Starting phenix.real_space_refine on Fri Aug 22 16:58:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8woz_37703/08_2025/8woz_37703.cif Found real_map, /net/cci-nas-00/data/ceres_data/8woz_37703/08_2025/8woz_37703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8woz_37703/08_2025/8woz_37703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8woz_37703/08_2025/8woz_37703.map" model { file = "/net/cci-nas-00/data/ceres_data/8woz_37703/08_2025/8woz_37703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8woz_37703/08_2025/8woz_37703.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 36 5.16 5 C 3994 2.51 5 N 1032 2.21 5 O 1181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6244 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4858 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 26, 'TRANS': 569} Chain: "B" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1385 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 160} 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: 1.43, per 1000 atoms: 0.23 Number of scatterers: 6244 At special positions: 0 Unit cell: (77.28, 97.98, 107.64, 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 36 16.00 O 1181 8.00 N 1032 7.00 C 3994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 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 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: 0.38 Conformation dependent library (CDL) restraints added in 298.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1450 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 4 sheets defined 54.9% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.876A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 78 removed outlier: 3.612A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.224A pdb=" N THR A 82 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.868A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.783A pdb=" N ALA A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.712A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.841A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 221 through 247 removed outlier: 3.516A pdb=" N GLU A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.659A pdb=" N PHE A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 removed outlier: 4.059A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.841A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.762A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 405 removed outlier: 3.927A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 413 removed outlier: 4.188A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.778A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 removed outlier: 3.512A pdb=" N THR A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.679A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.832A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.524A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 4.613A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.606A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.616A pdb=" N LEU B 355 " --> pdb=" O TYR B 352 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR B 356 " --> pdb=" O SER B 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 356' Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.358A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 377 " --> pdb=" O LEU B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 397 removed outlier: 4.323A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.610A 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 352 removed outlier: 6.143A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 341 through 345 Processing sheet with id=AA4, first strand: chain 'B' and resid 439 through 441 276 hydrogen bonds defined for protein. 774 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: 0.76 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1261 1.33 - 1.45: 1667 1.45 - 1.57: 3434 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6420 Sorted by residual: bond pdb=" N ASP A 292 " pdb=" CA ASP A 292 " ideal model delta sigma weight residual 1.457 1.502 -0.045 1.29e-02 6.01e+03 1.19e+01 bond pdb=" N HIS A 378 " pdb=" CA HIS A 378 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.21e-02 6.83e+03 8.43e+00 bond pdb=" N ASN A 90 " pdb=" CA ASN A 90 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.31e-02 5.83e+03 6.78e+00 bond pdb=" N VAL A 293 " pdb=" CA VAL A 293 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.38e+00 bond pdb=" C ASP A 292 " pdb=" O ASP A 292 " ideal model delta sigma weight residual 1.235 1.208 0.028 1.26e-02 6.30e+03 4.78e+00 ... (remaining 6415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 8592 2.45 - 4.91: 110 4.91 - 7.36: 18 7.36 - 9.81: 2 9.81 - 12.26: 2 Bond angle restraints: 8724 Sorted by residual: angle pdb=" CA HIS A 378 " pdb=" CB HIS A 378 " pdb=" CG HIS A 378 " ideal model delta sigma weight residual 113.80 119.10 -5.30 1.00e+00 1.00e+00 2.81e+01 angle pdb=" C ASP A 292 " pdb=" CA ASP A 292 " pdb=" CB ASP A 292 " ideal model delta sigma weight residual 110.42 99.96 10.46 1.99e+00 2.53e-01 2.76e+01 angle pdb=" C HIS A 378 " pdb=" CA HIS A 378 " pdb=" CB HIS A 378 " ideal model delta sigma weight residual 110.79 102.59 8.20 1.66e+00 3.63e-01 2.44e+01 angle pdb=" O GLY A 377 " pdb=" C GLY A 377 " pdb=" N HIS A 378 " ideal model delta sigma weight residual 122.19 117.62 4.57 9.60e-01 1.09e+00 2.27e+01 angle pdb=" CA GLY A 377 " pdb=" C GLY A 377 " pdb=" N HIS A 378 " ideal model delta sigma weight residual 117.04 121.49 -4.45 9.90e-01 1.02e+00 2.02e+01 ... (remaining 8719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 3262 17.74 - 35.49: 398 35.49 - 53.23: 113 53.23 - 70.97: 9 70.97 - 88.71: 8 Dihedral angle restraints: 3790 sinusoidal: 1530 harmonic: 2260 Sorted by residual: dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -126.19 40.19 1 1.00e+01 1.00e-02 2.27e+01 dihedral pdb=" CA TRP A 473 " pdb=" C TRP A 473 " pdb=" N MET A 474 " pdb=" CA MET A 474 " ideal model delta harmonic sigma weight residual 180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CB CYS B 467 " pdb=" SG CYS B 467 " pdb=" SG CYS B 474 " pdb=" CB CYS B 474 " ideal model delta sinusoidal sigma weight residual -86.00 -55.24 -30.76 1 1.00e+01 1.00e-02 1.35e+01 ... (remaining 3787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 578 0.035 - 0.071: 246 0.071 - 0.106: 65 0.106 - 0.141: 18 0.141 - 0.176: 3 Chirality restraints: 910 Sorted by residual: chirality pdb=" CG LEU A 267 " pdb=" CB LEU A 267 " pdb=" CD1 LEU A 267 " pdb=" CD2 LEU A 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CB VAL A 581 " pdb=" CA VAL A 581 " pdb=" CG1 VAL A 581 " pdb=" CG2 VAL A 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA HIS A 378 " pdb=" N HIS A 378 " pdb=" C HIS A 378 " pdb=" CB HIS A 378 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 907 not shown) Planarity restraints: 1127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 257 " -0.072 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO A 258 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 398 " 0.045 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO B 399 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 399 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 399 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 378 " -0.025 2.00e-02 2.50e+03 2.04e-02 6.24e+00 pdb=" CG HIS A 378 " 0.040 2.00e-02 2.50e+03 pdb=" ND1 HIS A 378 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS A 378 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS A 378 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS A 378 " -0.015 2.00e-02 2.50e+03 ... (remaining 1124 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 143 2.70 - 3.25: 6140 3.25 - 3.80: 9376 3.80 - 4.35: 11814 4.35 - 4.90: 19566 Nonbonded interactions: 47039 Sorted by model distance: nonbonded pdb=" O VAL A 293 " pdb=" OG1 THR A 294 " model vdw 2.147 3.040 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.241 3.120 nonbonded pdb=" OG SER B 362 " pdb=" O ALA B 422 " model vdw 2.243 3.040 nonbonded pdb=" ND2 ASN A 137 " pdb=" OE1 GLN A 139 " model vdw 2.249 3.120 nonbonded pdb=" OD1 ASP A 198 " pdb=" N ASP A 201 " model vdw 2.314 3.120 ... (remaining 47034 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: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.300 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 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 : 0.005 0.292 6426 Z= 0.208 Angle : 0.704 12.263 8732 Z= 0.395 Chirality : 0.042 0.176 910 Planarity : 0.006 0.107 1127 Dihedral : 16.315 88.714 2328 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.15 % Allowed : 22.88 % Favored : 76.97 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.32), residues: 764 helix: 0.44 (0.28), residues: 381 sheet: 0.84 (0.81), residues: 40 loop : -1.48 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 245 TYR 0.015 0.001 TYR A 183 PHE 0.018 0.001 PHE A 72 TRP 0.011 0.001 TRP A 594 HIS 0.012 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 6420) covalent geometry : angle 0.70384 ( 8724) SS BOND : bond 0.00146 ( 4) SS BOND : angle 0.85294 ( 8) hydrogen bonds : bond 0.17050 ( 276) hydrogen bonds : angle 6.19818 ( 774) metal coordination : bond 0.20680 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.160 Fit side-chains REVERT: A 207 TYR cc_start: 0.7010 (m-10) cc_final: 0.6729 (m-10) REVERT: A 247 LYS cc_start: 0.6663 (tptt) cc_final: 0.6414 (mmtt) REVERT: A 539 LEU cc_start: 0.8697 (tp) cc_final: 0.8487 (tt) outliers start: 1 outliers final: 1 residues processed: 118 average time/residue: 0.0676 time to fit residues: 10.7571 Evaluate side-chains 114 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4050 r_free = 0.4050 target = 0.158211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.137171 restraints weight = 9726.899| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.45 r_work: 0.3671 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6426 Z= 0.162 Angle : 0.609 12.251 8732 Z= 0.315 Chirality : 0.043 0.165 910 Planarity : 0.006 0.076 1127 Dihedral : 4.843 59.231 843 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.53 % Allowed : 20.51 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.31), residues: 764 helix: 0.56 (0.27), residues: 388 sheet: 0.89 (0.80), residues: 42 loop : -1.58 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 245 TYR 0.017 0.001 TYR A 183 PHE 0.016 0.001 PHE A 603 TRP 0.012 0.002 TRP A 165 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6420) covalent geometry : angle 0.60862 ( 8724) SS BOND : bond 0.00280 ( 4) SS BOND : angle 0.91762 ( 8) hydrogen bonds : bond 0.06469 ( 276) hydrogen bonds : angle 4.42601 ( 774) metal coordination : bond 0.00757 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 202 TYR cc_start: 0.7843 (t80) cc_final: 0.7600 (t80) REVERT: A 247 LYS cc_start: 0.7342 (tptt) cc_final: 0.6939 (mmtt) REVERT: A 471 GLU cc_start: 0.8446 (pm20) cc_final: 0.8065 (pm20) REVERT: A 539 LEU cc_start: 0.8892 (tp) cc_final: 0.8690 (tt) outliers start: 17 outliers final: 6 residues processed: 130 average time/residue: 0.0629 time to fit residues: 11.2794 Evaluate side-chains 119 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 337 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 62 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 27 optimal weight: 0.0970 chunk 50 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.4042 r_free = 0.4042 target = 0.157037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.135914 restraints weight = 9634.196| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.44 r_work: 0.3673 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6426 Z= 0.145 Angle : 0.586 12.186 8732 Z= 0.301 Chirality : 0.041 0.149 910 Planarity : 0.005 0.065 1127 Dihedral : 4.318 16.808 841 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.67 % Allowed : 20.95 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.31), residues: 764 helix: 0.65 (0.27), residues: 389 sheet: 1.03 (0.81), residues: 42 loop : -1.61 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 169 TYR 0.017 0.001 TYR A 183 PHE 0.016 0.001 PHE A 603 TRP 0.012 0.001 TRP A 165 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 6420) covalent geometry : angle 0.58533 ( 8724) SS BOND : bond 0.00167 ( 4) SS BOND : angle 0.83443 ( 8) hydrogen bonds : bond 0.06010 ( 276) hydrogen bonds : angle 4.25410 ( 774) metal coordination : bond 0.00433 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.262 Fit side-chains REVERT: A 182 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7423 (tm-30) REVERT: A 202 TYR cc_start: 0.7877 (t80) cc_final: 0.7642 (t80) REVERT: A 207 TYR cc_start: 0.7369 (m-10) cc_final: 0.7044 (m-10) REVERT: A 247 LYS cc_start: 0.7414 (tptt) cc_final: 0.6942 (mmtt) REVERT: A 471 GLU cc_start: 0.8480 (pm20) cc_final: 0.8007 (pm20) REVERT: A 474 MET cc_start: 0.6269 (mmt) cc_final: 0.6032 (mmt) REVERT: A 495 GLU cc_start: 0.6648 (tp30) cc_final: 0.6289 (tp30) REVERT: A 596 LYS cc_start: 0.8494 (mtpt) cc_final: 0.8149 (mtpp) outliers start: 18 outliers final: 9 residues processed: 131 average time/residue: 0.0638 time to fit residues: 11.3559 Evaluate side-chains 121 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 355 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 19 optimal weight: 0.0670 chunk 29 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 72 optimal weight: 0.0010 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 overall best weight: 0.4524 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.157963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.137042 restraints weight = 9729.563| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.46 r_work: 0.3686 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6426 Z= 0.126 Angle : 0.563 11.265 8732 Z= 0.289 Chirality : 0.041 0.147 910 Planarity : 0.005 0.059 1127 Dihedral : 4.191 16.189 841 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.82 % Allowed : 20.21 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.31), residues: 764 helix: 0.79 (0.27), residues: 388 sheet: 1.14 (0.83), residues: 42 loop : -1.59 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 169 TYR 0.015 0.001 TYR A 183 PHE 0.015 0.001 PHE A 603 TRP 0.012 0.001 TRP A 165 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6420) covalent geometry : angle 0.56259 ( 8724) SS BOND : bond 0.00114 ( 4) SS BOND : angle 0.79997 ( 8) hydrogen bonds : bond 0.05354 ( 276) hydrogen bonds : angle 4.08871 ( 774) metal coordination : bond 0.00286 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 202 TYR cc_start: 0.7579 (t80) cc_final: 0.7374 (t80) REVERT: A 207 TYR cc_start: 0.7020 (m-10) cc_final: 0.6809 (m-10) REVERT: A 247 LYS cc_start: 0.7397 (tptt) cc_final: 0.7011 (tptt) REVERT: A 364 VAL cc_start: 0.6831 (OUTLIER) cc_final: 0.6436 (t) REVERT: A 366 MET cc_start: 0.4913 (ttm) cc_final: 0.4249 (ttm) REVERT: A 471 GLU cc_start: 0.8213 (pm20) cc_final: 0.7734 (pm20) REVERT: A 474 MET cc_start: 0.5807 (mmt) cc_final: 0.5599 (mmt) REVERT: A 495 GLU cc_start: 0.6473 (tp30) cc_final: 0.6092 (tp30) REVERT: A 594 TRP cc_start: 0.7378 (OUTLIER) cc_final: 0.7048 (t-100) REVERT: A 596 LYS cc_start: 0.8427 (mtpt) cc_final: 0.8104 (mtpp) outliers start: 19 outliers final: 13 residues processed: 133 average time/residue: 0.0620 time to fit residues: 11.2841 Evaluate side-chains 132 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 594 TRP Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 355 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 6 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 chunk 56 optimal weight: 0.3980 chunk 74 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.158570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.137346 restraints weight = 9877.962| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.50 r_work: 0.3694 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6426 Z= 0.120 Angle : 0.560 10.438 8732 Z= 0.286 Chirality : 0.040 0.159 910 Planarity : 0.005 0.056 1127 Dihedral : 4.073 15.601 841 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.82 % Allowed : 21.69 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.31), residues: 764 helix: 0.87 (0.27), residues: 388 sheet: 1.21 (0.83), residues: 42 loop : -1.56 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.015 0.001 TYR A 215 PHE 0.015 0.001 PHE A 603 TRP 0.011 0.001 TRP A 165 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6420) covalent geometry : angle 0.55996 ( 8724) SS BOND : bond 0.00105 ( 4) SS BOND : angle 0.76374 ( 8) hydrogen bonds : bond 0.05012 ( 276) hydrogen bonds : angle 3.98814 ( 774) metal coordination : bond 0.00220 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 247 LYS cc_start: 0.7393 (tptt) cc_final: 0.7138 (tptt) REVERT: A 364 VAL cc_start: 0.6755 (OUTLIER) cc_final: 0.6388 (t) REVERT: A 470 LYS cc_start: 0.7181 (mmtm) cc_final: 0.6840 (mmtm) REVERT: A 471 GLU cc_start: 0.8265 (pm20) cc_final: 0.7814 (pm20) REVERT: A 495 GLU cc_start: 0.6437 (tp30) cc_final: 0.6054 (tp30) REVERT: A 596 LYS cc_start: 0.8406 (mtpt) cc_final: 0.8188 (mtmm) outliers start: 19 outliers final: 13 residues processed: 132 average time/residue: 0.0527 time to fit residues: 9.5941 Evaluate side-chains 128 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 355 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 35 optimal weight: 0.5980 chunk 71 optimal weight: 0.0370 chunk 70 optimal weight: 0.7980 chunk 19 optimal weight: 0.0470 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.3356 ------------------------------------------------------------------------------- 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** B 424 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.159416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.138415 restraints weight = 9781.600| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.43 r_work: 0.3708 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6426 Z= 0.116 Angle : 0.549 10.259 8732 Z= 0.279 Chirality : 0.040 0.125 910 Planarity : 0.005 0.055 1127 Dihedral : 3.994 15.237 841 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.67 % Allowed : 22.73 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.31), residues: 764 helix: 1.11 (0.27), residues: 378 sheet: 0.90 (0.83), residues: 44 loop : -1.39 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 169 TYR 0.015 0.001 TYR A 252 PHE 0.021 0.001 PHE A 438 TRP 0.008 0.001 TRP B 423 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 6420) covalent geometry : angle 0.54889 ( 8724) SS BOND : bond 0.00100 ( 4) SS BOND : angle 0.73705 ( 8) hydrogen bonds : bond 0.04766 ( 276) hydrogen bonds : angle 3.93498 ( 774) metal coordination : bond 0.00191 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 247 LYS cc_start: 0.7329 (tptt) cc_final: 0.7103 (tptt) REVERT: A 364 VAL cc_start: 0.6639 (OUTLIER) cc_final: 0.6274 (t) REVERT: A 470 LYS cc_start: 0.7131 (mmtm) cc_final: 0.6916 (mmtm) REVERT: A 471 GLU cc_start: 0.8253 (pm20) cc_final: 0.7809 (pm20) REVERT: A 474 MET cc_start: 0.5890 (mmm) cc_final: 0.5687 (mmm) REVERT: A 495 GLU cc_start: 0.6422 (tp30) cc_final: 0.6060 (tp30) REVERT: A 568 LEU cc_start: 0.8135 (tp) cc_final: 0.7871 (tp) REVERT: A 594 TRP cc_start: 0.7382 (OUTLIER) cc_final: 0.6970 (t-100) REVERT: A 596 LYS cc_start: 0.8384 (mtpt) cc_final: 0.8097 (mttp) outliers start: 18 outliers final: 13 residues processed: 132 average time/residue: 0.0597 time to fit residues: 10.7652 Evaluate side-chains 129 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 594 TRP Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 72 optimal weight: 0.0980 chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4059 r_free = 0.4059 target = 0.158349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.137229 restraints weight = 9806.067| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.46 r_work: 0.3693 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6426 Z= 0.133 Angle : 0.573 10.397 8732 Z= 0.294 Chirality : 0.041 0.164 910 Planarity : 0.005 0.055 1127 Dihedral : 4.029 15.629 841 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.42 % Allowed : 21.84 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.31), residues: 764 helix: 1.09 (0.27), residues: 380 sheet: 0.92 (0.83), residues: 44 loop : -1.46 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 255 TYR 0.016 0.001 TYR A 183 PHE 0.024 0.002 PHE A 438 TRP 0.010 0.001 TRP A 165 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 6420) covalent geometry : angle 0.57318 ( 8724) SS BOND : bond 0.00128 ( 4) SS BOND : angle 0.75748 ( 8) hydrogen bonds : bond 0.05182 ( 276) hydrogen bonds : angle 3.92852 ( 774) metal coordination : bond 0.00277 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 181 GLU cc_start: 0.7561 (tp30) cc_final: 0.6820 (tp30) REVERT: A 364 VAL cc_start: 0.6516 (OUTLIER) cc_final: 0.6163 (t) REVERT: A 471 GLU cc_start: 0.8270 (pm20) cc_final: 0.7832 (pm20) REVERT: A 485 VAL cc_start: 0.7743 (t) cc_final: 0.7324 (t) REVERT: A 495 GLU cc_start: 0.6463 (tp30) cc_final: 0.6110 (tp30) REVERT: A 594 TRP cc_start: 0.7447 (OUTLIER) cc_final: 0.6782 (t-100) REVERT: A 596 LYS cc_start: 0.8358 (mtpt) cc_final: 0.8086 (mttm) outliers start: 23 outliers final: 14 residues processed: 138 average time/residue: 0.0669 time to fit residues: 12.3606 Evaluate side-chains 134 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 594 TRP Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 61 optimal weight: 0.0010 chunk 44 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 0.0980 chunk 4 optimal weight: 3.9990 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4065 r_free = 0.4065 target = 0.158847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.137860 restraints weight = 9783.619| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.45 r_work: 0.3699 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6426 Z= 0.125 Angle : 0.576 10.122 8732 Z= 0.295 Chirality : 0.041 0.153 910 Planarity : 0.005 0.055 1127 Dihedral : 4.020 15.248 841 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.82 % Allowed : 23.48 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.31), residues: 764 helix: 1.11 (0.27), residues: 378 sheet: 0.91 (0.83), residues: 44 loop : -1.38 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 357 TYR 0.017 0.001 TYR A 215 PHE 0.027 0.001 PHE A 438 TRP 0.010 0.001 TRP A 165 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6420) covalent geometry : angle 0.57548 ( 8724) SS BOND : bond 0.00113 ( 4) SS BOND : angle 0.72875 ( 8) hydrogen bonds : bond 0.04965 ( 276) hydrogen bonds : angle 3.92305 ( 774) metal coordination : bond 0.00212 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.7235 (mtt180) cc_final: 0.7004 (mtt180) REVERT: A 364 VAL cc_start: 0.6442 (OUTLIER) cc_final: 0.6075 (t) REVERT: A 471 GLU cc_start: 0.8197 (pm20) cc_final: 0.7716 (pm20) REVERT: A 495 GLU cc_start: 0.6428 (tp30) cc_final: 0.6076 (tp30) REVERT: A 594 TRP cc_start: 0.7400 (OUTLIER) cc_final: 0.6757 (t-100) REVERT: A 596 LYS cc_start: 0.8349 (mtpt) cc_final: 0.8089 (mttm) outliers start: 19 outliers final: 14 residues processed: 134 average time/residue: 0.0662 time to fit residues: 11.7050 Evaluate side-chains 134 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 594 TRP Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 20 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 chunk 57 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.157706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.136430 restraints weight = 9845.494| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.52 r_work: 0.3677 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6426 Z= 0.147 Angle : 0.617 10.463 8732 Z= 0.316 Chirality : 0.042 0.180 910 Planarity : 0.005 0.055 1127 Dihedral : 4.119 15.822 841 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.53 % Allowed : 23.92 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.31), residues: 764 helix: 1.04 (0.27), residues: 378 sheet: 0.94 (0.83), residues: 44 loop : -1.40 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 95 TYR 0.018 0.001 TYR A 183 PHE 0.024 0.002 PHE A 438 TRP 0.011 0.001 TRP A 165 HIS 0.006 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 6420) covalent geometry : angle 0.61714 ( 8724) SS BOND : bond 0.00160 ( 4) SS BOND : angle 0.77505 ( 8) hydrogen bonds : bond 0.05565 ( 276) hydrogen bonds : angle 3.98312 ( 774) metal coordination : bond 0.00329 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 357 ARG cc_start: 0.7307 (mtt180) cc_final: 0.7038 (mtt180) REVERT: A 364 VAL cc_start: 0.6523 (OUTLIER) cc_final: 0.6145 (t) REVERT: A 471 GLU cc_start: 0.8228 (pm20) cc_final: 0.7707 (pm20) REVERT: A 474 MET cc_start: 0.6128 (mmm) cc_final: 0.5731 (mmm) REVERT: A 495 GLU cc_start: 0.6471 (tp30) cc_final: 0.6106 (tp30) REVERT: A 594 TRP cc_start: 0.7442 (OUTLIER) cc_final: 0.6722 (t-100) REVERT: A 596 LYS cc_start: 0.8369 (mtpt) cc_final: 0.8060 (mttm) outliers start: 17 outliers final: 14 residues processed: 134 average time/residue: 0.0565 time to fit residues: 10.3790 Evaluate side-chains 136 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 594 TRP Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 12 optimal weight: 0.0870 chunk 74 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 59 optimal weight: 0.0070 chunk 32 optimal weight: 0.9980 chunk 73 optimal weight: 0.0970 chunk 7 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 69 optimal weight: 0.0570 chunk 67 optimal weight: 0.9990 overall best weight: 0.2092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.161098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.140237 restraints weight = 9866.293| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.45 r_work: 0.3732 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6426 Z= 0.117 Angle : 0.596 9.475 8732 Z= 0.301 Chirality : 0.040 0.152 910 Planarity : 0.005 0.054 1127 Dihedral : 4.003 14.335 841 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.38 % Allowed : 24.52 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.32), residues: 764 helix: 1.28 (0.28), residues: 371 sheet: 0.89 (0.84), residues: 44 loop : -1.31 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 95 TYR 0.015 0.001 TYR A 183 PHE 0.028 0.001 PHE A 438 TRP 0.009 0.001 TRP A 328 HIS 0.003 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6420) covalent geometry : angle 0.59582 ( 8724) SS BOND : bond 0.00087 ( 4) SS BOND : angle 0.75276 ( 8) hydrogen bonds : bond 0.04378 ( 276) hydrogen bonds : angle 3.86396 ( 774) metal coordination : bond 0.00143 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8102 (t0) cc_final: 0.7893 (t0) REVERT: A 357 ARG cc_start: 0.7208 (mtt180) cc_final: 0.6930 (mtt180) REVERT: A 364 VAL cc_start: 0.6250 (OUTLIER) cc_final: 0.5949 (t) REVERT: A 471 GLU cc_start: 0.8157 (pm20) cc_final: 0.7932 (pm20) REVERT: A 495 GLU cc_start: 0.6405 (tp30) cc_final: 0.6014 (tp30) REVERT: A 568 LEU cc_start: 0.7716 (tp) cc_final: 0.7480 (mp) REVERT: A 594 TRP cc_start: 0.7373 (OUTLIER) cc_final: 0.6743 (t-100) outliers start: 16 outliers final: 13 residues processed: 135 average time/residue: 0.0624 time to fit residues: 11.3783 Evaluate side-chains 135 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 594 TRP Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 43 optimal weight: 0.0770 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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** B 424 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.158161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.137262 restraints weight = 9897.760| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.46 r_work: 0.3689 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6426 Z= 0.141 Angle : 0.613 9.930 8732 Z= 0.312 Chirality : 0.042 0.148 910 Planarity : 0.005 0.055 1127 Dihedral : 4.052 15.409 841 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.53 % Allowed : 24.22 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.31), residues: 764 helix: 1.25 (0.28), residues: 372 sheet: 0.92 (0.84), residues: 42 loop : -1.34 (0.34), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 95 TYR 0.018 0.001 TYR A 183 PHE 0.017 0.002 PHE A 72 TRP 0.012 0.001 TRP A 165 HIS 0.005 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6420) covalent geometry : angle 0.61329 ( 8724) SS BOND : bond 0.00143 ( 4) SS BOND : angle 0.75212 ( 8) hydrogen bonds : bond 0.05319 ( 276) hydrogen bonds : angle 3.94000 ( 774) metal coordination : bond 0.00288 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1341.07 seconds wall clock time: 23 minutes 41.92 seconds (1421.92 seconds total)