Starting phenix.real_space_refine on Thu Jul 2 01:55:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wwb_32865/07_2026/7wwb_32865.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wwb_32865/07_2026/7wwb_32865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wwb_32865/07_2026/7wwb_32865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wwb_32865/07_2026/7wwb_32865.map" model { file = "/net/cci-nas-00/data/ceres_data/7wwb_32865/07_2026/7wwb_32865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wwb_32865/07_2026/7wwb_32865.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wwb_32865/07_2026/7wwb_32865.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wwb_32865/07_2026/7wwb_32865.cif" } resolution = 3.86 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= 0.018 sd= 0.094 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 60 5.16 5 C 3682 2.51 5 N 834 2.21 5 O 852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5428 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2679 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 8, 'TRANS': 324} Chain breaks: 5 Chain: "B" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2679 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 8, 'TRANS': 324} Chain breaks: 5 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'CHT': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'CHT': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.35, per 1000 atoms: 0.25 Number of scatterers: 5428 At special positions: 0 Unit cell: (107.613, 120.657, 82.612, 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 60 16.00 O 852 8.00 N 834 7.00 C 3682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.47 Conformation dependent library (CDL) restraints added in 193.3 milliseconds 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1276 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 83.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 29 through 51 Processing helix chain 'A' and resid 228 through 245 removed outlier: 5.997A pdb=" N ARG A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR A 235 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG A 238 " --> pdb=" O ARG A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 310 through 331 Processing helix chain 'A' and resid 333 through 336 Processing helix chain 'A' and resid 337 through 356 removed outlier: 3.515A pdb=" N THR A 341 " --> pdb=" O GLN A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 416 removed outlier: 3.614A pdb=" N ILE A 393 " --> pdb=" O VAL A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 431 through 438 Processing helix chain 'A' and resid 439 through 466 removed outlier: 3.545A pdb=" N VAL A 443 " --> pdb=" O HIS A 439 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 479 through 508 Processing helix chain 'A' and resid 510 through 525 Processing helix chain 'A' and resid 525 through 554 Processing helix chain 'A' and resid 573 through 607 Processing helix chain 'B' and resid 29 through 51 Processing helix chain 'B' and resid 228 through 245 removed outlier: 5.997A pdb=" N ARG B 234 " --> pdb=" O MET B 230 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR B 235 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG B 238 " --> pdb=" O ARG B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 Processing helix chain 'B' and resid 310 through 331 Processing helix chain 'B' and resid 333 through 336 Processing helix chain 'B' and resid 337 through 356 removed outlier: 3.516A pdb=" N THR B 341 " --> pdb=" O GLN B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 416 removed outlier: 3.615A pdb=" N ILE B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 431 through 438 Processing helix chain 'B' and resid 439 through 466 removed outlier: 3.544A pdb=" N VAL B 443 " --> pdb=" O HIS B 439 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL B 453 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 479 through 508 Processing helix chain 'B' and resid 510 through 525 Processing helix chain 'B' and resid 525 through 554 Processing helix chain 'B' and resid 573 through 607 428 hydrogen bonds defined for protein. 1260 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: 0.82 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 756 1.30 - 1.43: 1504 1.43 - 1.56: 3180 1.56 - 1.68: 34 1.68 - 1.81: 90 Bond restraints: 5564 Sorted by residual: bond pdb=" C GLN B 337 " pdb=" O GLN B 337 " ideal model delta sigma weight residual 1.243 1.177 0.066 9.90e-03 1.02e+04 4.38e+01 bond pdb=" C GLN A 337 " pdb=" O GLN A 337 " ideal model delta sigma weight residual 1.243 1.178 0.065 9.90e-03 1.02e+04 4.35e+01 bond pdb=" C PHE B 339 " pdb=" O PHE B 339 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.29e-02 6.01e+03 1.26e+01 bond pdb=" C PHE A 339 " pdb=" O PHE A 339 " ideal model delta sigma weight residual 1.236 1.190 0.046 1.29e-02 6.01e+03 1.25e+01 bond pdb=" C17 CLR A 702 " pdb=" C20 CLR A 702 " ideal model delta sigma weight residual 1.535 1.596 -0.061 2.00e-02 2.50e+03 9.18e+00 ... (remaining 5559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 7256 2.16 - 4.32: 268 4.32 - 6.48: 32 6.48 - 8.64: 8 8.64 - 10.80: 4 Bond angle restraints: 7568 Sorted by residual: angle pdb=" C PHE B 339 " pdb=" N TRP B 340 " pdb=" CA TRP B 340 " ideal model delta sigma weight residual 120.31 109.51 10.80 1.52e+00 4.33e-01 5.05e+01 angle pdb=" C PHE A 339 " pdb=" N TRP A 340 " pdb=" CA TRP A 340 " ideal model delta sigma weight residual 120.31 109.53 10.78 1.52e+00 4.33e-01 5.03e+01 angle pdb=" N ILE A 428 " pdb=" CA ILE A 428 " pdb=" C ILE A 428 " ideal model delta sigma weight residual 113.53 107.83 5.70 9.80e-01 1.04e+00 3.38e+01 angle pdb=" N ILE B 428 " pdb=" CA ILE B 428 " pdb=" C ILE B 428 " ideal model delta sigma weight residual 113.53 107.85 5.68 9.80e-01 1.04e+00 3.36e+01 angle pdb=" C PHE B 336 " pdb=" N GLN B 337 " pdb=" CA GLN B 337 " ideal model delta sigma weight residual 120.58 128.05 -7.47 1.32e+00 5.74e-01 3.20e+01 ... (remaining 7563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 3110 17.14 - 34.28: 68 34.28 - 51.42: 6 51.42 - 68.56: 4 68.56 - 85.70: 4 Dihedral angle restraints: 3192 sinusoidal: 1238 harmonic: 1954 Sorted by residual: dihedral pdb=" CA TYR B 438 " pdb=" C TYR B 438 " pdb=" N HIS B 439 " pdb=" CA HIS B 439 " ideal model delta harmonic sigma weight residual 180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA TYR A 438 " pdb=" C TYR A 438 " pdb=" N HIS A 439 " pdb=" CA HIS A 439 " ideal model delta harmonic sigma weight residual -180.00 -159.85 -20.15 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CB GLU B 591 " pdb=" CG GLU B 591 " pdb=" CD GLU B 591 " pdb=" OE1 GLU B 591 " ideal model delta sinusoidal sigma weight residual 0.00 -85.70 85.70 1 3.00e+01 1.11e-03 9.87e+00 ... (remaining 3189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 642 0.063 - 0.125: 240 0.125 - 0.188: 32 0.188 - 0.251: 8 0.251 - 0.313: 8 Chirality restraints: 930 Sorted by residual: chirality pdb=" C13 CLR A 702 " pdb=" C12 CLR A 702 " pdb=" C14 CLR A 702 " pdb=" C17 CLR A 702 " both_signs ideal model delta sigma weight residual False -2.93 -3.25 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C13 CLR B 702 " pdb=" C12 CLR B 702 " pdb=" C14 CLR B 702 " pdb=" C17 CLR B 702 " both_signs ideal model delta sigma weight residual False -2.93 -3.25 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C14 CLR B 702 " pdb=" C13 CLR B 702 " pdb=" C15 CLR B 702 " pdb=" C8 CLR B 702 " both_signs ideal model delta sigma weight residual False -2.32 -2.63 0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 927 not shown) Planarity restraints: 860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 343 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.71e+00 pdb=" C PHE A 343 " 0.041 2.00e-02 2.50e+03 pdb=" O PHE A 343 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA A 344 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 343 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" C PHE B 343 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE B 343 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA B 344 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 493 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C LEU B 493 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU B 493 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN B 494 " 0.013 2.00e-02 2.50e+03 ... (remaining 857 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 2767 2.99 - 3.47: 5843 3.47 - 3.94: 8642 3.94 - 4.42: 9683 4.42 - 4.90: 15145 Nonbonded interactions: 42080 Sorted by model distance: nonbonded pdb=" NZ LYS B 326 " pdb=" OD2 ASP B 619 " model vdw 2.511 3.120 nonbonded pdb=" NZ LYS A 326 " pdb=" OD2 ASP A 619 " model vdw 2.512 3.120 nonbonded pdb=" O CYS B 26 " pdb=" OG1 THR B 27 " model vdw 2.531 3.040 nonbonded pdb=" O CYS A 26 " pdb=" OG1 THR A 27 " model vdw 2.531 3.040 nonbonded pdb=" N PHE B 336 " pdb=" N GLN B 337 " model vdw 2.561 2.560 ... (remaining 42075 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 6.650 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 : 0.008 0.066 5564 Z= 0.476 Angle : 0.969 10.801 7568 Z= 0.650 Chirality : 0.066 0.313 930 Planarity : 0.006 0.026 860 Dihedral : 9.509 85.703 1916 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 0.18 (0.31), residues: 642 helix: 0.69 (0.21), residues: 518 sheet: None (None), residues: 0 loop : -2.08 (0.51), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 311 TYR 0.001 0.000 TYR B 415 PHE 0.001 0.000 PHE B 348 TRP 0.001 0.000 TRP B 386 HIS 0.001 0.000 HIS B 464 Details of bonding type rmsd/Z covalent geometry : bond 0.00825 / 0.48 ( 5564) covalent geometry : angle 0.96944 / 0.65 ( 7568) hydrogen bonds : bond 0.21072 / 13.85 ( 428) hydrogen bonds : angle 6.93898 / 4.97 ( 1260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.8669 (mt) cc_final: 0.8421 (mt) REVERT: A 234 ARG cc_start: 0.7483 (ptt180) cc_final: 0.7160 (ptt-90) REVERT: A 326 LYS cc_start: 0.8897 (mttt) cc_final: 0.8602 (ttmm) REVERT: A 342 PHE cc_start: 0.7578 (t80) cc_final: 0.7357 (m-10) REVERT: A 352 TRP cc_start: 0.8852 (t60) cc_final: 0.8616 (t60) REVERT: A 354 MET cc_start: 0.8206 (mmm) cc_final: 0.7948 (tpp) REVERT: A 438 TYR cc_start: 0.7244 (m-80) cc_final: 0.7021 (m-10) REVERT: A 516 LYS cc_start: 0.6466 (mttt) cc_final: 0.6193 (mmtp) REVERT: A 528 ARG cc_start: 0.7817 (mtt90) cc_final: 0.7031 (mpt180) REVERT: A 581 LEU cc_start: 0.8942 (mt) cc_final: 0.8654 (tt) REVERT: B 340 TRP cc_start: 0.6592 (m-10) cc_final: 0.5815 (m100) REVERT: B 437 ARG cc_start: 0.7457 (tpt90) cc_final: 0.6957 (mmt180) REVERT: B 463 ILE cc_start: 0.8796 (mt) cc_final: 0.8573 (mm) REVERT: B 508 SER cc_start: 0.8865 (m) cc_final: 0.8507 (t) REVERT: B 516 LYS cc_start: 0.6949 (mttt) cc_final: 0.6378 (mptt) REVERT: B 534 THR cc_start: 0.8810 (m) cc_final: 0.8595 (p) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.0775 time to fit residues: 28.7292 Evaluate side-chains 178 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.0670 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 HIS A 466 GLN B 439 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.157838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.122257 restraints weight = 9206.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.125672 restraints weight = 5702.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.128018 restraints weight = 4306.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.129397 restraints weight = 3633.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.130017 restraints weight = 3280.709| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5564 Z= 0.152 Angle : 0.668 7.847 7568 Z= 0.337 Chirality : 0.038 0.180 930 Planarity : 0.004 0.028 860 Dihedral : 4.883 40.194 724 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 6.04 % Allowed : 14.93 % Favored : 79.03 % 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: 2.67 (0.34), residues: 642 helix: 2.65 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -2.45 (0.49), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 614 TYR 0.012 0.001 TYR A 414 PHE 0.019 0.001 PHE B 44 TRP 0.009 0.001 TRP B 487 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 ( 5564) covalent geometry : angle 0.66772 / 0.34 ( 7568) hydrogen bonds : bond 0.05427 / 3.47 ( 428) hydrogen bonds : angle 4.17736 / 2.97 ( 1260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 MET cc_start: 0.8006 (mmp) cc_final: 0.7679 (mmp) REVERT: A 342 PHE cc_start: 0.7858 (t80) cc_final: 0.7435 (m-10) REVERT: A 397 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: A 433 ASN cc_start: 0.7461 (p0) cc_final: 0.7084 (m-40) REVERT: A 516 LYS cc_start: 0.6417 (mttt) cc_final: 0.6192 (mmtp) REVERT: A 528 ARG cc_start: 0.7902 (mtt90) cc_final: 0.7180 (mpt180) REVERT: A 538 PHE cc_start: 0.8599 (t80) cc_final: 0.7673 (t80) REVERT: A 542 LEU cc_start: 0.8698 (mp) cc_final: 0.8463 (mp) REVERT: A 578 PHE cc_start: 0.8054 (t80) cc_final: 0.7623 (t80) REVERT: A 581 LEU cc_start: 0.9024 (mt) cc_final: 0.8792 (tt) REVERT: B 21 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6907 (pp) REVERT: B 340 TRP cc_start: 0.6787 (m-10) cc_final: 0.6562 (m-10) REVERT: B 352 TRP cc_start: 0.9181 (t60) cc_final: 0.8965 (t60) REVERT: B 516 LYS cc_start: 0.7078 (mttt) cc_final: 0.6277 (mmtt) outliers start: 36 outliers final: 20 residues processed: 216 average time/residue: 0.0662 time to fit residues: 18.9786 Evaluate side-chains 183 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 28 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 603 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 13 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.0470 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 439 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.160053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123646 restraints weight = 8993.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127190 restraints weight = 5708.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.129603 restraints weight = 4364.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.130970 restraints weight = 3709.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.131348 restraints weight = 3369.568| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5564 Z= 0.151 Angle : 0.650 7.002 7568 Z= 0.328 Chirality : 0.038 0.169 930 Planarity : 0.004 0.035 860 Dihedral : 4.913 38.461 724 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 6.21 % Allowed : 17.45 % Favored : 76.34 % 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: 2.89 (0.34), residues: 642 helix: 2.66 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -2.23 (0.58), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 614 TYR 0.027 0.002 TYR A 438 PHE 0.023 0.002 PHE B 343 TRP 0.015 0.001 TRP A 352 HIS 0.003 0.001 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 5564) covalent geometry : angle 0.65018 / 0.33 ( 7568) hydrogen bonds : bond 0.05112 / 3.27 ( 428) hydrogen bonds : angle 4.02384 / 2.84 ( 1260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.129 Fit side-chains REVERT: A 230 MET cc_start: 0.8122 (mmp) cc_final: 0.7907 (mmp) REVERT: A 307 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7619 (tpt) REVERT: A 342 PHE cc_start: 0.7792 (t80) cc_final: 0.7305 (m-10) REVERT: A 397 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: A 501 TYR cc_start: 0.9220 (m-10) cc_final: 0.8951 (m-10) REVERT: A 528 ARG cc_start: 0.7724 (mtt90) cc_final: 0.7284 (mpt180) REVERT: A 538 PHE cc_start: 0.8693 (t80) cc_final: 0.7845 (t80) REVERT: A 553 LEU cc_start: 0.7923 (mp) cc_final: 0.7579 (mm) REVERT: A 581 LEU cc_start: 0.9022 (mt) cc_final: 0.8666 (tt) REVERT: B 244 LEU cc_start: 0.9046 (tt) cc_final: 0.8774 (mm) REVERT: B 438 TYR cc_start: 0.8091 (m-80) cc_final: 0.7746 (m-80) REVERT: B 454 LYS cc_start: 0.8808 (ttmt) cc_final: 0.8210 (ttmm) REVERT: B 516 LYS cc_start: 0.7265 (mttt) cc_final: 0.6697 (mmtt) outliers start: 37 outliers final: 25 residues processed: 202 average time/residue: 0.0632 time to fit residues: 17.1268 Evaluate side-chains 172 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 1 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.158624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.122713 restraints weight = 9213.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.126184 restraints weight = 5819.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.128585 restraints weight = 4430.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130107 restraints weight = 3750.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.130604 restraints weight = 3384.795| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.6410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5564 Z= 0.144 Angle : 0.643 8.529 7568 Z= 0.325 Chirality : 0.038 0.174 930 Planarity : 0.004 0.029 860 Dihedral : 4.716 38.031 724 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 6.71 % Allowed : 20.13 % Favored : 73.15 % 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: 2.84 (0.34), residues: 642 helix: 2.63 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -2.28 (0.56), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 614 TYR 0.031 0.002 TYR A 438 PHE 0.020 0.001 PHE B 343 TRP 0.009 0.001 TRP A 31 HIS 0.002 0.001 HIS A 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 5564) covalent geometry : angle 0.64322 / 0.32 ( 7568) hydrogen bonds : bond 0.04741 / 3.04 ( 428) hydrogen bonds : angle 3.94712 / 2.78 ( 1260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 0.205 Fit side-chains REVERT: A 307 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7629 (tpt) REVERT: A 342 PHE cc_start: 0.7776 (t80) cc_final: 0.7362 (m-10) REVERT: A 384 MET cc_start: 0.5463 (mpp) cc_final: 0.5043 (mpp) REVERT: A 397 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: A 445 LYS cc_start: 0.8362 (tptm) cc_final: 0.7899 (tptm) REVERT: A 449 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8886 (mp) REVERT: A 501 TYR cc_start: 0.9207 (m-10) cc_final: 0.8951 (m-10) REVERT: A 528 ARG cc_start: 0.7655 (mtt90) cc_final: 0.7394 (mpt180) REVERT: A 538 PHE cc_start: 0.8579 (t80) cc_final: 0.8141 (t80) REVERT: A 581 LEU cc_start: 0.9016 (mt) cc_final: 0.8641 (tt) REVERT: B 42 MET cc_start: 0.8615 (tpt) cc_final: 0.8176 (tpp) REVERT: B 242 TRP cc_start: 0.7674 (OUTLIER) cc_final: 0.6934 (t60) REVERT: B 244 LEU cc_start: 0.8834 (tt) cc_final: 0.8616 (mm) REVERT: B 454 LYS cc_start: 0.8702 (ttmt) cc_final: 0.8404 (ttmt) REVERT: B 516 LYS cc_start: 0.7330 (mttt) cc_final: 0.6842 (mmtt) outliers start: 40 outliers final: 26 residues processed: 188 average time/residue: 0.0581 time to fit residues: 14.8299 Evaluate side-chains 173 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 466 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.150779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117362 restraints weight = 9441.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.119304 restraints weight = 6639.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120574 restraints weight = 4822.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121606 restraints weight = 4190.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.121805 restraints weight = 3895.706| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.6852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5564 Z= 0.159 Angle : 0.649 8.680 7568 Z= 0.334 Chirality : 0.039 0.178 930 Planarity : 0.004 0.027 860 Dihedral : 4.950 40.300 724 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 7.72 % Allowed : 20.81 % Favored : 71.48 % 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: 2.91 (0.34), residues: 642 helix: 2.73 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.99 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 614 TYR 0.020 0.002 TYR A 438 PHE 0.021 0.002 PHE B 343 TRP 0.011 0.001 TRP A 386 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 5564) covalent geometry : angle 0.64878 / 0.33 ( 7568) hydrogen bonds : bond 0.04939 / 3.16 ( 428) hydrogen bonds : angle 4.00627 / 2.82 ( 1260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 0.188 Fit side-chains REVERT: A 227 MET cc_start: 0.8064 (ppp) cc_final: 0.7716 (ptt) REVERT: A 242 TRP cc_start: 0.7646 (OUTLIER) cc_final: 0.7148 (m-10) REVERT: A 307 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7645 (tpt) REVERT: A 342 PHE cc_start: 0.7798 (t80) cc_final: 0.7326 (m-10) REVERT: A 384 MET cc_start: 0.5503 (mpp) cc_final: 0.5280 (mpp) REVERT: A 393 ILE cc_start: 0.8381 (mm) cc_final: 0.8011 (mt) REVERT: A 397 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: A 445 LYS cc_start: 0.8392 (tptm) cc_final: 0.7893 (tptm) REVERT: A 449 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8788 (mp) REVERT: A 458 MET cc_start: 0.7747 (tpt) cc_final: 0.7326 (tpt) REVERT: A 538 PHE cc_start: 0.8620 (t80) cc_final: 0.8340 (t80) REVERT: A 581 LEU cc_start: 0.9051 (mt) cc_final: 0.8661 (tt) REVERT: B 40 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8745 (mt) REVERT: B 42 MET cc_start: 0.8547 (tpt) cc_final: 0.8191 (tpp) REVERT: B 242 TRP cc_start: 0.7565 (OUTLIER) cc_final: 0.6757 (t60) REVERT: B 354 MET cc_start: 0.7285 (ttp) cc_final: 0.6918 (tmm) REVERT: B 419 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.7080 (p0) REVERT: B 438 TYR cc_start: 0.8059 (m-80) cc_final: 0.7805 (m-10) REVERT: B 454 LYS cc_start: 0.8734 (ttmt) cc_final: 0.8232 (ttmt) REVERT: B 516 LYS cc_start: 0.7271 (mttt) cc_final: 0.6738 (mmtt) outliers start: 46 outliers final: 29 residues processed: 181 average time/residue: 0.0575 time to fit residues: 14.3487 Evaluate side-chains 173 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 57 optimal weight: 0.4980 chunk 64 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 44 optimal weight: 0.0970 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.153567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.121851 restraints weight = 9386.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.122249 restraints weight = 6253.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.123816 restraints weight = 5627.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.124573 restraints weight = 4360.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124909 restraints weight = 4174.973| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.7202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5564 Z= 0.131 Angle : 0.639 8.104 7568 Z= 0.321 Chirality : 0.038 0.167 930 Planarity : 0.004 0.026 860 Dihedral : 4.685 41.955 724 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 6.88 % Allowed : 23.83 % Favored : 69.30 % 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: 3.01 (0.34), residues: 642 helix: 2.79 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.95 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 614 TYR 0.020 0.002 TYR B 351 PHE 0.024 0.002 PHE B 342 TRP 0.009 0.001 TRP B 386 HIS 0.002 0.000 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 5564) covalent geometry : angle 0.63850 / 0.32 ( 7568) hydrogen bonds : bond 0.04262 / 2.74 ( 428) hydrogen bonds : angle 3.83555 / 2.68 ( 1260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 0.214 Fit side-chains REVERT: A 42 MET cc_start: 0.8444 (ttm) cc_final: 0.8201 (ttt) REVERT: A 242 TRP cc_start: 0.7672 (OUTLIER) cc_final: 0.7191 (m-10) REVERT: A 307 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7659 (tpt) REVERT: A 342 PHE cc_start: 0.7800 (t80) cc_final: 0.7310 (m-10) REVERT: A 393 ILE cc_start: 0.8256 (mm) cc_final: 0.7915 (mt) REVERT: A 397 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: A 445 LYS cc_start: 0.8239 (tptm) cc_final: 0.7831 (tptm) REVERT: A 449 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8752 (mp) REVERT: A 458 MET cc_start: 0.7794 (tpt) cc_final: 0.7386 (tpt) REVERT: A 581 LEU cc_start: 0.9018 (mt) cc_final: 0.8644 (tt) REVERT: A 599 LEU cc_start: 0.8842 (tp) cc_final: 0.8276 (tt) REVERT: B 40 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8680 (mt) REVERT: B 42 MET cc_start: 0.8584 (tpt) cc_final: 0.8275 (tpp) REVERT: B 242 TRP cc_start: 0.7598 (OUTLIER) cc_final: 0.6909 (t60) REVERT: B 343 PHE cc_start: 0.8780 (t80) cc_final: 0.8383 (t80) REVERT: B 354 MET cc_start: 0.7279 (ttp) cc_final: 0.6834 (tmm) REVERT: B 397 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8312 (mm-30) REVERT: B 419 ASP cc_start: 0.7027 (OUTLIER) cc_final: 0.6703 (p0) REVERT: B 438 TYR cc_start: 0.8019 (m-80) cc_final: 0.7613 (m-10) REVERT: B 454 LYS cc_start: 0.8629 (ttmt) cc_final: 0.8098 (ttpt) REVERT: B 516 LYS cc_start: 0.7330 (mttt) cc_final: 0.6867 (mmtt) outliers start: 41 outliers final: 26 residues processed: 179 average time/residue: 0.0550 time to fit residues: 13.6634 Evaluate side-chains 178 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 620 LYS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 615 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 16 optimal weight: 0.0570 chunk 28 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.153106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.121461 restraints weight = 9336.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.123647 restraints weight = 6327.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.125075 restraints weight = 4539.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.125762 restraints weight = 3861.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.125900 restraints weight = 3693.061| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.7403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5564 Z= 0.131 Angle : 0.639 8.712 7568 Z= 0.319 Chirality : 0.038 0.177 930 Planarity : 0.004 0.027 860 Dihedral : 4.642 44.302 724 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 7.38 % Allowed : 24.83 % Favored : 67.79 % 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: 3.09 (0.34), residues: 642 helix: 2.86 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.95 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 614 TYR 0.018 0.002 TYR B 351 PHE 0.026 0.001 PHE A 538 TRP 0.011 0.001 TRP B 386 HIS 0.002 0.001 HIS B 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 5564) covalent geometry : angle 0.63861 / 0.32 ( 7568) hydrogen bonds : bond 0.04238 / 2.72 ( 428) hydrogen bonds : angle 3.84395 / 2.68 ( 1260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 242 TRP cc_start: 0.7679 (OUTLIER) cc_final: 0.7132 (m-10) REVERT: A 307 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7678 (tpt) REVERT: A 342 PHE cc_start: 0.7739 (t80) cc_final: 0.7281 (m-10) REVERT: A 393 ILE cc_start: 0.8287 (mm) cc_final: 0.7902 (mt) REVERT: A 397 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: A 445 LYS cc_start: 0.8231 (tptm) cc_final: 0.7835 (tptm) REVERT: A 449 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8739 (mp) REVERT: A 458 MET cc_start: 0.7770 (tpt) cc_final: 0.7360 (tpt) REVERT: A 460 LEU cc_start: 0.8768 (tp) cc_final: 0.8385 (tt) REVERT: A 516 LYS cc_start: 0.5929 (mmtp) cc_final: 0.5549 (mmtt) REVERT: A 581 LEU cc_start: 0.9017 (mt) cc_final: 0.8584 (tt) REVERT: A 599 LEU cc_start: 0.8869 (tp) cc_final: 0.8326 (tt) REVERT: B 40 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8794 (mt) REVERT: B 42 MET cc_start: 0.8570 (tpt) cc_final: 0.8261 (tpp) REVERT: B 343 PHE cc_start: 0.8654 (t80) cc_final: 0.8311 (t80) REVERT: B 354 MET cc_start: 0.7248 (ttp) cc_final: 0.6797 (tmm) REVERT: B 397 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8559 (mm-30) REVERT: B 419 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.6655 (p0) REVERT: B 438 TYR cc_start: 0.8022 (m-80) cc_final: 0.7606 (m-10) REVERT: B 454 LYS cc_start: 0.8658 (ttmt) cc_final: 0.8244 (ttmt) REVERT: B 516 LYS cc_start: 0.7346 (mttt) cc_final: 0.6910 (mmtt) outliers start: 44 outliers final: 29 residues processed: 181 average time/residue: 0.0483 time to fit residues: 12.1972 Evaluate side-chains 178 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 615 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 50 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 9 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 533 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 = 0.3928 r_free = 0.3928 target = 0.158794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125501 restraints weight = 9236.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.129054 restraints weight = 6449.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.130488 restraints weight = 4647.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.130802 restraints weight = 3642.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.131283 restraints weight = 3590.203| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.7652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5564 Z= 0.131 Angle : 0.674 9.172 7568 Z= 0.330 Chirality : 0.040 0.224 930 Planarity : 0.004 0.026 860 Dihedral : 4.612 46.969 724 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 6.21 % Allowed : 26.17 % Favored : 67.62 % 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: 3.13 (0.34), residues: 642 helix: 3.02 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -2.10 (0.54), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 418 TYR 0.019 0.002 TYR B 351 PHE 0.027 0.001 PHE B 342 TRP 0.012 0.001 TRP B 386 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 5564) covalent geometry : angle 0.67401 / 0.33 ( 7568) hydrogen bonds : bond 0.04148 / 2.67 ( 428) hydrogen bonds : angle 3.82222 / 2.67 ( 1260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.199 Fit side-chains revert: symmetry clash REVERT: A 242 TRP cc_start: 0.7740 (OUTLIER) cc_final: 0.7203 (m-10) REVERT: A 307 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7712 (tpt) REVERT: A 342 PHE cc_start: 0.7744 (t80) cc_final: 0.7209 (m-10) REVERT: A 393 ILE cc_start: 0.8273 (mm) cc_final: 0.7876 (mt) REVERT: A 397 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: A 445 LYS cc_start: 0.8214 (tptm) cc_final: 0.7828 (tptm) REVERT: A 449 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8722 (mp) REVERT: A 458 MET cc_start: 0.7746 (tpt) cc_final: 0.7422 (tpt) REVERT: A 581 LEU cc_start: 0.8916 (mt) cc_final: 0.8558 (tt) REVERT: A 599 LEU cc_start: 0.8805 (tp) cc_final: 0.8241 (tt) REVERT: B 40 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8754 (mt) REVERT: B 42 MET cc_start: 0.8566 (tpt) cc_final: 0.8290 (tpp) REVERT: B 235 TYR cc_start: 0.7103 (m-80) cc_final: 0.6856 (m-10) REVERT: B 354 MET cc_start: 0.7391 (ttp) cc_final: 0.6872 (tmm) REVERT: B 419 ASP cc_start: 0.6852 (OUTLIER) cc_final: 0.6529 (p0) REVERT: B 438 TYR cc_start: 0.7987 (m-80) cc_final: 0.7733 (m-80) REVERT: B 454 LYS cc_start: 0.8684 (ttmt) cc_final: 0.8246 (ttmt) REVERT: B 516 LYS cc_start: 0.7342 (mttt) cc_final: 0.6882 (mmtt) REVERT: B 549 CYS cc_start: 0.8884 (m) cc_final: 0.8576 (m) outliers start: 37 outliers final: 29 residues processed: 179 average time/residue: 0.0541 time to fit residues: 13.5084 Evaluate side-chains 183 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 615 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 4 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 533 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 = 0.3898 r_free = 0.3898 target = 0.156217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.122296 restraints weight = 9189.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124985 restraints weight = 6673.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.126264 restraints weight = 4640.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.126848 restraints weight = 4229.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.127172 restraints weight = 3994.822| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.7662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5564 Z= 0.149 Angle : 0.699 10.603 7568 Z= 0.342 Chirality : 0.040 0.242 930 Planarity : 0.004 0.026 860 Dihedral : 4.850 51.928 724 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 6.38 % Allowed : 25.84 % Favored : 67.79 % 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: 3.06 (0.34), residues: 642 helix: 2.91 (0.22), residues: 514 sheet: None (None), residues: 0 loop : -1.99 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 418 TYR 0.031 0.002 TYR A 438 PHE 0.025 0.001 PHE A 538 TRP 0.018 0.001 TRP B 386 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 5564) covalent geometry : angle 0.69915 / 0.34 ( 7568) hydrogen bonds : bond 0.04529 / 2.91 ( 428) hydrogen bonds : angle 3.91589 / 2.75 ( 1260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 230 MET cc_start: 0.8607 (mmp) cc_final: 0.8011 (mmp) REVERT: A 242 TRP cc_start: 0.7752 (OUTLIER) cc_final: 0.7254 (m-10) REVERT: A 307 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7725 (tpt) REVERT: A 342 PHE cc_start: 0.7809 (t80) cc_final: 0.7293 (m-10) REVERT: A 393 ILE cc_start: 0.8495 (mm) cc_final: 0.8060 (mt) REVERT: A 397 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: A 458 MET cc_start: 0.7762 (tpt) cc_final: 0.7436 (tpt) REVERT: A 460 LEU cc_start: 0.8733 (tp) cc_final: 0.8386 (tt) REVERT: A 538 PHE cc_start: 0.8696 (t80) cc_final: 0.8228 (t80) REVERT: A 544 LYS cc_start: 0.7439 (ptmt) cc_final: 0.6935 (ttmt) REVERT: A 581 LEU cc_start: 0.8937 (mt) cc_final: 0.8578 (tt) REVERT: A 599 LEU cc_start: 0.8868 (tp) cc_final: 0.8325 (tt) REVERT: B 40 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8785 (mt) REVERT: B 42 MET cc_start: 0.8639 (tpt) cc_final: 0.8356 (tpp) REVERT: B 235 TYR cc_start: 0.7342 (m-80) cc_final: 0.7081 (m-10) REVERT: B 419 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6579 (p0) REVERT: B 454 LYS cc_start: 0.8743 (ttmt) cc_final: 0.8280 (ttmt) REVERT: B 516 LYS cc_start: 0.7380 (mttt) cc_final: 0.6917 (mmtt) REVERT: B 549 CYS cc_start: 0.8917 (m) cc_final: 0.8605 (m) outliers start: 38 outliers final: 29 residues processed: 177 average time/residue: 0.0550 time to fit residues: 13.5884 Evaluate side-chains 178 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 615 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 533 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 = 0.3916 r_free = 0.3916 target = 0.157618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.123863 restraints weight = 9254.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.126300 restraints weight = 6801.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.127686 restraints weight = 4692.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.128538 restraints weight = 4182.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.128724 restraints weight = 3945.322| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.7859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5564 Z= 0.138 Angle : 0.703 10.524 7568 Z= 0.342 Chirality : 0.040 0.255 930 Planarity : 0.004 0.026 860 Dihedral : 4.866 58.855 724 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 5.37 % Allowed : 27.35 % Favored : 67.28 % 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: 3.09 (0.34), residues: 642 helix: 2.98 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -2.04 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 437 TYR 0.032 0.002 TYR B 438 PHE 0.030 0.002 PHE B 342 TRP 0.015 0.001 TRP B 386 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 5564) covalent geometry : angle 0.70296 / 0.34 ( 7568) hydrogen bonds : bond 0.04252 / 2.75 ( 428) hydrogen bonds : angle 3.89165 / 2.73 ( 1260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1284 Ramachandran restraints generated. 642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 230 MET cc_start: 0.8808 (mmp) cc_final: 0.8589 (mmp) REVERT: A 242 TRP cc_start: 0.7743 (OUTLIER) cc_final: 0.7171 (m-10) REVERT: A 307 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7737 (tpt) REVERT: A 342 PHE cc_start: 0.7807 (t80) cc_final: 0.7294 (m-10) REVERT: A 393 ILE cc_start: 0.8404 (mm) cc_final: 0.7988 (mt) REVERT: A 397 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: A 458 MET cc_start: 0.7784 (tpt) cc_final: 0.7455 (tpt) REVERT: A 460 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8401 (tt) REVERT: A 538 PHE cc_start: 0.8706 (t80) cc_final: 0.8152 (t80) REVERT: A 544 LYS cc_start: 0.7514 (ptmt) cc_final: 0.7030 (ttmt) REVERT: A 581 LEU cc_start: 0.8914 (mt) cc_final: 0.8573 (tt) REVERT: A 599 LEU cc_start: 0.8791 (tp) cc_final: 0.8576 (tp) REVERT: B 42 MET cc_start: 0.8629 (tpt) cc_final: 0.8365 (tpp) REVERT: B 235 TYR cc_start: 0.7262 (m-80) cc_final: 0.7000 (m-10) REVERT: B 419 ASP cc_start: 0.6809 (p0) cc_final: 0.6518 (p0) REVERT: B 454 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8285 (ttmt) REVERT: B 462 TYR cc_start: 0.8564 (t80) cc_final: 0.8056 (t80) REVERT: B 516 LYS cc_start: 0.7349 (mttt) cc_final: 0.6928 (mmtt) REVERT: B 549 CYS cc_start: 0.8852 (m) cc_final: 0.8523 (m) outliers start: 32 outliers final: 26 residues processed: 172 average time/residue: 0.0543 time to fit residues: 13.1225 Evaluate side-chains 176 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 242 TRP Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain A residue 556 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 615 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 32 optimal weight: 0.0370 chunk 37 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 533 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 = 0.3905 r_free = 0.3905 target = 0.156722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.125404 restraints weight = 9223.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.125830 restraints weight = 6556.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.127364 restraints weight = 5787.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.128304 restraints weight = 4498.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.128786 restraints weight = 4171.921| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.7894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 5564 Z= 0.142 Angle : 0.697 10.038 7568 Z= 0.343 Chirality : 0.040 0.243 930 Planarity : 0.004 0.026 860 Dihedral : 4.904 57.395 724 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 5.54 % Allowed : 27.18 % Favored : 67.28 % 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: 3.10 (0.34), residues: 642 helix: 2.94 (0.22), residues: 514 sheet: None (None), residues: 0 loop : -1.97 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 418 TYR 0.033 0.002 TYR B 438 PHE 0.025 0.001 PHE B 343 TRP 0.017 0.001 TRP B 386 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 5564) covalent geometry : angle 0.69674 / 0.34 ( 7568) hydrogen bonds : bond 0.04350 / 2.81 ( 428) hydrogen bonds : angle 3.91324 / 2.74 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 976.90 seconds wall clock time: 17 minutes 34.41 seconds (1054.41 seconds total)