Starting phenix.real_space_refine on Tue Aug 4 12:26:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uxs_64597/08_2026/9uxs_64597.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uxs_64597/08_2026/9uxs_64597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uxs_64597/08_2026/9uxs_64597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uxs_64597/08_2026/9uxs_64597.map" model { file = "/net/cci-nas-00/data/ceres_data/9uxs_64597/08_2026/9uxs_64597.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uxs_64597/08_2026/9uxs_64597.cif" } resolution = 3.4 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= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 13 5.16 5 C 1648 2.51 5 N 429 2.21 5 O 469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2559 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 951 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "B" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1608 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 13, 'TRANS': 186} Time building chain proxies: 0.63, per 1000 atoms: 0.25 Number of scatterers: 2559 At special positions: 0 Unit cell: (67.45, 74.1, 73.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 13 16.00 O 469 8.00 N 429 7.00 C 1648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 5 " - pdb=" SG CYS A 111 " distance=2.03 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 83 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 96.5 milliseconds 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 598 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 6 sheets defined 17.7% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 9 through 15 removed outlier: 4.012A pdb=" N MET A 15 " --> pdb=" O LYS A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.750A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 411 removed outlier: 3.716A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.727A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 41 removed outlier: 3.781A pdb=" N VAL A 85 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 109 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 93 removed outlier: 6.259A pdb=" N TYR A 91 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR A 99 " --> pdb=" O TYR A 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA5, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 454 70 hydrogen bonds defined for protein. 168 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: 0.36 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 408 1.31 - 1.44: 790 1.44 - 1.56: 1425 1.56 - 1.69: 0 1.69 - 1.81: 14 Bond restraints: 2637 Sorted by residual: bond pdb=" C HIS A 32 " pdb=" O HIS A 32 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.47e-02 4.63e+03 9.61e+00 bond pdb=" C HIS A 32 " pdb=" N HIS A 33 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.44e-02 4.82e+03 8.00e+00 bond pdb=" CA HIS A 32 " pdb=" C HIS A 32 " ideal model delta sigma weight residual 1.523 1.478 0.045 1.80e-02 3.09e+03 6.38e+00 bond pdb=" C PRO A 31 " pdb=" N HIS A 32 " ideal model delta sigma weight residual 1.331 1.298 0.033 1.62e-02 3.81e+03 4.10e+00 bond pdb=" N HIS A 32 " pdb=" CA HIS A 32 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.40e-02 5.10e+03 4.08e+00 ... (remaining 2632 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 3249 1.09 - 2.19: 276 2.19 - 3.28: 57 3.28 - 4.38: 4 4.38 - 5.47: 4 Bond angle restraints: 3590 Sorted by residual: angle pdb=" C LEU A 60 " pdb=" N ASN A 61 " pdb=" CA ASN A 61 " ideal model delta sigma weight residual 121.54 127.01 -5.47 1.91e+00 2.74e-01 8.21e+00 angle pdb=" N ILE A 34 " pdb=" CA ILE A 34 " pdb=" C ILE A 34 " ideal model delta sigma weight residual 110.05 107.23 2.82 1.09e+00 8.42e-01 6.71e+00 angle pdb=" N ASP A 58 " pdb=" CA ASP A 58 " pdb=" C ASP A 58 " ideal model delta sigma weight residual 108.17 103.44 4.73 1.85e+00 2.92e-01 6.53e+00 angle pdb=" O PRO A 31 " pdb=" C PRO A 31 " pdb=" N HIS A 32 " ideal model delta sigma weight residual 122.22 119.18 3.04 1.29e+00 6.01e-01 5.56e+00 angle pdb=" C TRP B 436 " pdb=" CA TRP B 436 " pdb=" CB TRP B 436 " ideal model delta sigma weight residual 113.33 108.03 5.30 2.26e+00 1.96e-01 5.50e+00 ... (remaining 3585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 1409 17.80 - 35.59: 126 35.59 - 53.39: 28 53.39 - 71.18: 2 71.18 - 88.98: 5 Dihedral angle restraints: 1570 sinusoidal: 632 harmonic: 938 Sorted by residual: dihedral pdb=" CB CYS A 5 " pdb=" SG CYS A 5 " pdb=" SG CYS A 111 " pdb=" CB CYS A 111 " ideal model delta sinusoidal sigma weight residual 93.00 176.73 -83.73 1 1.00e+01 1.00e-02 8.55e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 158.88 -65.88 1 1.00e+01 1.00e-02 5.68e+01 dihedral pdb=" CA ALA B 372 " pdb=" C ALA B 372 " pdb=" N PRO B 373 " pdb=" CA PRO B 373 " ideal model delta harmonic sigma weight residual 180.00 154.30 25.70 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 1567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 230 0.038 - 0.075: 103 0.075 - 0.113: 36 0.113 - 0.151: 5 0.151 - 0.188: 2 Chirality restraints: 376 Sorted by residual: chirality pdb=" CB VAL A 26 " pdb=" CA VAL A 26 " pdb=" CG1 VAL A 26 " pdb=" CG2 VAL A 26 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.86e-01 chirality pdb=" CB THR B 415 " pdb=" CA THR B 415 " pdb=" OG1 THR B 415 " pdb=" CG2 THR B 415 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CB ILE B 434 " pdb=" CA ILE B 434 " pdb=" CG1 ILE B 434 " pdb=" CG2 ILE B 434 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 373 not shown) Planarity restraints: 463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 526 " 0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO B 527 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 436 " 0.013 2.00e-02 2.50e+03 8.31e-03 1.73e+00 pdb=" CG TRP B 436 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP B 436 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP B 436 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 436 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 436 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 436 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 436 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 436 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 436 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 462 " 0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO B 463 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 463 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 463 " 0.018 5.00e-02 4.00e+02 ... (remaining 460 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 552 2.78 - 3.31: 2381 3.31 - 3.84: 4141 3.84 - 4.37: 4726 4.37 - 4.90: 8171 Nonbonded interactions: 19971 Sorted by model distance: nonbonded pdb=" OD2 ASP B 442 " pdb=" OH TYR B 451 " model vdw 2.249 3.040 nonbonded pdb=" OG SER B 359 " pdb=" OG1 THR B 523 " model vdw 2.255 3.040 nonbonded pdb=" O SER B 438 " pdb=" OG SER B 438 " model vdw 2.295 3.040 nonbonded pdb=" O VAL A 85 " pdb=" OG SER A 86 " model vdw 2.350 3.040 nonbonded pdb=" OG1 THR B 393 " pdb=" O GLU B 516 " model vdw 2.389 3.040 ... (remaining 19966 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.090 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:1.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 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 : 0.004 0.046 2643 Z= 0.209 Angle : 0.686 5.473 3602 Z= 0.399 Chirality : 0.048 0.188 376 Planarity : 0.005 0.033 463 Dihedral : 14.027 88.978 954 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: -1.55 (0.47), residues: 312 helix: -1.61 (0.99), residues: 27 sheet: -1.03 (0.55), residues: 67 loop : -0.96 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 403 TYR 0.017 0.002 TYR B 423 PHE 0.014 0.002 PHE B 374 TRP 0.022 0.002 TRP B 436 HIS 0.005 0.002 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.21 ( 2637) covalent geometry : angle 0.68557 / 0.40 ( 3590) SS BOND : bond 0.00206 / 0.10 ( 6) SS BOND : angle 0.82521 / 0.41 ( 12) hydrogen bonds : bond 0.17097 / 9.94 ( 70) hydrogen bonds : angle 9.03839 / 6.11 ( 168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.091 Fit side-chains REVERT: A 40 TYR cc_start: 0.7527 (m-10) cc_final: 0.7311 (m-10) REVERT: A 42 ASP cc_start: 0.7905 (t70) cc_final: 0.7676 (t0) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.0732 time to fit residues: 7.5737 Evaluate side-chains 72 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 10.0000 chunk 12 optimal weight: 0.0770 chunk 24 optimal weight: 0.0470 chunk 28 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.0020 chunk 8 optimal weight: 2.9990 chunk 30 optimal weight: 0.0770 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 0.1980 overall best weight: 0.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 417 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.161839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.130593 restraints weight = 4574.192| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 3.77 r_work: 0.3542 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2643 Z= 0.122 Angle : 0.674 10.575 3602 Z= 0.359 Chirality : 0.047 0.150 376 Planarity : 0.005 0.034 463 Dihedral : 6.134 22.445 356 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.14 % Allowed : 9.96 % Favored : 87.90 % 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: -1.27 (0.47), residues: 312 helix: -0.90 (0.95), residues: 33 sheet: -0.86 (0.52), residues: 77 loop : -0.80 (0.46), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 403 TYR 0.024 0.002 TYR A 91 PHE 0.016 0.002 PHE B 456 TRP 0.018 0.002 TRP B 436 HIS 0.002 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 2637) covalent geometry : angle 0.63609 / 0.34 ( 3590) SS BOND : bond 0.00119 / 0.07 ( 6) SS BOND : angle 3.88776 / 2.51 ( 12) hydrogen bonds : bond 0.03954 / 2.63 ( 70) hydrogen bonds : angle 7.64320 / 5.36 ( 168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.058 Fit side-chains revert: symmetry clash REVERT: A 42 ASP cc_start: 0.8163 (t70) cc_final: 0.7760 (t0) REVERT: A 79 LYS cc_start: 0.7310 (ttmt) cc_final: 0.7110 (ttmm) REVERT: A 82 LYS cc_start: 0.8495 (pttm) cc_final: 0.8143 (pttm) REVERT: B 456 PHE cc_start: 0.8284 (m-80) cc_final: 0.8033 (m-80) outliers start: 6 outliers final: 5 residues processed: 79 average time/residue: 0.0469 time to fit residues: 4.3583 Evaluate side-chains 77 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain B residue 405 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 4 optimal weight: 0.0970 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 32 HIS ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.157532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.125178 restraints weight = 4611.520| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 3.74 r_work: 0.3457 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2643 Z= 0.183 Angle : 0.672 10.220 3602 Z= 0.358 Chirality : 0.048 0.184 376 Planarity : 0.005 0.030 463 Dihedral : 6.160 21.889 356 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.91 % Allowed : 13.52 % Favored : 82.56 % 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: -1.08 (0.47), residues: 312 helix: -0.31 (1.06), residues: 25 sheet: -0.83 (0.52), residues: 75 loop : -0.70 (0.45), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 454 TYR 0.017 0.002 TYR A 91 PHE 0.010 0.001 PHE B 400 TRP 0.015 0.002 TRP B 436 HIS 0.005 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 2637) covalent geometry : angle 0.64221 / 0.35 ( 3590) SS BOND : bond 0.00420 / 0.26 ( 6) SS BOND : angle 3.46460 / 2.30 ( 12) hydrogen bonds : bond 0.04028 / 2.49 ( 70) hydrogen bonds : angle 7.50953 / 5.22 ( 168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.8606 (pttm) cc_final: 0.8266 (pttm) REVERT: B 406 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: B 456 PHE cc_start: 0.8333 (m-80) cc_final: 0.8063 (m-10) outliers start: 11 outliers final: 8 residues processed: 84 average time/residue: 0.0517 time to fit residues: 5.1905 Evaluate side-chains 82 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.0670 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 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 = 0.3999 r_free = 0.3999 target = 0.156958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.124281 restraints weight = 4594.685| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.72 r_work: 0.3449 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2643 Z= 0.187 Angle : 0.688 10.201 3602 Z= 0.363 Chirality : 0.049 0.196 376 Planarity : 0.004 0.028 463 Dihedral : 6.153 21.596 356 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.20 % Allowed : 18.51 % Favored : 78.29 % 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: -1.21 (0.47), residues: 312 helix: -0.86 (0.90), residues: 31 sheet: -0.76 (0.52), residues: 75 loop : -0.79 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 18 TYR 0.015 0.002 TYR A 93 PHE 0.009 0.001 PHE B 400 TRP 0.014 0.002 TRP B 436 HIS 0.006 0.002 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 ( 2637) covalent geometry : angle 0.65907 / 0.35 ( 3590) SS BOND : bond 0.00328 / 0.21 ( 6) SS BOND : angle 3.48148 / 2.30 ( 12) hydrogen bonds : bond 0.03941 / 2.42 ( 70) hydrogen bonds : angle 7.55651 / 5.23 ( 168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.059 Fit side-chains revert: symmetry clash REVERT: B 406 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7808 (pm20) REVERT: B 456 PHE cc_start: 0.8399 (m-80) cc_final: 0.8061 (m-10) outliers start: 9 outliers final: 7 residues processed: 83 average time/residue: 0.0532 time to fit residues: 5.2047 Evaluate side-chains 81 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.0020 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 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 = 0.4008 r_free = 0.4008 target = 0.157530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.124516 restraints weight = 4596.920| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 3.77 r_work: 0.3452 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2643 Z= 0.185 Angle : 0.687 10.262 3602 Z= 0.363 Chirality : 0.049 0.198 376 Planarity : 0.004 0.029 463 Dihedral : 6.105 21.312 356 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.34 % Allowed : 18.51 % Favored : 76.16 % 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: -1.09 (0.47), residues: 312 helix: -0.28 (1.05), residues: 25 sheet: -0.72 (0.52), residues: 75 loop : -0.77 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 18 TYR 0.012 0.002 TYR A 93 PHE 0.010 0.001 PHE B 429 TRP 0.014 0.002 TRP B 436 HIS 0.006 0.002 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 ( 2637) covalent geometry : angle 0.65801 / 0.35 ( 3590) SS BOND : bond 0.00239 / 0.14 ( 6) SS BOND : angle 3.47692 / 2.31 ( 12) hydrogen bonds : bond 0.03902 / 2.38 ( 70) hydrogen bonds : angle 7.65747 / 5.29 ( 168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.8533 (pttm) cc_final: 0.8187 (pttm) REVERT: B 406 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7821 (pm20) REVERT: B 427 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7926 (m-30) REVERT: B 456 PHE cc_start: 0.8462 (m-80) cc_final: 0.8221 (m-80) outliers start: 15 outliers final: 10 residues processed: 83 average time/residue: 0.0546 time to fit residues: 5.4816 Evaluate side-chains 86 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 15 optimal weight: 0.0370 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 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 = 0.4030 r_free = 0.4030 target = 0.159417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.126612 restraints weight = 4615.068| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 3.75 r_work: 0.3488 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2643 Z= 0.144 Angle : 0.664 9.883 3602 Z= 0.353 Chirality : 0.048 0.178 376 Planarity : 0.004 0.029 463 Dihedral : 5.964 22.653 356 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 5.34 % Allowed : 21.00 % Favored : 73.67 % 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: -1.06 (0.48), residues: 312 helix: -0.66 (0.93), residues: 31 sheet: -0.61 (0.52), residues: 75 loop : -0.72 (0.47), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 498 TYR 0.015 0.002 TYR A 57 PHE 0.010 0.001 PHE B 429 TRP 0.016 0.001 TRP B 436 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 2637) covalent geometry : angle 0.63400 / 0.34 ( 3590) SS BOND : bond 0.00246 / 0.16 ( 6) SS BOND : angle 3.47833 / 2.31 ( 12) hydrogen bonds : bond 0.03669 / 2.26 ( 70) hydrogen bonds : angle 7.61937 / 5.26 ( 168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: A 40 TYR cc_start: 0.7520 (m-10) cc_final: 0.7317 (m-10) REVERT: A 82 LYS cc_start: 0.8528 (pttm) cc_final: 0.8103 (pttm) REVERT: B 406 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7816 (pm20) REVERT: B 427 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7936 (m-30) REVERT: B 456 PHE cc_start: 0.8454 (m-80) cc_final: 0.8163 (m-80) outliers start: 15 outliers final: 11 residues processed: 86 average time/residue: 0.0560 time to fit residues: 5.7338 Evaluate side-chains 90 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 4 optimal weight: 0.0060 chunk 22 optimal weight: 0.0170 chunk 16 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 25 optimal weight: 0.0070 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.0970 chunk 19 optimal weight: 0.0980 chunk 26 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.0450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.165744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.134297 restraints weight = 4607.934| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.75 r_work: 0.3585 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2643 Z= 0.105 Angle : 0.651 8.193 3602 Z= 0.342 Chirality : 0.047 0.130 376 Planarity : 0.004 0.031 463 Dihedral : 5.656 23.877 356 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.85 % Allowed : 23.13 % Favored : 74.02 % 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: -0.90 (0.48), residues: 312 helix: -0.60 (0.96), residues: 31 sheet: -0.58 (0.53), residues: 78 loop : -0.56 (0.46), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 498 TYR 0.014 0.001 TYR A 93 PHE 0.012 0.001 PHE B 374 TRP 0.020 0.002 TRP B 436 HIS 0.002 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 2637) covalent geometry : angle 0.62402 / 0.33 ( 3590) SS BOND : bond 0.00354 / 0.24 ( 6) SS BOND : angle 3.28653 / 2.14 ( 12) hydrogen bonds : bond 0.03331 / 2.07 ( 70) hydrogen bonds : angle 7.68907 / 5.25 ( 168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: A 68 LEU cc_start: 0.9012 (tp) cc_final: 0.8772 (tt) REVERT: A 82 LYS cc_start: 0.8505 (pttm) cc_final: 0.8221 (pttm) REVERT: B 427 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7942 (m-30) REVERT: B 452 LEU cc_start: 0.7548 (mt) cc_final: 0.7021 (pt) outliers start: 8 outliers final: 6 residues processed: 85 average time/residue: 0.0703 time to fit residues: 6.9940 Evaluate side-chains 82 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 427 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 28 optimal weight: 0.0970 chunk 22 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 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 = 0.4060 r_free = 0.4060 target = 0.161751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.129487 restraints weight = 4697.942| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 3.75 r_work: 0.3522 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 2643 Z= 0.160 Angle : 0.678 9.754 3602 Z= 0.357 Chirality : 0.047 0.173 376 Planarity : 0.005 0.032 463 Dihedral : 5.938 26.612 356 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 4.98 % Allowed : 18.51 % Favored : 76.51 % 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: -0.98 (0.48), residues: 312 helix: -0.65 (0.97), residues: 31 sheet: -0.50 (0.53), residues: 75 loop : -0.69 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 96 TYR 0.016 0.002 TYR A 93 PHE 0.061 0.002 PHE B 456 TRP 0.014 0.002 TRP B 436 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 2637) covalent geometry : angle 0.65276 / 0.35 ( 3590) SS BOND : bond 0.00238 / 0.15 ( 6) SS BOND : angle 3.22024 / 2.24 ( 12) hydrogen bonds : bond 0.03772 / 2.28 ( 70) hydrogen bonds : angle 7.43170 / 5.05 ( 168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.069 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.8567 (pttm) cc_final: 0.8239 (pttm) REVERT: A 98 TYR cc_start: 0.7642 (t80) cc_final: 0.7413 (t80) REVERT: B 356 LYS cc_start: 0.8527 (tppt) cc_final: 0.8319 (tptp) REVERT: B 403 ARG cc_start: 0.7742 (mtp180) cc_final: 0.7075 (mtm-85) REVERT: B 427 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: B 452 LEU cc_start: 0.7523 (mt) cc_final: 0.6965 (pt) outliers start: 14 outliers final: 10 residues processed: 84 average time/residue: 0.0760 time to fit residues: 7.3508 Evaluate side-chains 84 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 30 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 0.0670 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 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 = 0.4051 r_free = 0.4051 target = 0.161221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.128862 restraints weight = 4727.576| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 3.77 r_work: 0.3514 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2643 Z= 0.159 Angle : 0.685 9.787 3602 Z= 0.360 Chirality : 0.048 0.167 376 Planarity : 0.005 0.036 463 Dihedral : 5.960 26.409 356 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 3.91 % Allowed : 20.64 % Favored : 75.44 % 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: -1.01 (0.48), residues: 312 helix: -0.63 (0.97), residues: 31 sheet: -0.58 (0.54), residues: 75 loop : -0.69 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 454 TYR 0.016 0.002 TYR A 93 PHE 0.016 0.002 PHE B 429 TRP 0.014 0.002 TRP B 436 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 2637) covalent geometry : angle 0.66121 / 0.35 ( 3590) SS BOND : bond 0.00209 / 0.12 ( 6) SS BOND : angle 3.20121 / 2.20 ( 12) hydrogen bonds : bond 0.03768 / 2.28 ( 70) hydrogen bonds : angle 7.44875 / 5.07 ( 168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.058 Fit side-chains revert: symmetry clash REVERT: B 356 LYS cc_start: 0.8534 (tppt) cc_final: 0.8321 (tptp) REVERT: B 427 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7983 (m-30) REVERT: B 452 LEU cc_start: 0.7543 (mt) cc_final: 0.6997 (pt) outliers start: 11 outliers final: 10 residues processed: 82 average time/residue: 0.0498 time to fit residues: 4.7609 Evaluate side-chains 89 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 0.0270 chunk 21 optimal weight: 0.5980 chunk 25 optimal weight: 0.0970 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 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 = 0.4054 r_free = 0.4054 target = 0.161565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.129634 restraints weight = 4673.857| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 3.73 r_work: 0.3529 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2643 Z= 0.154 Angle : 0.698 9.676 3602 Z= 0.368 Chirality : 0.047 0.162 376 Planarity : 0.005 0.033 463 Dihedral : 6.126 29.674 356 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.27 % Allowed : 21.00 % Favored : 74.73 % 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: -0.96 (0.47), residues: 312 helix: -0.52 (0.97), residues: 31 sheet: -0.57 (0.54), residues: 75 loop : -0.66 (0.45), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 454 TYR 0.021 0.002 TYR A 98 PHE 0.015 0.002 PHE B 429 TRP 0.014 0.002 TRP B 436 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 ( 2637) covalent geometry : angle 0.67477 / 0.36 ( 3590) SS BOND : bond 0.00187 / 0.11 ( 6) SS BOND : angle 3.15274 / 2.15 ( 12) hydrogen bonds : bond 0.03713 / 2.27 ( 70) hydrogen bonds : angle 7.36540 / 5.00 ( 168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.095 Fit side-chains revert: symmetry clash REVERT: B 356 LYS cc_start: 0.8535 (tppt) cc_final: 0.8316 (tptp) REVERT: B 403 ARG cc_start: 0.7697 (mtp180) cc_final: 0.6986 (mtm-85) REVERT: B 427 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: B 452 LEU cc_start: 0.7552 (mt) cc_final: 0.6915 (pt) REVERT: B 498 ARG cc_start: 0.7448 (mmt180) cc_final: 0.7129 (mmt180) outliers start: 12 outliers final: 10 residues processed: 82 average time/residue: 0.0687 time to fit residues: 6.5207 Evaluate side-chains 85 residues out of total 281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 CYS Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 523 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 409 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 = 0.4029 r_free = 0.4029 target = 0.158915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.126330 restraints weight = 4683.305| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 3.77 r_work: 0.3479 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 2643 Z= 0.212 Angle : 0.743 9.966 3602 Z= 0.392 Chirality : 0.049 0.187 376 Planarity : 0.005 0.037 463 Dihedral : 6.340 28.998 356 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 4.27 % Allowed : 22.06 % Favored : 73.67 % 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: -1.25 (0.46), residues: 312 helix: -0.64 (0.87), residues: 37 sheet: -0.52 (0.56), residues: 71 loop : -0.98 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 454 TYR 0.035 0.003 TYR A 57 PHE 0.015 0.002 PHE B 429 TRP 0.014 0.002 TRP B 353 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 ( 2637) covalent geometry : angle 0.72162 / 0.38 ( 3590) SS BOND : bond 0.00178 / 0.09 ( 6) SS BOND : angle 3.14900 / 2.18 ( 12) hydrogen bonds : bond 0.04083 / 2.44 ( 70) hydrogen bonds : angle 7.58465 / 5.17 ( 168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1013.10 seconds wall clock time: 18 minutes 2.93 seconds (1082.93 seconds total)