Starting phenix.real_space_refine on Tue Feb 3 15:46:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kvy_62604/02_2026/9kvy_62604.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kvy_62604/02_2026/9kvy_62604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kvy_62604/02_2026/9kvy_62604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kvy_62604/02_2026/9kvy_62604.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kvy_62604/02_2026/9kvy_62604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kvy_62604/02_2026/9kvy_62604.map" } resolution = 3.34 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= 0.000 sd= 0.009 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 Mn 1 7.51 5 S 31 5.16 5 C 2909 2.51 5 N 727 2.21 5 O 786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4454 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2197 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 13, 'TRANS': 274} Chain breaks: 2 Chain: "B" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2256 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.15, per 1000 atoms: 0.26 Number of scatterers: 4454 At special positions: 0 Unit cell: (74.56, 59.648, 113.704, 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) Mn 1 24.99 S 31 16.00 O 786 8.00 N 727 7.00 C 2909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 273 " - pdb=" SG CYS A 277 " distance=2.05 Simple disulfide: pdb=" SG CYS A 404 " - pdb=" SG CYS A 409 " distance=2.03 Simple disulfide: pdb=" SG CYS B 273 " - pdb=" SG CYS B 277 " distance=2.05 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: 0.34 Conformation dependent library (CDL) restraints added in 317.3 milliseconds 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1092 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 4 sheets defined 67.8% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 10 through 33 removed outlier: 3.600A pdb=" N TYR A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 62 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 76 through 106 Processing helix chain 'A' and resid 112 through 133 removed outlier: 3.928A pdb=" N GLY A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 264 removed outlier: 3.689A pdb=" N GLY A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 307 removed outlier: 3.913A pdb=" N TYR A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 279 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASP A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Proline residue: A 281 - end of helix Proline residue: A 297 - end of helix Processing helix chain 'A' and resid 315 through 325 Processing helix chain 'A' and resid 359 through 374 Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.517A pdb=" N ALA A 410 " --> pdb=" O LYS A 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 23 Processing helix chain 'B' and resid 24 through 26 No H-bonds generated for 'chain 'B' and resid 24 through 26' Processing helix chain 'B' and resid 33 through 37 removed outlier: 4.421A pdb=" N ALA B 36 " --> pdb=" O ASN B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 62 removed outlier: 3.643A pdb=" N LEU B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 76 through 106 Processing helix chain 'B' and resid 112 through 132 removed outlier: 3.723A pdb=" N VAL B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 265 Processing helix chain 'B' and resid 274 through 306 removed outlier: 3.585A pdb=" N TYR B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Proline residue: B 281 - end of helix Proline residue: B 297 - end of helix removed outlier: 3.735A pdb=" N ALA B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 326 removed outlier: 3.922A pdb=" N SER B 321 " --> pdb=" O GLU B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 373 removed outlier: 3.898A pdb=" N THR B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 3.641A pdb=" N LYS B 411 " --> pdb=" O GLY B 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 341 removed outlier: 6.452A pdb=" N VAL A 332 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LYS A 352 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU A 334 " --> pdb=" O HIS A 350 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS A 350 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 377 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 331 through 341 removed outlier: 6.452A pdb=" N VAL A 332 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LYS A 352 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU A 334 " --> pdb=" O HIS A 350 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N HIS A 350 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LYS A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 331 through 332 removed outlier: 4.356A pdb=" N SER B 331 " --> pdb=" O LYS B 352 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 337 through 341 removed outlier: 5.515A pdb=" N GLU B 339 " --> pdb=" O ILE B 346 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE B 346 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL B 341 " --> pdb=" O LYS B 344 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN B 377 " --> pdb=" O ILE B 345 " (cutoff:3.500A) 301 hydrogen bonds defined for protein. 885 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: 0.74 Time building geometry restraints manager: 0.43 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: 1047 1.33 - 1.46: 1041 1.46 - 1.58: 2401 1.58 - 1.71: 0 1.71 - 1.83: 45 Bond restraints: 4534 Sorted by residual: bond pdb=" N ILE A 279 " pdb=" CA ILE A 279 " ideal model delta sigma weight residual 1.459 1.508 -0.049 1.30e-02 5.92e+03 1.40e+01 bond pdb=" C ALA A 410 " pdb=" N LYS A 411 " ideal model delta sigma weight residual 1.335 1.293 0.042 1.38e-02 5.25e+03 9.29e+00 bond pdb=" N VAL A 98 " pdb=" CA VAL A 98 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.35e+00 bond pdb=" N ASP B 280 " pdb=" CA ASP B 280 " ideal model delta sigma weight residual 1.462 1.439 0.023 8.50e-03 1.38e+04 7.30e+00 bond pdb=" N CYS A 277 " pdb=" CA CYS A 277 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.26e-02 6.30e+03 6.65e+00 ... (remaining 4529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 5964 1.86 - 3.72: 159 3.72 - 5.58: 28 5.58 - 7.44: 8 7.44 - 9.30: 6 Bond angle restraints: 6165 Sorted by residual: angle pdb=" C LYS A 411 " pdb=" CA LYS A 411 " pdb=" CB LYS A 411 " ideal model delta sigma weight residual 110.67 101.37 9.30 1.92e+00 2.71e-01 2.35e+01 angle pdb=" C CYS A 277 " pdb=" CA CYS A 277 " pdb=" CB CYS A 277 " ideal model delta sigma weight residual 110.70 101.86 8.84 1.83e+00 2.99e-01 2.33e+01 angle pdb=" N TRP A 275 " pdb=" CA TRP A 275 " pdb=" C TRP A 275 " ideal model delta sigma weight residual 111.28 106.77 4.51 1.09e+00 8.42e-01 1.71e+01 angle pdb=" C CYS A 273 " pdb=" CA CYS A 273 " pdb=" CB CYS A 273 " ideal model delta sigma weight residual 109.54 116.96 -7.42 1.84e+00 2.95e-01 1.63e+01 angle pdb=" C ASN A 274 " pdb=" N TRP A 275 " pdb=" CA TRP A 275 " ideal model delta sigma weight residual 120.28 115.23 5.05 1.34e+00 5.57e-01 1.42e+01 ... (remaining 6160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 2298 17.13 - 34.25: 319 34.25 - 51.38: 80 51.38 - 68.50: 17 68.50 - 85.63: 9 Dihedral angle restraints: 2723 sinusoidal: 1038 harmonic: 1685 Sorted by residual: dihedral pdb=" CB CYS A 404 " pdb=" SG CYS A 404 " pdb=" SG CYS A 409 " pdb=" CB CYS A 409 " ideal model delta sinusoidal sigma weight residual -86.00 -7.62 -78.38 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" C CYS A 273 " pdb=" N CYS A 273 " pdb=" CA CYS A 273 " pdb=" CB CYS A 273 " ideal model delta harmonic sigma weight residual -122.60 -134.63 12.03 0 2.50e+00 1.60e-01 2.32e+01 dihedral pdb=" CA ASN B 33 " pdb=" C ASN B 33 " pdb=" N SER B 34 " pdb=" CA SER B 34 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 2720 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 705 0.085 - 0.170: 60 0.170 - 0.255: 5 0.255 - 0.340: 0 0.340 - 0.425: 1 Chirality restraints: 771 Sorted by residual: chirality pdb=" CA CYS A 273 " pdb=" N CYS A 273 " pdb=" C CYS A 273 " pdb=" CB CYS A 273 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CA LYS A 411 " pdb=" N LYS A 411 " pdb=" C LYS A 411 " pdb=" CB LYS A 411 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA CYS A 277 " pdb=" N CYS A 277 " pdb=" C CYS A 277 " pdb=" CB CYS A 277 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 768 not shown) Planarity restraints: 755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 353 " -0.056 5.00e-02 4.00e+02 8.50e-02 1.15e+01 pdb=" N PRO B 354 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 354 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 354 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 275 " -0.023 2.00e-02 2.50e+03 1.55e-02 6.00e+00 pdb=" CG TRP A 275 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 275 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 275 " 0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP A 275 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 275 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 275 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 275 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 275 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 275 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 411 " 0.011 2.00e-02 2.50e+03 2.35e-02 5.53e+00 pdb=" C LYS A 411 " -0.041 2.00e-02 2.50e+03 pdb=" O LYS A 411 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN A 412 " 0.014 2.00e-02 2.50e+03 ... (remaining 752 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 22 2.55 - 3.14: 3623 3.14 - 3.73: 7114 3.73 - 4.31: 8983 4.31 - 4.90: 15401 Nonbonded interactions: 35143 Sorted by model distance: nonbonded pdb=" OD1 ASP A 40 " pdb="MN MN A 501 " model vdw 1.968 2.320 nonbonded pdb=" OG SER A 252 " pdb="MN MN A 501 " model vdw 1.990 2.320 nonbonded pdb=" OD1 ASN A 127 " pdb="MN MN A 501 " model vdw 2.189 2.320 nonbonded pdb=" NH1 ARG A 103 " pdb=" OE1 GLU A 108 " model vdw 2.244 3.120 nonbonded pdb=" O SER B 34 " pdb=" OG SER B 34 " model vdw 2.301 3.040 ... (remaining 35138 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 385 or resid 398 or resid 405 through 416)) selection = (chain 'B' and (resid 10 through 133 or resid 243 through 385 or resid 387 throu \ gh 416)) } 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: 1.240 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.490 Find NCS groups from input model: 0.050 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 0.055 4537 Z= 0.247 Angle : 0.773 9.305 6171 Z= 0.419 Chirality : 0.050 0.425 771 Planarity : 0.006 0.085 755 Dihedral : 17.440 85.626 1622 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.00 % Allowed : 26.65 % Favored : 72.34 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.53 (0.37), residues: 571 helix: 2.32 (0.28), residues: 342 sheet: -0.81 (0.75), residues: 50 loop : -1.07 (0.49), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 367 TYR 0.006 0.001 TYR B 278 PHE 0.016 0.001 PHE A 21 TRP 0.032 0.004 TRP A 275 HIS 0.007 0.002 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 4534) covalent geometry : angle 0.77091 ( 6165) SS BOND : bond 0.01478 ( 3) SS BOND : angle 1.90233 ( 6) hydrogen bonds : bond 0.12743 ( 296) hydrogen bonds : angle 4.95680 ( 885) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 298 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7298 (m110) cc_final: 0.6598 (m110) REVERT: A 349 LEU cc_start: 0.8516 (tt) cc_final: 0.8262 (tt) REVERT: B 33 ASN cc_start: 0.7960 (p0) cc_final: 0.7735 (p0) outliers start: 5 outliers final: 1 residues processed: 299 average time/residue: 0.0671 time to fit residues: 24.8949 Evaluate side-chains 211 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 243 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN B 127 ASN B 276 GLN B 360 GLN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.107518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.088493 restraints weight = 10706.935| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 5.13 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4537 Z= 0.158 Angle : 0.755 12.972 6171 Z= 0.368 Chirality : 0.043 0.170 771 Planarity : 0.005 0.046 755 Dihedral : 4.858 53.717 616 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.21 % Allowed : 30.86 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.73 (0.36), residues: 571 helix: 2.25 (0.27), residues: 351 sheet: -0.36 (0.75), residues: 50 loop : -0.75 (0.49), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 367 TYR 0.023 0.002 TYR A 353 PHE 0.013 0.001 PHE A 88 TRP 0.016 0.001 TRP A 275 HIS 0.004 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 4534) covalent geometry : angle 0.75467 ( 6165) SS BOND : bond 0.00346 ( 3) SS BOND : angle 0.96365 ( 6) hydrogen bonds : bond 0.04155 ( 296) hydrogen bonds : angle 4.33294 ( 885) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 34 SER cc_start: 0.9573 (t) cc_final: 0.9224 (t) REVERT: A 40 ASP cc_start: 0.8764 (t0) cc_final: 0.8525 (t70) REVERT: A 99 GLU cc_start: 0.9068 (tp30) cc_final: 0.8819 (tp30) REVERT: A 268 LYS cc_start: 0.9129 (tptp) cc_final: 0.8488 (tptp) REVERT: A 308 GLN cc_start: 0.9234 (mp10) cc_final: 0.8585 (mp10) REVERT: A 316 MET cc_start: 0.9121 (tmm) cc_final: 0.8633 (tmm) REVERT: A 317 GLU cc_start: 0.9443 (tp30) cc_final: 0.9215 (tp30) REVERT: B 33 ASN cc_start: 0.7965 (p0) cc_final: 0.7417 (p0) REVERT: B 68 PHE cc_start: 0.9071 (OUTLIER) cc_final: 0.8460 (m-80) REVERT: B 108 GLU cc_start: 0.9095 (tp30) cc_final: 0.8860 (tp30) REVERT: B 287 MET cc_start: 0.8709 (tmm) cc_final: 0.8442 (tmm) REVERT: B 292 LEU cc_start: 0.9371 (mt) cc_final: 0.9156 (mm) REVERT: B 309 MET cc_start: 0.9359 (mtm) cc_final: 0.9081 (mtm) REVERT: B 315 ASN cc_start: 0.8065 (p0) cc_final: 0.7851 (p0) REVERT: B 334 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8117 (mt-10) REVERT: B 355 LYS cc_start: 0.9556 (tptm) cc_final: 0.9296 (tppp) REVERT: B 379 THR cc_start: 0.9495 (m) cc_final: 0.9091 (p) outliers start: 21 outliers final: 15 residues processed: 224 average time/residue: 0.0594 time to fit residues: 16.9938 Evaluate side-chains 217 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 329 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 27 optimal weight: 0.0370 chunk 17 optimal weight: 0.0570 chunk 46 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 ASN B 237 ASN B 381 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.109128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.090548 restraints weight = 10536.911| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 5.10 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4537 Z= 0.138 Angle : 0.685 11.074 6171 Z= 0.336 Chirality : 0.042 0.151 771 Planarity : 0.004 0.041 755 Dihedral : 4.289 22.720 614 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 6.81 % Allowed : 32.87 % Favored : 60.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.71 (0.36), residues: 571 helix: 2.11 (0.27), residues: 360 sheet: -0.90 (0.67), residues: 48 loop : -0.40 (0.51), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 367 TYR 0.016 0.002 TYR A 72 PHE 0.009 0.001 PHE A 13 TRP 0.011 0.001 TRP A 338 HIS 0.005 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 4534) covalent geometry : angle 0.68423 ( 6165) SS BOND : bond 0.00950 ( 3) SS BOND : angle 1.36706 ( 6) hydrogen bonds : bond 0.03859 ( 296) hydrogen bonds : angle 4.16931 ( 885) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 222 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: A 34 SER cc_start: 0.9430 (t) cc_final: 0.9048 (t) REVERT: A 40 ASP cc_start: 0.8836 (t0) cc_final: 0.8577 (t70) REVERT: A 99 GLU cc_start: 0.9192 (tp30) cc_final: 0.8942 (tp30) REVERT: A 114 GLU cc_start: 0.8034 (pt0) cc_final: 0.7270 (pm20) REVERT: A 276 GLN cc_start: 0.9199 (mt0) cc_final: 0.8639 (tt0) REVERT: A 308 GLN cc_start: 0.9315 (mp10) cc_final: 0.8618 (mp10) REVERT: A 309 MET cc_start: 0.9138 (mmm) cc_final: 0.8762 (mmm) REVERT: A 339 GLU cc_start: 0.8575 (tt0) cc_final: 0.8375 (tt0) REVERT: A 412 GLN cc_start: 0.9100 (mp10) cc_final: 0.8864 (mp10) REVERT: B 33 ASN cc_start: 0.7974 (p0) cc_final: 0.7398 (p0) REVERT: B 108 GLU cc_start: 0.9049 (tp30) cc_final: 0.8820 (tp30) REVERT: B 287 MET cc_start: 0.8874 (tmm) cc_final: 0.8524 (tmm) REVERT: B 307 LEU cc_start: 0.9435 (tp) cc_final: 0.9139 (tt) REVERT: B 309 MET cc_start: 0.9322 (mtm) cc_final: 0.8764 (mtm) REVERT: B 315 ASN cc_start: 0.8147 (p0) cc_final: 0.7749 (p0) REVERT: B 317 GLU cc_start: 0.8598 (pm20) cc_final: 0.8073 (pm20) REVERT: B 320 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7695 (mmm) REVERT: B 331 SER cc_start: 0.8293 (t) cc_final: 0.8076 (m) REVERT: B 334 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8085 (mt-10) REVERT: B 355 LYS cc_start: 0.9596 (tptm) cc_final: 0.9317 (tppp) outliers start: 34 outliers final: 18 residues processed: 233 average time/residue: 0.0484 time to fit residues: 14.5711 Evaluate side-chains 224 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 21 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 26 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 381 GLN ** 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 = 0.3576 r_free = 0.3576 target = 0.107197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.088553 restraints weight = 10747.327| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 5.12 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4537 Z= 0.160 Angle : 0.690 10.787 6171 Z= 0.342 Chirality : 0.043 0.159 771 Planarity : 0.004 0.041 755 Dihedral : 4.379 23.038 614 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.21 % Allowed : 36.47 % Favored : 58.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.69 (0.36), residues: 571 helix: 2.16 (0.27), residues: 355 sheet: -1.00 (0.68), residues: 48 loop : -0.46 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 103 TYR 0.023 0.002 TYR B 72 PHE 0.013 0.001 PHE A 88 TRP 0.013 0.002 TRP A 275 HIS 0.006 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 4534) covalent geometry : angle 0.68939 ( 6165) SS BOND : bond 0.00711 ( 3) SS BOND : angle 0.88984 ( 6) hydrogen bonds : bond 0.03854 ( 296) hydrogen bonds : angle 4.25342 ( 885) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: A 34 SER cc_start: 0.9399 (t) cc_final: 0.9057 (t) REVERT: A 40 ASP cc_start: 0.8828 (t0) cc_final: 0.8507 (t70) REVERT: A 99 GLU cc_start: 0.9197 (tp30) cc_final: 0.8922 (tp30) REVERT: A 114 GLU cc_start: 0.8009 (pt0) cc_final: 0.7582 (pm20) REVERT: A 276 GLN cc_start: 0.9138 (mt0) cc_final: 0.8619 (tt0) REVERT: A 309 MET cc_start: 0.9198 (mmm) cc_final: 0.8862 (mmm) REVERT: A 316 MET cc_start: 0.9307 (tmm) cc_final: 0.8690 (tmm) REVERT: A 368 GLU cc_start: 0.9136 (tt0) cc_final: 0.8627 (tm-30) REVERT: A 412 GLN cc_start: 0.9134 (mp10) cc_final: 0.8855 (mp10) REVERT: B 33 ASN cc_start: 0.8226 (p0) cc_final: 0.7597 (p0) REVERT: B 108 GLU cc_start: 0.9031 (tp30) cc_final: 0.8796 (tp30) REVERT: B 287 MET cc_start: 0.8944 (tmm) cc_final: 0.8556 (tmm) REVERT: B 309 MET cc_start: 0.9370 (mtm) cc_final: 0.9027 (mtm) REVERT: B 315 ASN cc_start: 0.8207 (p0) cc_final: 0.7747 (p0) REVERT: B 317 GLU cc_start: 0.8653 (pm20) cc_final: 0.8194 (pm20) REVERT: B 334 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8082 (mt-10) REVERT: B 355 LYS cc_start: 0.9635 (tptm) cc_final: 0.9361 (tppp) outliers start: 26 outliers final: 19 residues processed: 217 average time/residue: 0.0498 time to fit residues: 13.7631 Evaluate side-chains 212 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 38 optimal weight: 0.0770 chunk 33 optimal weight: 2.9990 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 381 GLN ** 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 = 0.3601 r_free = 0.3601 target = 0.109237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.091451 restraints weight = 10666.775| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 4.90 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 4537 Z= 0.139 Angle : 0.695 9.380 6171 Z= 0.345 Chirality : 0.043 0.169 771 Planarity : 0.004 0.043 755 Dihedral : 4.346 21.445 614 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.41 % Allowed : 37.88 % Favored : 58.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.59 (0.36), residues: 571 helix: 2.05 (0.27), residues: 358 sheet: -1.02 (0.68), residues: 49 loop : -0.46 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 103 TYR 0.018 0.002 TYR A 353 PHE 0.014 0.001 PHE A 88 TRP 0.011 0.001 TRP A 275 HIS 0.003 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 4534) covalent geometry : angle 0.69510 ( 6165) SS BOND : bond 0.00438 ( 3) SS BOND : angle 0.96959 ( 6) hydrogen bonds : bond 0.03752 ( 296) hydrogen bonds : angle 4.22396 ( 885) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 205 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: A 34 SER cc_start: 0.9322 (t) cc_final: 0.8956 (t) REVERT: A 40 ASP cc_start: 0.8927 (t0) cc_final: 0.8676 (t70) REVERT: A 99 GLU cc_start: 0.9287 (tp30) cc_final: 0.8975 (tp30) REVERT: A 114 GLU cc_start: 0.7871 (pt0) cc_final: 0.7151 (pm20) REVERT: A 268 LYS cc_start: 0.9065 (tptp) cc_final: 0.8111 (mmtm) REVERT: A 270 GLU cc_start: 0.9579 (pp20) cc_final: 0.9304 (pm20) REVERT: A 276 GLN cc_start: 0.9099 (mt0) cc_final: 0.8664 (tt0) REVERT: A 309 MET cc_start: 0.9192 (mmm) cc_final: 0.8875 (mmm) REVERT: A 317 GLU cc_start: 0.9477 (tp30) cc_final: 0.9167 (tp30) REVERT: A 339 GLU cc_start: 0.8408 (tt0) cc_final: 0.8208 (tt0) REVERT: A 368 GLU cc_start: 0.9072 (tt0) cc_final: 0.8621 (tm-30) REVERT: A 412 GLN cc_start: 0.9106 (mp10) cc_final: 0.8814 (mp10) REVERT: B 33 ASN cc_start: 0.8192 (p0) cc_final: 0.7563 (p0) REVERT: B 108 GLU cc_start: 0.9054 (tp30) cc_final: 0.8828 (tp30) REVERT: B 287 MET cc_start: 0.8865 (tmm) cc_final: 0.8426 (tmm) REVERT: B 309 MET cc_start: 0.9356 (mtm) cc_final: 0.8949 (mtm) REVERT: B 315 ASN cc_start: 0.8250 (p0) cc_final: 0.7769 (p0) REVERT: B 317 GLU cc_start: 0.8685 (pm20) cc_final: 0.8217 (pm20) REVERT: B 334 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8153 (mt-10) REVERT: B 355 LYS cc_start: 0.9682 (tptm) cc_final: 0.9396 (tppp) outliers start: 17 outliers final: 13 residues processed: 214 average time/residue: 0.0428 time to fit residues: 12.0226 Evaluate side-chains 209 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** B 381 GLN ** 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 = 0.3598 r_free = 0.3598 target = 0.108809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.090889 restraints weight = 10722.410| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 4.95 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4537 Z= 0.139 Angle : 0.702 9.285 6171 Z= 0.347 Chirality : 0.044 0.200 771 Planarity : 0.004 0.039 755 Dihedral : 4.286 22.939 614 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.21 % Allowed : 37.07 % Favored : 58.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.64 (0.37), residues: 571 helix: 2.10 (0.27), residues: 357 sheet: -1.24 (0.67), residues: 49 loop : -0.36 (0.53), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 103 TYR 0.016 0.002 TYR A 72 PHE 0.022 0.002 PHE A 97 TRP 0.013 0.001 TRP A 275 HIS 0.005 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 4534) covalent geometry : angle 0.70181 ( 6165) SS BOND : bond 0.00345 ( 3) SS BOND : angle 0.98401 ( 6) hydrogen bonds : bond 0.03801 ( 296) hydrogen bonds : angle 4.26179 ( 885) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.107 Fit side-chains revert: symmetry clash REVERT: A 34 SER cc_start: 0.9413 (t) cc_final: 0.9055 (t) REVERT: A 99 GLU cc_start: 0.9305 (tp30) cc_final: 0.8993 (tp30) REVERT: A 108 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8470 (mm-30) REVERT: A 114 GLU cc_start: 0.7805 (pt0) cc_final: 0.7080 (pm20) REVERT: A 260 ILE cc_start: 0.8668 (mp) cc_final: 0.8462 (mp) REVERT: A 268 LYS cc_start: 0.9041 (tptp) cc_final: 0.8001 (mmtm) REVERT: A 270 GLU cc_start: 0.9544 (pp20) cc_final: 0.9310 (pm20) REVERT: A 276 GLN cc_start: 0.9077 (mt0) cc_final: 0.8649 (tt0) REVERT: A 309 MET cc_start: 0.9204 (mmm) cc_final: 0.8906 (mmm) REVERT: A 315 ASN cc_start: 0.8654 (t0) cc_final: 0.8200 (t0) REVERT: A 317 GLU cc_start: 0.9477 (tp30) cc_final: 0.8929 (tp30) REVERT: A 318 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8787 (tm-30) REVERT: A 339 GLU cc_start: 0.8376 (tt0) cc_final: 0.8141 (tt0) REVERT: A 368 GLU cc_start: 0.9109 (tt0) cc_final: 0.8655 (tm-30) REVERT: B 33 ASN cc_start: 0.8219 (p0) cc_final: 0.7597 (p0) REVERT: B 108 GLU cc_start: 0.9048 (tp30) cc_final: 0.8827 (tp30) REVERT: B 236 LEU cc_start: 0.9630 (mm) cc_final: 0.9389 (mp) REVERT: B 287 MET cc_start: 0.8906 (tmm) cc_final: 0.8466 (tmm) REVERT: B 309 MET cc_start: 0.9407 (mtm) cc_final: 0.8986 (mtm) REVERT: B 315 ASN cc_start: 0.8286 (p0) cc_final: 0.7738 (p0) REVERT: B 317 GLU cc_start: 0.8740 (pm20) cc_final: 0.8310 (pm20) REVERT: B 318 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8885 (mt-10) REVERT: B 355 LYS cc_start: 0.9705 (tptm) cc_final: 0.9430 (tppp) outliers start: 21 outliers final: 17 residues processed: 201 average time/residue: 0.0507 time to fit residues: 13.2709 Evaluate side-chains 207 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 0.0370 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 381 GLN ** 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 = 0.3596 r_free = 0.3596 target = 0.108553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.090690 restraints weight = 10723.424| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 4.90 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4537 Z= 0.144 Angle : 0.730 9.956 6171 Z= 0.357 Chirality : 0.044 0.267 771 Planarity : 0.004 0.036 755 Dihedral : 4.255 22.541 614 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.41 % Allowed : 37.27 % Favored : 58.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.64 (0.37), residues: 571 helix: 2.07 (0.27), residues: 357 sheet: -1.17 (0.67), residues: 49 loop : -0.32 (0.54), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 103 TYR 0.019 0.002 TYR B 72 PHE 0.020 0.001 PHE A 97 TRP 0.013 0.001 TRP A 275 HIS 0.005 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 4534) covalent geometry : angle 0.73015 ( 6165) SS BOND : bond 0.00319 ( 3) SS BOND : angle 0.88773 ( 6) hydrogen bonds : bond 0.03832 ( 296) hydrogen bonds : angle 4.29860 ( 885) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: A 34 SER cc_start: 0.9435 (t) cc_final: 0.9083 (t) REVERT: A 99 GLU cc_start: 0.9315 (tp30) cc_final: 0.9007 (tp30) REVERT: A 108 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8405 (mm-30) REVERT: A 111 ASP cc_start: 0.8291 (m-30) cc_final: 0.8052 (m-30) REVERT: A 114 GLU cc_start: 0.7794 (pt0) cc_final: 0.7389 (pm20) REVERT: A 260 ILE cc_start: 0.8691 (mp) cc_final: 0.8434 (mp) REVERT: A 268 LYS cc_start: 0.9055 (tptp) cc_final: 0.7933 (mmtm) REVERT: A 270 GLU cc_start: 0.9541 (pp20) cc_final: 0.9299 (pm20) REVERT: A 276 GLN cc_start: 0.9054 (mt0) cc_final: 0.8650 (tt0) REVERT: A 309 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8911 (mmm) REVERT: A 315 ASN cc_start: 0.8706 (t0) cc_final: 0.8231 (t0) REVERT: A 317 GLU cc_start: 0.9446 (tp30) cc_final: 0.8948 (tp30) REVERT: A 318 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8756 (tm-30) REVERT: A 339 GLU cc_start: 0.8384 (tt0) cc_final: 0.8156 (tt0) REVERT: A 355 LYS cc_start: 0.9243 (tptp) cc_final: 0.8931 (tppt) REVERT: A 368 GLU cc_start: 0.9072 (tt0) cc_final: 0.8636 (tm-30) REVERT: A 412 GLN cc_start: 0.8968 (mp10) cc_final: 0.8686 (mp10) REVERT: B 33 ASN cc_start: 0.8249 (p0) cc_final: 0.7621 (p0) REVERT: B 108 GLU cc_start: 0.9019 (tp30) cc_final: 0.8790 (tp30) REVERT: B 236 LEU cc_start: 0.9626 (mm) cc_final: 0.9401 (mp) REVERT: B 287 MET cc_start: 0.8900 (tmm) cc_final: 0.8451 (tmm) REVERT: B 301 GLU cc_start: 0.9112 (tp30) cc_final: 0.8718 (tp30) REVERT: B 309 MET cc_start: 0.9395 (mtm) cc_final: 0.8994 (mtm) REVERT: B 315 ASN cc_start: 0.8335 (p0) cc_final: 0.7752 (p0) REVERT: B 317 GLU cc_start: 0.8764 (pm20) cc_final: 0.8364 (pm20) REVERT: B 318 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8885 (mt-10) outliers start: 22 outliers final: 16 residues processed: 204 average time/residue: 0.0562 time to fit residues: 14.7954 Evaluate side-chains 210 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 193 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 29 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 45 optimal weight: 0.0030 chunk 8 optimal weight: 2.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 381 GLN ** 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 = 0.3592 r_free = 0.3592 target = 0.108782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.090993 restraints weight = 10641.209| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 4.90 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4537 Z= 0.140 Angle : 0.737 10.393 6171 Z= 0.363 Chirality : 0.047 0.357 771 Planarity : 0.004 0.033 755 Dihedral : 4.264 22.698 614 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.21 % Allowed : 38.88 % Favored : 57.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.65 (0.37), residues: 571 helix: 2.04 (0.27), residues: 357 sheet: -1.14 (0.67), residues: 49 loop : -0.23 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.017 0.002 TYR B 72 PHE 0.019 0.001 PHE A 97 TRP 0.012 0.001 TRP A 275 HIS 0.005 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 4534) covalent geometry : angle 0.73663 ( 6165) SS BOND : bond 0.00322 ( 3) SS BOND : angle 0.93919 ( 6) hydrogen bonds : bond 0.03854 ( 296) hydrogen bonds : angle 4.33794 ( 885) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 34 SER cc_start: 0.9370 (t) cc_final: 0.8985 (t) REVERT: A 99 GLU cc_start: 0.9336 (tp30) cc_final: 0.9050 (tp30) REVERT: A 108 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8409 (mm-30) REVERT: A 111 ASP cc_start: 0.8316 (m-30) cc_final: 0.8079 (m-30) REVERT: A 114 GLU cc_start: 0.7798 (pt0) cc_final: 0.7366 (pm20) REVERT: A 260 ILE cc_start: 0.8664 (mp) cc_final: 0.8401 (mp) REVERT: A 268 LYS cc_start: 0.9023 (tptp) cc_final: 0.8117 (mmtm) REVERT: A 276 GLN cc_start: 0.9010 (mt0) cc_final: 0.8595 (tt0) REVERT: A 309 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8900 (mmm) REVERT: A 315 ASN cc_start: 0.8704 (t0) cc_final: 0.8242 (t0) REVERT: A 317 GLU cc_start: 0.9426 (tp30) cc_final: 0.8972 (tp30) REVERT: A 318 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8748 (tm-30) REVERT: A 368 GLU cc_start: 0.9056 (tt0) cc_final: 0.8674 (tm-30) REVERT: A 412 GLN cc_start: 0.8962 (mp10) cc_final: 0.8701 (mp10) REVERT: B 33 ASN cc_start: 0.8259 (p0) cc_final: 0.7624 (p0) REVERT: B 108 GLU cc_start: 0.9001 (tp30) cc_final: 0.8784 (tp30) REVERT: B 236 LEU cc_start: 0.9649 (mm) cc_final: 0.9430 (mp) REVERT: B 287 MET cc_start: 0.8883 (tmm) cc_final: 0.8433 (tmm) REVERT: B 301 GLU cc_start: 0.9151 (tp30) cc_final: 0.8739 (tp30) REVERT: B 309 MET cc_start: 0.9415 (mtm) cc_final: 0.9014 (mtm) REVERT: B 315 ASN cc_start: 0.8291 (p0) cc_final: 0.7720 (p0) REVERT: B 317 GLU cc_start: 0.8817 (pm20) cc_final: 0.8511 (pm20) REVERT: B 318 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8940 (mt-10) REVERT: B 360 GLN cc_start: 0.9278 (tm-30) cc_final: 0.9034 (tm-30) outliers start: 16 outliers final: 13 residues processed: 191 average time/residue: 0.0526 time to fit residues: 13.0545 Evaluate side-chains 201 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 9.9990 chunk 54 optimal weight: 0.0980 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 381 GLN ** 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 = 0.3610 r_free = 0.3610 target = 0.109645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.091904 restraints weight = 10655.779| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 4.89 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4537 Z= 0.140 Angle : 0.759 11.006 6171 Z= 0.373 Chirality : 0.046 0.405 771 Planarity : 0.004 0.033 755 Dihedral : 4.296 22.783 614 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.41 % Allowed : 39.48 % Favored : 57.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.62 (0.37), residues: 571 helix: 2.00 (0.27), residues: 357 sheet: -1.07 (0.68), residues: 49 loop : -0.22 (0.55), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 103 TYR 0.012 0.001 TYR B 72 PHE 0.019 0.001 PHE A 97 TRP 0.010 0.001 TRP A 275 HIS 0.006 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 4534) covalent geometry : angle 0.75917 ( 6165) SS BOND : bond 0.00374 ( 3) SS BOND : angle 0.98246 ( 6) hydrogen bonds : bond 0.03822 ( 296) hydrogen bonds : angle 4.32808 ( 885) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 34 SER cc_start: 0.9378 (t) cc_final: 0.9052 (t) REVERT: A 99 GLU cc_start: 0.9341 (tp30) cc_final: 0.9086 (tp30) REVERT: A 103 ARG cc_start: 0.8504 (mtp85) cc_final: 0.8296 (mtp85) REVERT: A 108 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8330 (mm-30) REVERT: A 111 ASP cc_start: 0.8313 (m-30) cc_final: 0.8083 (m-30) REVERT: A 114 GLU cc_start: 0.7781 (pt0) cc_final: 0.7019 (pm20) REVERT: A 260 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8358 (mp) REVERT: A 276 GLN cc_start: 0.8999 (mt0) cc_final: 0.8670 (tt0) REVERT: A 309 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8900 (mmm) REVERT: A 315 ASN cc_start: 0.8680 (t0) cc_final: 0.8205 (t0) REVERT: A 318 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8778 (tm-30) REVERT: A 353 TYR cc_start: 0.7815 (p90) cc_final: 0.7405 (p90) REVERT: A 355 LYS cc_start: 0.9291 (tptp) cc_final: 0.9063 (tppt) REVERT: A 368 GLU cc_start: 0.9043 (tt0) cc_final: 0.8671 (tm-30) REVERT: A 412 GLN cc_start: 0.8949 (mp10) cc_final: 0.8700 (mp10) REVERT: B 33 ASN cc_start: 0.8413 (p0) cc_final: 0.7750 (p0) REVERT: B 108 GLU cc_start: 0.9020 (tp30) cc_final: 0.8800 (tp30) REVERT: B 236 LEU cc_start: 0.9626 (mm) cc_final: 0.9378 (mp) REVERT: B 287 MET cc_start: 0.8887 (tmm) cc_final: 0.8434 (tmm) REVERT: B 309 MET cc_start: 0.9423 (mtm) cc_final: 0.8933 (mtm) REVERT: B 315 ASN cc_start: 0.8288 (p0) cc_final: 0.7750 (p0) REVERT: B 317 GLU cc_start: 0.8821 (pm20) cc_final: 0.8565 (pm20) REVERT: B 318 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8953 (mt-10) outliers start: 17 outliers final: 14 residues processed: 195 average time/residue: 0.0477 time to fit residues: 12.1594 Evaluate side-chains 207 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 4 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 16 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 20 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 384 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 = 0.3615 r_free = 0.3615 target = 0.110304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.092478 restraints weight = 10685.221| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 4.98 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4537 Z= 0.140 Angle : 0.753 10.964 6171 Z= 0.373 Chirality : 0.045 0.210 771 Planarity : 0.004 0.033 755 Dihedral : 4.290 22.995 614 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.01 % Allowed : 39.48 % Favored : 56.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.61 (0.37), residues: 571 helix: 1.96 (0.27), residues: 358 sheet: -1.02 (0.69), residues: 49 loop : -0.16 (0.56), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 103 TYR 0.014 0.002 TYR B 72 PHE 0.020 0.002 PHE A 42 TRP 0.010 0.001 TRP A 275 HIS 0.005 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 4534) covalent geometry : angle 0.75289 ( 6165) SS BOND : bond 0.00303 ( 3) SS BOND : angle 0.90554 ( 6) hydrogen bonds : bond 0.03896 ( 296) hydrogen bonds : angle 4.35796 ( 885) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1142 Ramachandran restraints generated. 571 Oldfield, 0 Emsley, 571 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: A 34 SER cc_start: 0.9389 (t) cc_final: 0.9055 (t) REVERT: A 69 SER cc_start: 0.9282 (p) cc_final: 0.9050 (t) REVERT: A 99 GLU cc_start: 0.9344 (tp30) cc_final: 0.9092 (tp30) REVERT: A 108 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8304 (mm-30) REVERT: A 111 ASP cc_start: 0.8332 (m-30) cc_final: 0.8108 (m-30) REVERT: A 114 GLU cc_start: 0.7703 (pt0) cc_final: 0.6948 (pm20) REVERT: A 260 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8394 (mp) REVERT: A 270 GLU cc_start: 0.9347 (pp20) cc_final: 0.9114 (pp20) REVERT: A 276 GLN cc_start: 0.8990 (mt0) cc_final: 0.8664 (tt0) REVERT: A 309 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8912 (mmm) REVERT: A 315 ASN cc_start: 0.8698 (t0) cc_final: 0.8234 (t0) REVERT: A 317 GLU cc_start: 0.9352 (tp30) cc_final: 0.9064 (tp30) REVERT: A 318 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8785 (tm-30) REVERT: A 368 GLU cc_start: 0.9039 (tt0) cc_final: 0.8680 (tm-30) REVERT: A 384 ASN cc_start: 0.8832 (m-40) cc_final: 0.8281 (t0) REVERT: A 412 GLN cc_start: 0.8966 (mp10) cc_final: 0.8720 (mp10) REVERT: B 33 ASN cc_start: 0.8432 (p0) cc_final: 0.7767 (p0) REVERT: B 108 GLU cc_start: 0.8988 (tp30) cc_final: 0.8771 (tp30) REVERT: B 236 LEU cc_start: 0.9607 (mm) cc_final: 0.9357 (mp) REVERT: B 287 MET cc_start: 0.8902 (tmm) cc_final: 0.8451 (tmm) REVERT: B 309 MET cc_start: 0.9403 (mtm) cc_final: 0.8981 (mtm) REVERT: B 315 ASN cc_start: 0.8310 (p0) cc_final: 0.7796 (p0) REVERT: B 317 GLU cc_start: 0.8831 (pm20) cc_final: 0.8631 (pm20) REVERT: B 318 GLU cc_start: 0.9214 (mt-10) cc_final: 0.9001 (mt-10) outliers start: 20 outliers final: 16 residues processed: 203 average time/residue: 0.0424 time to fit residues: 11.2971 Evaluate side-chains 208 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 282 SER Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 326 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 20 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 0.0370 chunk 43 optimal weight: 3.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 381 GLN ** 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 = 0.3613 r_free = 0.3613 target = 0.109765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.091766 restraints weight = 10640.633| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 4.97 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.5852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4537 Z= 0.148 Angle : 0.778 11.191 6171 Z= 0.386 Chirality : 0.045 0.260 771 Planarity : 0.004 0.033 755 Dihedral : 4.274 22.646 614 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.81 % Allowed : 40.68 % Favored : 55.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.63 (0.37), residues: 571 helix: 1.93 (0.27), residues: 358 sheet: -0.84 (0.69), residues: 49 loop : -0.11 (0.56), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 76 TYR 0.014 0.002 TYR B 72 PHE 0.019 0.002 PHE A 42 TRP 0.011 0.001 TRP A 275 HIS 0.005 0.001 HIS B 336 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 4534) covalent geometry : angle 0.77818 ( 6165) SS BOND : bond 0.00317 ( 3) SS BOND : angle 0.91226 ( 6) hydrogen bonds : bond 0.03887 ( 296) hydrogen bonds : angle 4.37269 ( 885) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 867.11 seconds wall clock time: 15 minutes 42.31 seconds (942.31 seconds total)