Starting phenix.real_space_refine on Fri Dec 27 15:13:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wwb_32865/12_2024/7wwb_32865.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wwb_32865/12_2024/7wwb_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_32865/12_2024/7wwb_32865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wwb_32865/12_2024/7wwb_32865.map" model { file = "/net/cci-nas-00/data/ceres_data/7wwb_32865/12_2024/7wwb_32865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wwb_32865/12_2024/7wwb_32865.cif" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.018 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 3.85, per 1000 atoms: 0.71 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: 1.52 Conformation dependent library (CDL) restraints added in 657.3 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: 0.43 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: 1.53 Time building geometry restraints manager: 1.76 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: 3222 17.14 - 34.28: 68 34.28 - 51.42: 6 51.42 - 68.56: 4 68.56 - 85.70: 4 Dihedral angle restraints: 3304 sinusoidal: 1350 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 3301 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: 0.00 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.180 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 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= 0.529 Angle : 0.969 10.801 7568 Z= 0.650 Chirality : 0.066 0.313 930 Planarity : 0.006 0.026 860 Dihedral : 9.324 85.703 2028 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (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 TRP 0.001 0.000 TRP B 386 HIS 0.001 0.000 HIS B 464 PHE 0.001 0.000 PHE B 348 TYR 0.001 0.000 TYR B 415 ARG 0.001 0.000 ARG B 311 *********************** 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 : 0.642 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: 0.7161 (ptt-90) REVERT: A 326 LYS cc_start: 0.8897 (mttt) cc_final: 0.8603 (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: 0.6192 (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: 0.6958 (mmt180) REVERT: B 463 ILE cc_start: 0.8796 (mt) cc_final: 0.8568 (mm) REVERT: B 508 SER cc_start: 0.8865 (m) cc_final: 0.8506 (t) REVERT: B 516 LYS cc_start: 0.6949 (mttt) cc_final: 0.6379 (mptt) REVERT: B 534 THR cc_start: 0.8810 (m) cc_final: 0.8596 (p) outliers start: 0 outliers final: 0 residues processed: 290 average time/residue: 0.1829 time to fit residues: 66.6027 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 : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS A 466 GLN B 439 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5564 Z= 0.217 Angle : 0.680 7.472 7568 Z= 0.344 Chirality : 0.039 0.184 930 Planarity : 0.004 0.028 860 Dihedral : 4.735 31.905 836 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 6.38 % Allowed : 14.93 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.34), residues: 642 helix: 2.65 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -2.41 (0.50), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 340 HIS 0.002 0.001 HIS B 330 PHE 0.020 0.001 PHE B 44 TYR 0.012 0.001 TYR B 415 ARG 0.006 0.001 ARG B 614 *********************** 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 223 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: A 433 ASN cc_start: 0.7292 (p0) cc_final: 0.6950 (m-40) REVERT: A 445 LYS cc_start: 0.8490 (tptm) cc_final: 0.8158 (tptm) REVERT: A 528 ARG cc_start: 0.7850 (mtt90) cc_final: 0.7214 (mpt180) REVERT: A 538 PHE cc_start: 0.8670 (t80) cc_final: 0.7783 (t80) REVERT: A 542 LEU cc_start: 0.8797 (mp) cc_final: 0.8592 (mp) REVERT: A 578 PHE cc_start: 0.8182 (t80) cc_final: 0.7717 (t80) REVERT: A 581 LEU cc_start: 0.9029 (mt) cc_final: 0.8761 (tt) REVERT: B 21 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7210 (pp) REVERT: B 234 ARG cc_start: 0.8711 (ptp90) cc_final: 0.8457 (ptp90) REVERT: B 340 TRP cc_start: 0.7024 (m-10) cc_final: 0.6766 (m-10) REVERT: B 508 SER cc_start: 0.8835 (m) cc_final: 0.8628 (t) REVERT: B 516 LYS cc_start: 0.7132 (mttt) cc_final: 0.6348 (mmtt) outliers start: 38 outliers final: 26 residues processed: 216 average time/residue: 0.1750 time to fit residues: 48.7159 Evaluate side-chains 181 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 455 ILE 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 577 LEU 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 40 ILE Chi-restraints excluded: chain B residue 451 THR Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 506 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 33 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 439 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5564 Z= 0.239 Angle : 0.663 6.887 7568 Z= 0.336 Chirality : 0.038 0.174 930 Planarity : 0.004 0.037 860 Dihedral : 4.859 32.603 836 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 7.05 % Allowed : 16.78 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.34), residues: 642 helix: 2.63 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -2.23 (0.58), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 352 HIS 0.004 0.001 HIS A 439 PHE 0.022 0.001 PHE B 48 TYR 0.029 0.002 TYR A 438 ARG 0.005 0.001 ARG B 614 *********************** 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 213 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 0.641 Fit side-chains REVERT: A 230 MET cc_start: 0.8067 (mmp) cc_final: 0.7709 (mmp) REVERT: A 307 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7723 (tpt) REVERT: A 397 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: A 466 GLN cc_start: 0.8978 (tm-30) cc_final: 0.8700 (tm-30) REVERT: A 528 ARG cc_start: 0.7589 (mtt90) cc_final: 0.7247 (mpt180) REVERT: A 538 PHE cc_start: 0.8709 (t80) cc_final: 0.7858 (t80) REVERT: A 581 LEU cc_start: 0.9076 (mt) cc_final: 0.8665 (tt) REVERT: B 244 LEU cc_start: 0.9139 (tt) cc_final: 0.8830 (mm) REVERT: B 397 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8609 (mm-30) REVERT: B 454 LYS cc_start: 0.8896 (ttmt) cc_final: 0.8398 (ttpt) REVERT: B 516 LYS cc_start: 0.7314 (mttt) cc_final: 0.6682 (mmtt) outliers start: 42 outliers final: 24 residues processed: 202 average time/residue: 0.1514 time to fit residues: 40.2953 Evaluate side-chains 166 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 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 486 LEU Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 509 THR 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 588 SER Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 33 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.6585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5564 Z= 0.218 Angle : 0.662 8.602 7568 Z= 0.334 Chirality : 0.038 0.190 930 Planarity : 0.004 0.028 860 Dihedral : 4.971 33.066 836 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 6.88 % Allowed : 20.64 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.34), residues: 642 helix: 2.73 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.93 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 386 HIS 0.002 0.001 HIS B 330 PHE 0.019 0.001 PHE B 48 TYR 0.023 0.002 TYR A 438 ARG 0.004 0.001 ARG B 614 *********************** 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 198 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 0.613 Fit side-chains REVERT: A 307 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7733 (tpt) REVERT: A 347 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8951 (tt) REVERT: A 384 MET cc_start: 0.5651 (mpp) cc_final: 0.5227 (mpp) REVERT: A 393 ILE cc_start: 0.8337 (mm) cc_final: 0.8022 (mt) REVERT: A 397 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: A 445 LYS cc_start: 0.8503 (tptm) cc_final: 0.7960 (tptm) REVERT: A 449 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.8979 (mp) REVERT: A 501 TYR cc_start: 0.9210 (m-10) cc_final: 0.8994 (m-10) REVERT: A 528 ARG cc_start: 0.7635 (mtt90) cc_final: 0.7358 (mpt180) REVERT: A 538 PHE cc_start: 0.8660 (t80) cc_final: 0.8246 (t80) REVERT: A 581 LEU cc_start: 0.9027 (mt) cc_final: 0.8594 (tt) REVERT: B 42 MET cc_start: 0.8701 (tpt) cc_final: 0.8466 (tpp) REVERT: B 242 TRP cc_start: 0.7544 (OUTLIER) cc_final: 0.6840 (t60) REVERT: B 244 LEU cc_start: 0.9007 (tt) cc_final: 0.8750 (mm) REVERT: B 397 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8632 (mm-30) REVERT: B 419 ASP cc_start: 0.7463 (p0) cc_final: 0.7176 (p0) REVERT: B 438 TYR cc_start: 0.7972 (m-80) cc_final: 0.7621 (m-10) REVERT: B 454 LYS cc_start: 0.8699 (ttmt) cc_final: 0.8147 (ttmt) REVERT: B 516 LYS cc_start: 0.7291 (mttt) cc_final: 0.6709 (mmtt) outliers start: 41 outliers final: 27 residues processed: 187 average time/residue: 0.1492 time to fit residues: 37.0895 Evaluate side-chains 179 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 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 488 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 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 594 VAL Chi-restraints excluded: chain B residue 21 LEU 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 452 LEU 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 577 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 36 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.6938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5564 Z= 0.220 Angle : 0.646 7.821 7568 Z= 0.329 Chirality : 0.039 0.249 930 Planarity : 0.004 0.027 860 Dihedral : 5.064 37.286 836 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 7.38 % Allowed : 21.64 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.34), residues: 642 helix: 2.68 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -2.00 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 386 HIS 0.003 0.001 HIS B 330 PHE 0.024 0.001 PHE B 343 TYR 0.023 0.002 TYR A 438 ARG 0.003 0.001 ARG B 614 *********************** 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 193 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 0.610 Fit side-chains REVERT: A 307 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7709 (tpt) REVERT: A 384 MET cc_start: 0.5946 (mpp) cc_final: 0.5698 (mpp) REVERT: A 393 ILE cc_start: 0.8397 (mm) cc_final: 0.8027 (mt) REVERT: A 397 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: A 445 LYS cc_start: 0.8468 (tptm) cc_final: 0.7956 (tptm) REVERT: A 449 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8842 (mp) REVERT: A 458 MET cc_start: 0.7581 (tpt) cc_final: 0.7158 (tpt) REVERT: A 538 PHE cc_start: 0.8642 (t80) cc_final: 0.8394 (t80) REVERT: A 581 LEU cc_start: 0.9053 (mt) cc_final: 0.8616 (tt) REVERT: A 599 LEU cc_start: 0.8991 (tp) cc_final: 0.8483 (tt) REVERT: B 42 MET cc_start: 0.8770 (tpt) cc_final: 0.8310 (tpp) REVERT: B 242 TRP cc_start: 0.7498 (OUTLIER) cc_final: 0.6719 (t60) REVERT: B 244 LEU cc_start: 0.8966 (tt) cc_final: 0.8752 (mm) REVERT: B 354 MET cc_start: 0.7398 (ttp) cc_final: 0.6938 (tmm) REVERT: B 397 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8659 (mm-30) REVERT: B 454 LYS cc_start: 0.8700 (ttmt) cc_final: 0.8182 (ttmt) REVERT: B 516 LYS cc_start: 0.7448 (mttt) cc_final: 0.6907 (mmtt) outliers start: 44 outliers final: 27 residues processed: 182 average time/residue: 0.1415 time to fit residues: 34.6836 Evaluate side-chains 171 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 307 MET 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 594 VAL 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 387 TYR Chi-restraints excluded: chain B residue 452 LEU 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 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 37 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 63 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.7295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5564 Z= 0.258 Angle : 0.688 8.374 7568 Z= 0.348 Chirality : 0.040 0.237 930 Planarity : 0.004 0.027 860 Dihedral : 5.397 42.284 836 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 7.72 % Allowed : 23.49 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.34), residues: 642 helix: 2.64 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -2.06 (0.56), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 386 HIS 0.003 0.001 HIS B 330 PHE 0.023 0.002 PHE B 342 TYR 0.025 0.002 TYR A 438 ARG 0.004 0.001 ARG B 234 *********************** 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 196 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 307 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7682 (tpt) REVERT: A 393 ILE cc_start: 0.8671 (mm) cc_final: 0.8249 (mt) REVERT: A 397 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: A 445 LYS cc_start: 0.8399 (tptm) cc_final: 0.7953 (tptm) REVERT: A 449 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8862 (mp) REVERT: A 458 MET cc_start: 0.7616 (tpt) cc_final: 0.7195 (tpt) REVERT: A 508 SER cc_start: 0.8997 (OUTLIER) cc_final: 0.8549 (t) REVERT: A 516 LYS cc_start: 0.6348 (mttt) cc_final: 0.5978 (mmtp) REVERT: A 581 LEU cc_start: 0.9087 (mt) cc_final: 0.8639 (tt) REVERT: B 242 TRP cc_start: 0.7520 (OUTLIER) cc_final: 0.6704 (t60) REVERT: B 244 LEU cc_start: 0.8987 (tt) cc_final: 0.8776 (mm) REVERT: B 354 MET cc_start: 0.7311 (ttp) cc_final: 0.6889 (tmm) REVERT: B 419 ASP cc_start: 0.7158 (OUTLIER) cc_final: 0.6781 (p0) REVERT: B 438 TYR cc_start: 0.8133 (m-80) cc_final: 0.7790 (m-10) REVERT: B 516 LYS cc_start: 0.7469 (mttt) cc_final: 0.6941 (mmtt) REVERT: B 549 CYS cc_start: 0.8714 (m) cc_final: 0.8473 (m) outliers start: 46 outliers final: 33 residues processed: 185 average time/residue: 0.1451 time to fit residues: 35.7795 Evaluate side-chains 185 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 146 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 307 MET Chi-restraints excluded: chain A residue 335 VAL 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 488 CYS Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 527 LEU 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 577 LEU 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 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 451 THR Chi-restraints excluded: chain B residue 452 LEU 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 577 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 605 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 0.0970 chunk 53 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.0040 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.7545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5564 Z= 0.179 Angle : 0.654 10.089 7568 Z= 0.326 Chirality : 0.038 0.231 930 Planarity : 0.004 0.030 860 Dihedral : 4.911 34.080 836 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 6.04 % Allowed : 24.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.34), residues: 642 helix: 2.78 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.91 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 386 HIS 0.002 0.001 HIS B 388 PHE 0.023 0.001 PHE A 538 TYR 0.025 0.002 TYR A 438 ARG 0.004 0.001 ARG B 418 *********************** 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 191 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.635 Fit side-chains REVERT: A 307 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7704 (tpt) REVERT: A 393 ILE cc_start: 0.8352 (mm) cc_final: 0.8005 (mt) REVERT: A 397 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: A 458 MET cc_start: 0.7631 (tpt) cc_final: 0.7206 (tpt) REVERT: A 460 LEU cc_start: 0.8646 (mp) cc_final: 0.8340 (tt) REVERT: A 508 SER cc_start: 0.9018 (OUTLIER) cc_final: 0.8546 (t) REVERT: A 581 LEU cc_start: 0.9004 (mt) cc_final: 0.8589 (tt) REVERT: A 599 LEU cc_start: 0.8915 (tp) cc_final: 0.8364 (tt) REVERT: B 242 TRP cc_start: 0.7489 (OUTLIER) cc_final: 0.7022 (t60) REVERT: B 244 LEU cc_start: 0.8938 (tt) cc_final: 0.8730 (mm) REVERT: B 354 MET cc_start: 0.7402 (ttp) cc_final: 0.6972 (tmm) REVERT: B 462 TYR cc_start: 0.8508 (t80) cc_final: 0.8060 (t80) REVERT: B 516 LYS cc_start: 0.7342 (mttt) cc_final: 0.6886 (mmtt) REVERT: B 549 CYS cc_start: 0.8843 (m) cc_final: 0.8524 (m) outliers start: 36 outliers final: 28 residues processed: 184 average time/residue: 0.1293 time to fit residues: 33.0154 Evaluate side-chains 175 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 307 MET 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 463 ILE Chi-restraints excluded: chain A residue 485 CYS Chi-restraints excluded: chain A residue 488 CYS Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 508 SER 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 594 VAL Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 242 TRP Chi-restraints excluded: chain B residue 333 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 452 LEU Chi-restraints excluded: chain B residue 479 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 57 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.7728 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= 0.190 Angle : 0.642 8.713 7568 Z= 0.322 Chirality : 0.037 0.170 930 Planarity : 0.004 0.026 860 Dihedral : 4.919 33.996 836 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 5.37 % Allowed : 26.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.34), residues: 642 helix: 2.80 (0.22), residues: 522 sheet: None (None), residues: 0 loop : -1.85 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 386 HIS 0.002 0.001 HIS B 330 PHE 0.026 0.001 PHE B 343 TYR 0.021 0.002 TYR A 438 ARG 0.004 0.000 ARG B 418 *********************** 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 187 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 307 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7732 (tpt) REVERT: A 393 ILE cc_start: 0.8421 (mm) cc_final: 0.8049 (mt) REVERT: A 397 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: A 458 MET cc_start: 0.7645 (tpt) cc_final: 0.7225 (tpt) REVERT: A 460 LEU cc_start: 0.8621 (mp) cc_final: 0.8328 (tt) REVERT: A 508 SER cc_start: 0.9011 (OUTLIER) cc_final: 0.8552 (t) REVERT: A 538 PHE cc_start: 0.8642 (t80) cc_final: 0.7981 (t80) REVERT: A 544 LYS cc_start: 0.7627 (ptmt) cc_final: 0.7072 (ttmt) REVERT: A 581 LEU cc_start: 0.8978 (mt) cc_final: 0.8573 (tt) REVERT: A 599 LEU cc_start: 0.8954 (tp) cc_final: 0.8415 (tt) REVERT: B 235 TYR cc_start: 0.7384 (m-80) cc_final: 0.7106 (m-10) REVERT: B 354 MET cc_start: 0.7552 (ttp) cc_final: 0.7037 (tmm) REVERT: B 462 TYR cc_start: 0.8550 (t80) cc_final: 0.8087 (t80) REVERT: B 516 LYS cc_start: 0.7319 (mttt) cc_final: 0.6920 (mmtt) REVERT: B 549 CYS cc_start: 0.8817 (m) cc_final: 0.8585 (m) outliers start: 32 outliers final: 24 residues processed: 179 average time/residue: 0.1280 time to fit residues: 31.5474 Evaluate side-chains 175 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 307 MET 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 508 SER 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 605 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 479 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.7861 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= 0.202 Angle : 0.679 8.084 7568 Z= 0.338 Chirality : 0.038 0.198 930 Planarity : 0.004 0.026 860 Dihedral : 4.898 31.674 836 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 5.37 % Allowed : 27.68 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.34), residues: 642 helix: 2.94 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -2.13 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 386 HIS 0.002 0.001 HIS B 330 PHE 0.016 0.001 PHE B 416 TYR 0.020 0.002 TYR A 438 ARG 0.004 0.001 ARG B 418 *********************** 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 177 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 307 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7747 (tpt) REVERT: A 393 ILE cc_start: 0.8470 (mm) cc_final: 0.8107 (mt) REVERT: A 397 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: A 458 MET cc_start: 0.7594 (tpt) cc_final: 0.7283 (tpt) REVERT: A 460 LEU cc_start: 0.8621 (mp) cc_final: 0.8342 (tt) REVERT: A 508 SER cc_start: 0.9008 (OUTLIER) cc_final: 0.8554 (t) REVERT: A 516 LYS cc_start: 0.5955 (mmtp) cc_final: 0.5646 (mmtt) REVERT: A 538 PHE cc_start: 0.8652 (t80) cc_final: 0.8183 (t80) REVERT: A 544 LYS cc_start: 0.7880 (ptmt) cc_final: 0.7342 (ttmt) REVERT: A 581 LEU cc_start: 0.8931 (mt) cc_final: 0.8516 (tt) REVERT: A 599 LEU cc_start: 0.8953 (tp) cc_final: 0.8446 (tt) REVERT: B 235 TYR cc_start: 0.7214 (m-80) cc_final: 0.6942 (m-10) REVERT: B 462 TYR cc_start: 0.8544 (t80) cc_final: 0.8098 (t80) REVERT: B 516 LYS cc_start: 0.7464 (mttt) cc_final: 0.7037 (mmtt) REVERT: B 549 CYS cc_start: 0.8807 (m) cc_final: 0.8487 (m) outliers start: 32 outliers final: 25 residues processed: 169 average time/residue: 0.1328 time to fit residues: 30.7925 Evaluate side-chains 169 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 307 MET 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 508 SER 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 605 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 452 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 0.4980 chunk 52 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.7962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5564 Z= 0.194 Angle : 0.684 8.190 7568 Z= 0.339 Chirality : 0.039 0.283 930 Planarity : 0.004 0.027 860 Dihedral : 4.861 31.227 836 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.70 % Allowed : 28.19 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.34), residues: 642 helix: 2.97 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -2.18 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 386 HIS 0.002 0.000 HIS B 330 PHE 0.029 0.001 PHE B 342 TYR 0.028 0.002 TYR A 438 ARG 0.004 0.000 ARG B 418 ********************** 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 171 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 307 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7781 (tpt) REVERT: A 393 ILE cc_start: 0.8459 (mm) cc_final: 0.8107 (mt) REVERT: A 397 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: A 438 TYR cc_start: 0.7901 (m-80) cc_final: 0.7694 (m-10) REVERT: A 458 MET cc_start: 0.7594 (tpt) cc_final: 0.7281 (tpt) REVERT: A 538 PHE cc_start: 0.8626 (t80) cc_final: 0.8245 (t80) REVERT: A 581 LEU cc_start: 0.8859 (mt) cc_final: 0.8475 (tt) REVERT: A 599 LEU cc_start: 0.8929 (tp) cc_final: 0.8400 (tt) REVERT: B 42 MET cc_start: 0.8948 (tpp) cc_final: 0.8622 (tpp) REVERT: B 235 TYR cc_start: 0.7137 (m-80) cc_final: 0.6930 (m-10) REVERT: B 462 TYR cc_start: 0.8542 (t80) cc_final: 0.8115 (t80) REVERT: B 516 LYS cc_start: 0.7540 (mttt) cc_final: 0.7124 (mmtt) REVERT: B 549 CYS cc_start: 0.8812 (m) cc_final: 0.8534 (m) outliers start: 28 outliers final: 23 residues processed: 165 average time/residue: 0.1341 time to fit residues: 30.1535 Evaluate side-chains 163 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 307 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 455 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 605 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 384 MET Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 452 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 37 optimal weight: 0.0870 chunk 60 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 44 optimal weight: 0.0770 overall best weight: 0.8118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3901 r_free = 0.3901 target = 0.156686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.123839 restraints weight = 9318.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.126501 restraints weight = 6662.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.128145 restraints weight = 4634.346| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.8078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5564 Z= 0.201 Angle : 0.703 7.740 7568 Z= 0.350 Chirality : 0.040 0.248 930 Planarity : 0.004 0.028 860 Dihedral : 4.918 30.317 836 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.53 % Allowed : 29.19 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.34), residues: 642 helix: 2.95 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -2.17 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 386 HIS 0.002 0.000 HIS B 330 PHE 0.016 0.001 PHE B 38 TYR 0.026 0.002 TYR A 438 ARG 0.003 0.000 ARG B 418 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1361.77 seconds wall clock time: 25 minutes 56.45 seconds (1556.45 seconds total)