = "/net/cci-nas-00/data/ceres_data/7wsg_32757/06_2025/7wsg_32757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wsg_32757/06_2025/7wsg_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-5710/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: 5.02, per 1000 atoms: 0.78 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: 1.59 Conformation dependent library (CDL) restraints added in 879.8 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: 0.64 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: 1.65 Time building geometry restraints manager: 1.90 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.620 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:2.940 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.470 ------------------------------------------------------------------------------- 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 6609 Z= 0.117 Angle : 0.524 8.195 8984 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 Details of bonding type rmsd hydrogen bonds : bond 0.28332 ( 263) hydrogen bonds : angle 9.52979 ( 759) metal coordination : bond 0.00144 ( 2) SS BOND : bond 0.00228 ( 6) SS BOND : angle 0.60592 ( 12) covalent geometry : bond 0.00257 ( 6601) covalent geometry : angle 0.52388 ( 8972) *********************** 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 : 0.691 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: 0.2018 time to fit residues: 41.4325 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 : 0.681 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.183995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.162215 restraints weight = 9103.406| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 2.12 r_work: 0.4004 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3884 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 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 6609 Z= 0.144 Angle : 0.596 8.053 8984 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 Details of bonding type rmsd hydrogen bonds : bond 0.05522 ( 263) hydrogen bonds : angle 6.04451 ( 759) metal coordination : bond 0.00082 ( 2) SS BOND : bond 0.00206 ( 6) SS BOND : angle 0.50150 ( 12) covalent geometry : bond 0.00305 ( 6601) covalent geometry : angle 0.59600 ( 8972) *********************** 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 : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.6872 (OUTLIER) cc_final: 0.5941 (t70) REVERT: A 485 VAL cc_start: 0.7177 (OUTLIER) cc_final: 0.6884 (t) REVERT: A 597 GLU cc_start: 0.8122 (tt0) cc_final: 0.7820 (tm-30) REVERT: B 328 VAL cc_start: 0.5030 (OUTLIER) cc_final: 0.4792 (p) REVERT: B 396 GLN cc_start: 0.6811 (OUTLIER) cc_final: 0.6424 (mt0) outliers start: 25 outliers final: 16 residues processed: 133 average time/residue: 0.1603 time to fit residues: 29.3145 Evaluate side-chains 115 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 328 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 72 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 24 optimal weight: 0.4980 chunk 40 optimal weight: 0.0270 chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 overall best weight: 0.3838 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.186921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.164575 restraints weight = 9405.326| |-----------------------------------------------------------------------------| r_work (start): 0.4124 rms_B_bonded: 2.20 r_work: 0.4027 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3904 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6609 Z= 0.112 Angle : 0.532 7.664 8984 Z= 0.274 Chirality : 0.040 0.129 926 Planarity : 0.004 0.037 1163 Dihedral : 6.958 61.954 884 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.74 % Allowed : 15.97 % Favored : 80.29 % 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: -0.67 (0.29), residues: 783 helix: 0.04 (0.27), residues: 354 sheet: -1.26 (1.26), residues: 23 loop : -0.75 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.020 0.001 PHE B 364 TYR 0.024 0.001 TYR A 237 ARG 0.004 0.000 ARG B 495 Details of bonding type rmsd hydrogen bonds : bond 0.04637 ( 263) hydrogen bonds : angle 5.51964 ( 759) metal coordination : bond 0.00037 ( 2) SS BOND : bond 0.00150 ( 6) SS BOND : angle 0.36179 ( 12) covalent geometry : bond 0.00234 ( 6601) covalent geometry : angle 0.53250 ( 8972) *********************** 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 137 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.6779 (OUTLIER) cc_final: 0.5841 (t70) REVERT: A 148 LEU cc_start: 0.4628 (OUTLIER) cc_final: 0.4108 (mp) REVERT: A 485 VAL cc_start: 0.7143 (OUTLIER) cc_final: 0.6778 (t) REVERT: A 573 VAL cc_start: 0.8147 (OUTLIER) cc_final: 0.7876 (p) REVERT: A 597 GLU cc_start: 0.8052 (tt0) cc_final: 0.7800 (tm-30) REVERT: B 328 VAL cc_start: 0.5008 (OUTLIER) cc_final: 0.4780 (p) REVERT: B 396 GLN cc_start: 0.6770 (OUTLIER) cc_final: 0.6493 (mt0) outliers start: 26 outliers final: 13 residues processed: 131 average time/residue: 0.1655 time to fit residues: 29.5653 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 : 0.725 ------------------------------------------------------------------------------- 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 473 TRP Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 328 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 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 63 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 69 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.184520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.162643 restraints weight = 9373.707| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.18 r_work: 0.4011 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3888 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6609 Z= 0.127 Angle : 0.552 9.352 8984 Z= 0.279 Chirality : 0.041 0.205 926 Planarity : 0.004 0.050 1163 Dihedral : 6.857 57.829 883 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.17 % Allowed : 17.70 % Favored : 78.13 % 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: -0.53 (0.29), residues: 783 helix: 0.15 (0.27), residues: 354 sheet: -1.05 (1.29), residues: 23 loop : -0.68 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.015 0.001 PHE A 523 TYR 0.022 0.002 TYR A 385 ARG 0.007 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 263) hydrogen bonds : angle 5.46432 ( 759) metal coordination : bond 0.00076 ( 2) SS BOND : bond 0.00222 ( 6) SS BOND : angle 0.52541 ( 12) covalent geometry : bond 0.00282 ( 6601) covalent geometry : angle 0.55192 ( 8972) *********************** 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 128 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.6876 (OUTLIER) cc_final: 0.5862 (t70) REVERT: A 148 LEU cc_start: 0.4682 (OUTLIER) cc_final: 0.4203 (mp) REVERT: A 485 VAL cc_start: 0.7183 (OUTLIER) cc_final: 0.6904 (t) REVERT: A 597 GLU cc_start: 0.8130 (tt0) cc_final: 0.7835 (tm-30) REVERT: B 367 TYR cc_start: 0.7013 (m-80) cc_final: 0.6570 (m-80) outliers start: 29 outliers final: 20 residues processed: 121 average time/residue: 0.1652 time to fit residues: 27.8455 Evaluate side-chains 111 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 463 VAL 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 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 475 TYR 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 20 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 42 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.184815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.162765 restraints weight = 9325.319| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.17 r_work: 0.4013 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3891 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6609 Z= 0.123 Angle : 0.536 7.163 8984 Z= 0.274 Chirality : 0.041 0.181 926 Planarity : 0.004 0.038 1163 Dihedral : 6.418 58.657 880 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.88 % Allowed : 17.27 % Favored : 78.85 % 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: -0.51 (0.29), residues: 783 helix: 0.16 (0.27), residues: 362 sheet: -0.87 (1.29), residues: 23 loop : -0.70 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.015 0.001 PHE A 523 TYR 0.022 0.002 TYR A 385 ARG 0.006 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 263) hydrogen bonds : angle 5.34068 ( 759) metal coordination : bond 0.00079 ( 2) SS BOND : bond 0.00198 ( 6) SS BOND : angle 0.44946 ( 12) covalent geometry : bond 0.00273 ( 6601) covalent geometry : angle 0.53660 ( 8972) *********************** 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 124 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.6895 (OUTLIER) cc_final: 0.5853 (t70) REVERT: A 148 LEU cc_start: 0.4629 (OUTLIER) cc_final: 0.4148 (mp) REVERT: A 485 VAL cc_start: 0.7153 (OUTLIER) cc_final: 0.6884 (t) REVERT: A 597 GLU cc_start: 0.8073 (tt0) cc_final: 0.7835 (tm-30) REVERT: B 328 VAL cc_start: 0.5041 (OUTLIER) cc_final: 0.4793 (p) outliers start: 27 outliers final: 20 residues processed: 117 average time/residue: 0.1624 time to fit residues: 26.9912 Evaluate side-chains 115 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 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 328 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 53 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 34 optimal weight: 0.0370 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 54 optimal weight: 0.3980 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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** A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.186334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.164553 restraints weight = 9288.329| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 2.18 r_work: 0.4034 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3910 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6609 Z= 0.105 Angle : 0.514 6.798 8984 Z= 0.263 Chirality : 0.040 0.157 926 Planarity : 0.004 0.038 1163 Dihedral : 6.052 59.288 879 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.74 % Allowed : 17.55 % Favored : 78.71 % 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: 0.29 (0.27), residues: 364 sheet: -0.81 (1.30), residues: 23 loop : -0.68 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.014 0.001 PHE A 523 TYR 0.020 0.001 TYR A 385 ARG 0.005 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 263) hydrogen bonds : angle 5.19295 ( 759) metal coordination : bond 0.00087 ( 2) SS BOND : bond 0.00148 ( 6) SS BOND : angle 0.36978 ( 12) covalent geometry : bond 0.00228 ( 6601) covalent geometry : angle 0.51415 ( 8972) *********************** 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 129 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.6904 (OUTLIER) cc_final: 0.5882 (t70) REVERT: A 485 VAL cc_start: 0.7195 (OUTLIER) cc_final: 0.6977 (t) REVERT: A 597 GLU cc_start: 0.8074 (tt0) cc_final: 0.7818 (tm-30) outliers start: 26 outliers final: 16 residues processed: 122 average time/residue: 0.1538 time to fit residues: 26.6506 Evaluate side-chains 112 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 223 ILE 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 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 425 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 475 TYR 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 73 optimal weight: 0.0670 chunk 50 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 0.0770 chunk 14 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.186260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.164844 restraints weight = 9298.782| |-----------------------------------------------------------------------------| r_work (start): 0.4132 rms_B_bonded: 2.12 r_work: 0.4040 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3917 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6609 Z= 0.108 Angle : 0.527 6.876 8984 Z= 0.271 Chirality : 0.041 0.243 926 Planarity : 0.004 0.038 1163 Dihedral : 5.699 59.112 874 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.60 % Allowed : 17.84 % 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: -0.25 (0.30), residues: 783 helix: 0.40 (0.27), residues: 362 sheet: -0.74 (1.29), residues: 23 loop : -0.58 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.015 0.001 PHE A 523 TYR 0.019 0.001 TYR A 385 ARG 0.004 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 263) hydrogen bonds : angle 5.16947 ( 759) metal coordination : bond 0.00030 ( 2) SS BOND : bond 0.00152 ( 6) SS BOND : angle 0.37106 ( 12) covalent geometry : bond 0.00234 ( 6601) covalent geometry : angle 0.52704 ( 8972) *********************** 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 123 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.6935 (OUTLIER) cc_final: 0.5921 (t70) REVERT: A 203 TRP cc_start: 0.7064 (OUTLIER) cc_final: 0.6507 (t60) REVERT: A 485 VAL cc_start: 0.7094 (OUTLIER) cc_final: 0.6796 (t) REVERT: A 597 GLU cc_start: 0.8054 (tt0) cc_final: 0.7828 (tm-30) outliers start: 25 outliers final: 18 residues processed: 114 average time/residue: 0.1835 time to fit residues: 30.4352 Evaluate side-chains 117 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 1.343 ------------------------------------------------------------------------------- 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 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 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 B residue 325 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 69 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.185229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.163347 restraints weight = 9305.175| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 2.17 r_work: 0.4022 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3898 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6609 Z= 0.119 Angle : 0.535 6.831 8984 Z= 0.275 Chirality : 0.041 0.247 926 Planarity : 0.004 0.038 1163 Dihedral : 5.544 56.799 872 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.60 % Allowed : 17.55 % Favored : 78.85 % 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: -0.22 (0.30), residues: 783 helix: 0.43 (0.27), residues: 361 sheet: -0.85 (1.28), residues: 23 loop : -0.56 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.016 0.001 PHE A 523 TYR 0.021 0.001 TYR A 385 ARG 0.004 0.000 ARG B 495 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 263) hydrogen bonds : angle 5.15985 ( 759) metal coordination : bond 0.00142 ( 2) SS BOND : bond 0.00191 ( 6) SS BOND : angle 0.40096 ( 12) covalent geometry : bond 0.00265 ( 6601) covalent geometry : angle 0.53493 ( 8972) *********************** 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 123 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7054 (OUTLIER) cc_final: 0.6008 (t70) REVERT: A 485 VAL cc_start: 0.7204 (OUTLIER) cc_final: 0.6932 (t) REVERT: A 597 GLU cc_start: 0.8062 (tt0) cc_final: 0.7815 (tm-30) outliers start: 25 outliers final: 19 residues processed: 114 average time/residue: 0.1517 time to fit residues: 24.6454 Evaluate side-chains 116 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP 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 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 475 TYR 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 76 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 0.0370 chunk 55 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.185658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.163847 restraints weight = 9395.039| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.14 r_work: 0.4025 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3902 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6609 Z= 0.117 Angle : 0.537 6.962 8984 Z= 0.275 Chirality : 0.041 0.239 926 Planarity : 0.004 0.038 1163 Dihedral : 5.470 54.989 872 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.31 % Allowed : 18.13 % 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: -0.16 (0.30), residues: 783 helix: 0.46 (0.27), residues: 362 sheet: -0.85 (1.26), residues: 23 loop : -0.51 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.016 0.001 PHE A 523 TYR 0.020 0.001 TYR A 385 ARG 0.004 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 263) hydrogen bonds : angle 5.14548 ( 759) metal coordination : bond 0.00075 ( 2) SS BOND : bond 0.00190 ( 6) SS BOND : angle 0.35666 ( 12) covalent geometry : bond 0.00263 ( 6601) covalent geometry : angle 0.53679 ( 8972) *********************** 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 119 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6007 (t70) REVERT: A 203 TRP cc_start: 0.7113 (OUTLIER) cc_final: 0.6604 (t60) REVERT: A 325 GLN cc_start: 0.6132 (tp40) cc_final: 0.5746 (tp-100) REVERT: A 485 VAL cc_start: 0.7154 (OUTLIER) cc_final: 0.6865 (t) REVERT: A 597 GLU cc_start: 0.8042 (tt0) cc_final: 0.7823 (tm-30) outliers start: 23 outliers final: 16 residues processed: 112 average time/residue: 0.1499 time to fit residues: 23.9841 Evaluate side-chains 114 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 57 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 53 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 232 GLN A 378 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.185828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.163942 restraints weight = 9395.072| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 2.19 r_work: 0.4017 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3895 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.785 6609 Z= 0.345 Angle : 0.546 6.980 8984 Z= 0.280 Chirality : 0.041 0.220 926 Planarity : 0.004 0.037 1163 Dihedral : 5.477 54.104 872 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.31 % Allowed : 17.84 % Favored : 78.85 % 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: -0.27 (0.29), residues: 783 helix: 0.36 (0.27), residues: 369 sheet: -0.89 (1.26), residues: 23 loop : -0.56 (0.31), residues: 391 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 0.015 0.001 PHE A 523 TYR 0.021 0.002 TYR A 385 ARG 0.004 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 263) hydrogen bonds : angle 5.16818 ( 759) metal coordination : bond 0.55508 ( 2) SS BOND : bond 0.00215 ( 6) SS BOND : angle 0.39654 ( 12) covalent geometry : bond 0.00281 ( 6601) covalent geometry : angle 0.54604 ( 8972) ********************** 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 124 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6015 (t70) REVERT: A 203 TRP cc_start: 0.7115 (OUTLIER) cc_final: 0.6621 (t60) REVERT: A 376 MET cc_start: 0.7368 (mtm) cc_final: 0.7126 (mtm) REVERT: A 485 VAL cc_start: 0.7127 (OUTLIER) cc_final: 0.6872 (t) REVERT: A 597 GLU cc_start: 0.8050 (tt0) cc_final: 0.7845 (tm-30) REVERT: B 508 LEU cc_start: 0.2892 (OUTLIER) cc_final: 0.2558 (tm) outliers start: 23 outliers final: 17 residues processed: 115 average time/residue: 0.1589 time to fit residues: 25.8751 Evaluate side-chains 115 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP 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 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 505 LEU 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 46 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN A 522 GLN A 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.180961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.158731 restraints weight = 9649.976| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 2.29 r_work: 0.3958 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6609 Z= 0.200 Angle : 0.629 7.514 8984 Z= 0.326 Chirality : 0.045 0.272 926 Planarity : 0.004 0.044 1163 Dihedral : 5.988 58.394 872 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.17 % Allowed : 18.27 % 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: -0.63 (0.29), residues: 783 helix: -0.09 (0.26), residues: 380 sheet: -1.23 (1.22), residues: 23 loop : -0.58 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 163 HIS 0.011 0.002 HIS A 241 PHE 0.019 0.002 PHE A 523 TYR 0.026 0.002 TYR A 385 ARG 0.004 0.001 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.04691 ( 263) hydrogen bonds : angle 5.46615 ( 759) metal coordination : bond 0.00472 ( 2) SS BOND : bond 0.00379 ( 6) SS BOND : angle 0.55873 ( 12) covalent geometry : bond 0.00463 ( 6601) covalent geometry : angle 0.62900 ( 8972) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3969.99 seconds wall clock time: 69 minutes 10.41 seconds (4150.41 seconds total)