Starting phenix.real_space_refine on Thu Jul 24 18:20:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i4h_35173/07_2025/8i4h_35173.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i4h_35173/07_2025/8i4h_35173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i4h_35173/07_2025/8i4h_35173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i4h_35173/07_2025/8i4h_35173.map" model { file = "/net/cci-nas-00/data/ceres_data/8i4h_35173/07_2025/8i4h_35173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i4h_35173/07_2025/8i4h_35173.cif" } resolution = 3.81 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= 0.002 sd= 0.029 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 32 5.16 5 C 4194 2.51 5 N 1075 2.21 5 O 1238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6539 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4724 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 32, 'TRANS': 565} Chain breaks: 6 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1815 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Time building chain proxies: 4.45, per 1000 atoms: 0.68 Number of scatterers: 6539 At special positions: 0 Unit cell: (71.288, 90.44, 131.936, 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 32 16.00 O 1238 8.00 N 1075 7.00 C 4194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 234 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 922.8 milliseconds 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 19 sheets defined 3.5% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.687A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 4.348A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 removed outlier: 3.700A pdb=" N THR B 229 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.724A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.923A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.688A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 95 removed outlier: 5.911A pdb=" N SER A 203 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 120 removed outlier: 3.611A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.528A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 651 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR A 645 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU A 650 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA8, first strand: chain 'A' and resid 355 through 357 removed outlier: 3.883A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.371A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 655 through 660 removed outlier: 6.527A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.862A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 674 through 675 Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AB6, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.662A pdb=" N MET B 82 " --> pdb=" O LEU B 18 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 56 through 59 removed outlier: 3.800A pdb=" N ARG B 56 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET B 34 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 37 " --> pdb=" O TYR B 94 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR B 94 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR B 93 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 112 " --> pdb=" O TYR B 93 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 149 through 150 Processing sheet with id=AB9, first strand: chain 'B' and resid 157 through 161 removed outlier: 3.529A pdb=" N THR B 207 " --> pdb=" O GLN B 220 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 171 through 173 removed outlier: 3.631A pdb=" N ALA B 235 " --> pdb=" O SER B 173 " (cutoff:3.500A) 112 hydrogen bonds defined for protein. 264 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: 1.99 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2080 1.35 - 1.46: 1704 1.46 - 1.58: 2878 1.58 - 1.70: 0 1.70 - 1.81: 41 Bond restraints: 6703 Sorted by residual: bond pdb=" C GLU A 212 " pdb=" N PRO A 213 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.92e-01 bond pdb=" C ILE A 664 " pdb=" O ILE A 664 " ideal model delta sigma weight residual 1.240 1.231 0.009 1.26e-02 6.30e+03 5.02e-01 bond pdb=" C GLN A 173 " pdb=" N PRO A 174 " ideal model delta sigma weight residual 1.330 1.338 -0.008 1.19e-02 7.06e+03 4.31e-01 bond pdb=" CB PRO A 330 " pdb=" CG PRO A 330 " ideal model delta sigma weight residual 1.492 1.523 -0.031 5.00e-02 4.00e+02 3.96e-01 bond pdb=" N ASP B 26 " pdb=" CA ASP B 26 " ideal model delta sigma weight residual 1.460 1.469 -0.009 1.54e-02 4.22e+03 3.31e-01 ... (remaining 6698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 8836 1.03 - 2.06: 207 2.06 - 3.09: 64 3.09 - 4.12: 9 4.12 - 5.15: 2 Bond angle restraints: 9118 Sorted by residual: angle pdb=" N ASP A 80 " pdb=" CA ASP A 80 " pdb=" C ASP A 80 " ideal model delta sigma weight residual 114.56 111.04 3.52 1.27e+00 6.20e-01 7.68e+00 angle pdb=" CA ASP A 80 " pdb=" C ASP A 80 " pdb=" N ASN A 81 " ideal model delta sigma weight residual 119.26 116.87 2.39 1.14e+00 7.69e-01 4.40e+00 angle pdb=" CA ASP A 80 " pdb=" C ASP A 80 " pdb=" O ASP A 80 " ideal model delta sigma weight residual 118.55 120.50 -1.95 1.14e+00 7.69e-01 2.94e+00 angle pdb=" C SER B 25 " pdb=" N ASP B 26 " pdb=" CA ASP B 26 " ideal model delta sigma weight residual 122.46 124.71 -2.25 1.41e+00 5.03e-01 2.55e+00 angle pdb=" C PHE A 559 " pdb=" N LEU A 560 " pdb=" CA LEU A 560 " ideal model delta sigma weight residual 121.80 125.69 -3.89 2.44e+00 1.68e-01 2.54e+00 ... (remaining 9113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 3736 16.03 - 32.05: 166 32.05 - 48.08: 35 48.08 - 64.10: 6 64.10 - 80.13: 1 Dihedral angle restraints: 3944 sinusoidal: 1525 harmonic: 2419 Sorted by residual: dihedral pdb=" N LYS A 424 " pdb=" CA LYS A 424 " pdb=" CB LYS A 424 " pdb=" CG LYS A 424 " ideal model delta sinusoidal sigma weight residual -180.00 -120.01 -59.99 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LEU A 390 " pdb=" CA LEU A 390 " pdb=" CB LEU A 390 " pdb=" CG LEU A 390 " ideal model delta sinusoidal sigma weight residual -60.00 -116.77 56.77 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" N PHE A 329 " pdb=" CA PHE A 329 " pdb=" CB PHE A 329 " pdb=" CG PHE A 329 " ideal model delta sinusoidal sigma weight residual -180.00 -125.13 -54.87 3 1.50e+01 4.44e-03 9.31e+00 ... (remaining 3941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 572 0.025 - 0.050: 259 0.050 - 0.076: 83 0.076 - 0.101: 60 0.101 - 0.126: 29 Chirality restraints: 1003 Sorted by residual: chirality pdb=" CA ILE A 101 " pdb=" N ILE A 101 " pdb=" C ILE A 101 " pdb=" CB ILE A 101 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE A 584 " pdb=" N ILE A 584 " pdb=" C ILE A 584 " pdb=" CB ILE A 584 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ILE A 235 " pdb=" N ILE A 235 " pdb=" C ILE A 235 " pdb=" CB ILE A 235 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 1000 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 173 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO A 174 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 174 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 174 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 321 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO A 322 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 336 " 0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO A 337 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.016 5.00e-02 4.00e+02 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1589 2.79 - 3.32: 5895 3.32 - 3.84: 10478 3.84 - 4.37: 11962 4.37 - 4.90: 20458 Nonbonded interactions: 50382 Sorted by model distance: nonbonded pdb=" O ASP B 89 " pdb=" OH TYR B 93 " model vdw 2.262 3.040 nonbonded pdb=" O VAL A 130 " pdb=" OG1 THR A 167 " model vdw 2.270 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR A 470 " pdb=" OG SER B 54 " model vdw 2.277 3.040 nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.295 3.040 ... (remaining 50377 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.530 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.070 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.050 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 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 : 0.001 0.031 6714 Z= 0.080 Angle : 0.433 5.155 9140 Z= 0.240 Chirality : 0.040 0.126 1003 Planarity : 0.004 0.056 1175 Dihedral : 9.227 80.126 2367 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 5.85 % Allowed : 7.52 % Favored : 86.63 % 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: -4.65 (0.24), residues: 815 helix: -2.48 (1.17), residues: 14 sheet: -2.96 (0.34), residues: 172 loop : -3.44 (0.20), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 99 HIS 0.001 0.000 HIS A 49 PHE 0.005 0.001 PHE A 192 TYR 0.005 0.001 TYR B 169 ARG 0.001 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.22635 ( 112) hydrogen bonds : angle 9.04735 ( 264) SS BOND : bond 0.00135 ( 11) SS BOND : angle 0.42984 ( 22) covalent geometry : bond 0.00149 ( 6703) covalent geometry : angle 0.43270 ( 9118) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 246 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.5984 (t80) cc_final: 0.5726 (t80) REVERT: A 95 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7597 (tp) REVERT: A 177 MET cc_start: 0.6113 (mmt) cc_final: 0.5836 (mmt) REVERT: A 294 ASP cc_start: 0.7943 (p0) cc_final: 0.7654 (p0) REVERT: A 357 ARG cc_start: 0.6937 (ttp80) cc_final: 0.6561 (ttp80) REVERT: A 368 LEU cc_start: 0.7611 (mm) cc_final: 0.7289 (tp) REVERT: A 387 LEU cc_start: 0.8674 (mt) cc_final: 0.8255 (tp) REVERT: A 388 ASN cc_start: 0.7787 (m110) cc_final: 0.7455 (p0) REVERT: A 394 ASN cc_start: 0.7343 (m-40) cc_final: 0.7117 (m-40) REVERT: A 395 VAL cc_start: 0.7655 (m) cc_final: 0.7377 (t) REVERT: A 408 ARG cc_start: 0.7980 (ttp-170) cc_final: 0.7476 (ttp-170) REVERT: A 417 ASN cc_start: 0.7679 (t0) cc_final: 0.7403 (t0) REVERT: A 428 ASP cc_start: 0.7345 (p0) cc_final: 0.7010 (p0) REVERT: A 452 LEU cc_start: 0.7605 (mp) cc_final: 0.7186 (tt) REVERT: A 470 THR cc_start: 0.7394 (p) cc_final: 0.7114 (p) REVERT: A 490 PHE cc_start: 0.8416 (t80) cc_final: 0.8200 (t80) REVERT: A 537 LYS cc_start: 0.7724 (tppp) cc_final: 0.7195 (mmmm) REVERT: A 562 PHE cc_start: 0.6663 (t80) cc_final: 0.5858 (t80) REVERT: A 699 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8382 (pt) REVERT: B 82 MET cc_start: 0.8750 (mtt) cc_final: 0.8326 (mtt) REVERT: B 93 TYR cc_start: 0.6581 (m-80) cc_final: 0.5874 (m-80) REVERT: B 167 PHE cc_start: 0.6732 (m-80) cc_final: 0.6530 (m-80) REVERT: B 215 ASN cc_start: 0.8693 (m-40) cc_final: 0.8446 (t0) REVERT: B 252 THR cc_start: 0.8471 (t) cc_final: 0.8266 (p) outliers start: 42 outliers final: 14 residues processed: 270 average time/residue: 0.2340 time to fit residues: 82.6860 Evaluate side-chains 218 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 208 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 0.0870 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS A 87 ASN A 173 GLN A 271 GLN A 280 ASN A 321 GLN A 360 ASN A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN A 563 GLN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 13 GLN B 81 GLN B 110 GLN B 141 GLN B 212 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.177621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.145945 restraints weight = 12744.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.152049 restraints weight = 7508.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.156158 restraints weight = 5017.129| |-----------------------------------------------------------------------------| r_work (final): 0.4119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6714 Z= 0.136 Angle : 0.619 7.679 9140 Z= 0.312 Chirality : 0.045 0.256 1003 Planarity : 0.004 0.054 1175 Dihedral : 6.475 81.573 950 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 6.55 % Allowed : 14.07 % Favored : 79.39 % 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: -4.20 (0.25), residues: 815 helix: -2.58 (1.17), residues: 16 sheet: -2.82 (0.33), residues: 197 loop : -3.01 (0.22), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 174 HIS 0.017 0.003 HIS A 519 PHE 0.034 0.001 PHE A 306 TYR 0.010 0.001 TYR A 160 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.03239 ( 112) hydrogen bonds : angle 7.31996 ( 264) SS BOND : bond 0.00665 ( 11) SS BOND : angle 1.55820 ( 22) covalent geometry : bond 0.00295 ( 6703) covalent geometry : angle 0.61455 ( 9118) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 224 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7670 (tm-30) cc_final: 0.7338 (tp40) REVERT: A 67 VAL cc_start: 0.8073 (p) cc_final: 0.7316 (m) REVERT: A 92 PHE cc_start: 0.6444 (t80) cc_final: 0.6169 (t80) REVERT: A 177 MET cc_start: 0.6150 (mmt) cc_final: 0.5858 (mmt) REVERT: A 204 LYS cc_start: 0.8179 (tttp) cc_final: 0.7947 (tttp) REVERT: A 241 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8173 (mm) REVERT: A 265 TYR cc_start: 0.6680 (m-80) cc_final: 0.6366 (m-80) REVERT: A 319 ARG cc_start: 0.7862 (ptp90) cc_final: 0.7486 (tpt170) REVERT: A 340 GLU cc_start: 0.7522 (mp0) cc_final: 0.7307 (mp0) REVERT: A 357 ARG cc_start: 0.7079 (ttp80) cc_final: 0.6689 (ttp80) REVERT: A 359 SER cc_start: 0.8134 (OUTLIER) cc_final: 0.7646 (t) REVERT: A 368 LEU cc_start: 0.8103 (mm) cc_final: 0.7578 (tp) REVERT: A 387 LEU cc_start: 0.8690 (mt) cc_final: 0.8300 (tp) REVERT: A 396 TYR cc_start: 0.7072 (m-80) cc_final: 0.6452 (m-80) REVERT: A 408 ARG cc_start: 0.8076 (ttp-170) cc_final: 0.7620 (ttp-170) REVERT: A 417 ASN cc_start: 0.7844 (t0) cc_final: 0.7470 (t0) REVERT: A 424 LYS cc_start: 0.8108 (tmtm) cc_final: 0.7724 (tmtm) REVERT: A 452 LEU cc_start: 0.7772 (mp) cc_final: 0.7243 (tt) REVERT: A 462 LYS cc_start: 0.8281 (tptp) cc_final: 0.7830 (tptp) REVERT: A 490 PHE cc_start: 0.8250 (t80) cc_final: 0.7969 (t80) REVERT: A 501 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.7310 (t80) REVERT: A 528 LYS cc_start: 0.7599 (mttm) cc_final: 0.6922 (mttp) REVERT: A 537 LYS cc_start: 0.7796 (tppp) cc_final: 0.7343 (mmmm) REVERT: A 588 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8647 (p) REVERT: A 598 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8144 (tp) REVERT: A 664 ILE cc_start: 0.8781 (pt) cc_final: 0.8489 (pt) REVERT: B 38 ARG cc_start: 0.7226 (ttp-170) cc_final: 0.6640 (ttp-170) REVERT: B 64 LYS cc_start: 0.8303 (tptt) cc_final: 0.7968 (tptt) REVERT: B 93 TYR cc_start: 0.6815 (m-80) cc_final: 0.5991 (m-80) REVERT: B 189 ILE cc_start: 0.8667 (mm) cc_final: 0.8321 (mm) REVERT: B 211 ASP cc_start: 0.7878 (t0) cc_final: 0.7660 (t0) REVERT: B 252 THR cc_start: 0.8444 (t) cc_final: 0.8162 (m) outliers start: 47 outliers final: 21 residues processed: 249 average time/residue: 0.3209 time to fit residues: 103.2560 Evaluate side-chains 243 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 208 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 35 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 63 optimal weight: 0.0060 chunk 16 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 234 ASN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.170629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.138587 restraints weight = 12604.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.144445 restraints weight = 7464.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.148478 restraints weight = 5025.878| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6714 Z= 0.117 Angle : 0.617 8.360 9140 Z= 0.309 Chirality : 0.045 0.157 1003 Planarity : 0.005 0.058 1175 Dihedral : 6.223 80.353 940 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 4.46 % Allowed : 19.64 % Favored : 75.91 % 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: -3.79 (0.26), residues: 815 helix: -2.57 (1.23), residues: 16 sheet: -2.44 (0.38), residues: 167 loop : -2.77 (0.22), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 174 HIS 0.010 0.002 HIS A 519 PHE 0.026 0.002 PHE A 306 TYR 0.015 0.001 TYR B 107 ARG 0.005 0.000 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.03038 ( 112) hydrogen bonds : angle 7.12942 ( 264) SS BOND : bond 0.00453 ( 11) SS BOND : angle 1.22812 ( 22) covalent geometry : bond 0.00260 ( 6703) covalent geometry : angle 0.61479 ( 9118) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 1.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7688 (tm130) cc_final: 0.7272 (tp40) REVERT: A 67 VAL cc_start: 0.8035 (p) cc_final: 0.7353 (m) REVERT: A 92 PHE cc_start: 0.6468 (t80) cc_final: 0.6149 (t80) REVERT: A 177 MET cc_start: 0.6205 (mmt) cc_final: 0.5901 (mmt) REVERT: A 265 TYR cc_start: 0.6533 (m-80) cc_final: 0.6257 (m-80) REVERT: A 313 TYR cc_start: 0.5845 (m-80) cc_final: 0.5366 (m-80) REVERT: A 319 ARG cc_start: 0.7821 (ptp90) cc_final: 0.7572 (tpt170) REVERT: A 340 GLU cc_start: 0.7641 (mp0) cc_final: 0.7427 (mp0) REVERT: A 355 ARG cc_start: 0.7689 (mtp85) cc_final: 0.7244 (mtp85) REVERT: A 357 ARG cc_start: 0.7145 (ttp80) cc_final: 0.6714 (ttp80) REVERT: A 359 SER cc_start: 0.7926 (m) cc_final: 0.7436 (t) REVERT: A 368 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7918 (tp) REVERT: A 396 TYR cc_start: 0.6836 (m-80) cc_final: 0.6267 (m-80) REVERT: A 408 ARG cc_start: 0.8028 (ttp-170) cc_final: 0.7577 (ttp-170) REVERT: A 417 ASN cc_start: 0.7808 (t0) cc_final: 0.7406 (t0) REVERT: A 452 LEU cc_start: 0.7553 (mp) cc_final: 0.7052 (tt) REVERT: A 490 PHE cc_start: 0.8027 (t80) cc_final: 0.7776 (t80) REVERT: A 501 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.7317 (t80) REVERT: A 537 LYS cc_start: 0.7879 (tppp) cc_final: 0.7397 (mmmm) REVERT: A 564 GLN cc_start: 0.7854 (pp30) cc_final: 0.7631 (tm-30) REVERT: A 588 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8693 (p) REVERT: B 64 LYS cc_start: 0.8255 (tptt) cc_final: 0.7960 (tptt) REVERT: B 93 TYR cc_start: 0.6685 (m-80) cc_final: 0.6215 (m-80) REVERT: B 107 TYR cc_start: 0.5569 (t80) cc_final: 0.5018 (t80) REVERT: B 158 LEU cc_start: 0.7754 (mm) cc_final: 0.6854 (mt) REVERT: B 159 SER cc_start: 0.8033 (OUTLIER) cc_final: 0.7724 (t) REVERT: B 189 ILE cc_start: 0.8677 (mm) cc_final: 0.8381 (mm) REVERT: B 211 ASP cc_start: 0.7888 (t0) cc_final: 0.7610 (t0) REVERT: B 217 LEU cc_start: 0.8355 (tt) cc_final: 0.8058 (tt) REVERT: B 252 THR cc_start: 0.8252 (t) cc_final: 0.8032 (m) outliers start: 32 outliers final: 20 residues processed: 232 average time/residue: 0.4251 time to fit residues: 126.5835 Evaluate side-chains 220 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 231 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 57 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN B 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.162164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.129862 restraints weight = 12715.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.135709 restraints weight = 7401.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.139675 restraints weight = 4924.994| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6714 Z= 0.202 Angle : 0.681 7.221 9140 Z= 0.354 Chirality : 0.046 0.155 1003 Planarity : 0.005 0.064 1175 Dihedral : 6.862 81.598 938 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.88 % Favored : 87.12 % Rotamer: Outliers : 5.99 % Allowed : 19.08 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.58 (0.27), residues: 815 helix: -1.21 (1.80), residues: 10 sheet: -2.43 (0.36), residues: 191 loop : -2.58 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP B 174 HIS 0.004 0.001 HIS A 66 PHE 0.040 0.002 PHE A 275 TYR 0.017 0.002 TYR B 107 ARG 0.007 0.001 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 112) hydrogen bonds : angle 7.50174 ( 264) SS BOND : bond 0.00621 ( 11) SS BOND : angle 1.35023 ( 22) covalent geometry : bond 0.00422 ( 6703) covalent geometry : angle 0.67878 ( 9118) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 221 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7572 (tm130) cc_final: 0.7175 (tp40) REVERT: A 177 MET cc_start: 0.6392 (mmt) cc_final: 0.6059 (mmt) REVERT: A 340 GLU cc_start: 0.7985 (mp0) cc_final: 0.7690 (mp0) REVERT: A 357 ARG cc_start: 0.7682 (ttp80) cc_final: 0.6879 (ttp80) REVERT: A 360 ASN cc_start: 0.8569 (p0) cc_final: 0.8298 (p0) REVERT: A 377 PHE cc_start: 0.7231 (t80) cc_final: 0.6863 (t80) REVERT: A 387 LEU cc_start: 0.8637 (mt) cc_final: 0.8409 (tp) REVERT: A 396 TYR cc_start: 0.6939 (m-80) cc_final: 0.6181 (m-10) REVERT: A 401 VAL cc_start: 0.8065 (t) cc_final: 0.7702 (m) REVERT: A 408 ARG cc_start: 0.8011 (ttp-170) cc_final: 0.7630 (ttp-170) REVERT: A 417 ASN cc_start: 0.8108 (t0) cc_final: 0.7738 (t0) REVERT: A 424 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7929 (tmtm) REVERT: A 442 ASP cc_start: 0.8253 (p0) cc_final: 0.7895 (p0) REVERT: A 452 LEU cc_start: 0.7732 (mp) cc_final: 0.7180 (tt) REVERT: A 490 PHE cc_start: 0.8056 (t80) cc_final: 0.7850 (t80) REVERT: A 501 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7412 (t80) REVERT: A 537 LYS cc_start: 0.7974 (tppp) cc_final: 0.7460 (mmmm) REVERT: A 562 PHE cc_start: 0.7108 (t80) cc_final: 0.6561 (t80) REVERT: B 45 PRO cc_start: 0.8819 (Cg_endo) cc_final: 0.8573 (Cg_exo) REVERT: B 64 LYS cc_start: 0.8391 (tptt) cc_final: 0.8030 (tptt) REVERT: B 189 ILE cc_start: 0.8779 (mm) cc_final: 0.8477 (mm) REVERT: B 211 ASP cc_start: 0.7982 (t0) cc_final: 0.7580 (t0) REVERT: B 217 LEU cc_start: 0.8483 (tt) cc_final: 0.8271 (tt) REVERT: B 252 THR cc_start: 0.8087 (t) cc_final: 0.7824 (m) outliers start: 43 outliers final: 28 residues processed: 244 average time/residue: 0.4267 time to fit residues: 130.8106 Evaluate side-chains 233 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 58 TYR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 4.9990 chunk 55 optimal weight: 0.0670 chunk 9 optimal weight: 9.9990 chunk 68 optimal weight: 0.1980 chunk 77 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 63 optimal weight: 0.0070 chunk 79 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 overall best weight: 0.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 321 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 564 GLN A 607 GLN A 690 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.168226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.136243 restraints weight = 12623.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.141858 restraints weight = 7325.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.145811 restraints weight = 4888.432| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6714 Z= 0.118 Angle : 0.680 8.387 9140 Z= 0.343 Chirality : 0.046 0.158 1003 Planarity : 0.005 0.061 1175 Dihedral : 6.792 79.389 938 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.80 % Favored : 89.20 % Rotamer: Outliers : 4.74 % Allowed : 22.84 % Favored : 72.42 % 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: -3.38 (0.27), residues: 815 helix: -0.59 (1.55), residues: 10 sheet: -2.29 (0.37), residues: 182 loop : -2.45 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 174 HIS 0.013 0.002 HIS A 519 PHE 0.048 0.002 PHE A 275 TYR 0.020 0.001 TYR A 660 ARG 0.006 0.001 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.03039 ( 112) hydrogen bonds : angle 6.99782 ( 264) SS BOND : bond 0.00536 ( 11) SS BOND : angle 0.91909 ( 22) covalent geometry : bond 0.00261 ( 6703) covalent geometry : angle 0.67926 ( 9118) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7056 (mmp80) cc_final: 0.6387 (mtp85) REVERT: A 52 GLN cc_start: 0.7418 (tm130) cc_final: 0.7125 (tp40) REVERT: A 55 PHE cc_start: 0.7373 (m-80) cc_final: 0.7087 (m-80) REVERT: A 86 PHE cc_start: 0.8375 (t80) cc_final: 0.7778 (t80) REVERT: A 92 PHE cc_start: 0.6419 (t80) cc_final: 0.6214 (t80) REVERT: A 170 TYR cc_start: 0.8683 (t80) cc_final: 0.8427 (t80) REVERT: A 177 MET cc_start: 0.6259 (mmt) cc_final: 0.5957 (mmt) REVERT: A 224 GLU cc_start: 0.7149 (pm20) cc_final: 0.6647 (pm20) REVERT: A 313 TYR cc_start: 0.6013 (m-80) cc_final: 0.5405 (m-80) REVERT: A 340 GLU cc_start: 0.8062 (mp0) cc_final: 0.7745 (mp0) REVERT: A 355 ARG cc_start: 0.7748 (mtp85) cc_final: 0.7390 (mtp85) REVERT: A 357 ARG cc_start: 0.7473 (ttp80) cc_final: 0.6833 (ttp80) REVERT: A 360 ASN cc_start: 0.8448 (p0) cc_final: 0.8182 (p0) REVERT: A 386 LYS cc_start: 0.8405 (ttpp) cc_final: 0.8120 (ptmm) REVERT: A 387 LEU cc_start: 0.8643 (mt) cc_final: 0.8385 (mt) REVERT: A 395 VAL cc_start: 0.7912 (m) cc_final: 0.7684 (t) REVERT: A 396 TYR cc_start: 0.6900 (m-80) cc_final: 0.6554 (m-10) REVERT: A 408 ARG cc_start: 0.7860 (ttp-170) cc_final: 0.7486 (ttp-170) REVERT: A 424 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7616 (tptt) REVERT: A 442 ASP cc_start: 0.8296 (p0) cc_final: 0.7805 (p0) REVERT: A 452 LEU cc_start: 0.7443 (mp) cc_final: 0.6862 (tt) REVERT: A 465 GLU cc_start: 0.7383 (pt0) cc_final: 0.7170 (pt0) REVERT: A 490 PHE cc_start: 0.8133 (t80) cc_final: 0.7841 (t80) REVERT: A 501 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.7371 (t80) REVERT: A 659 SER cc_start: 0.7889 (m) cc_final: 0.7344 (t) REVERT: A 673 SER cc_start: 0.8120 (t) cc_final: 0.7919 (m) REVERT: B 29 PHE cc_start: 0.8029 (m-80) cc_final: 0.7472 (m-80) REVERT: B 45 PRO cc_start: 0.8760 (Cg_endo) cc_final: 0.8386 (Cg_exo) REVERT: B 64 LYS cc_start: 0.8264 (tptt) cc_final: 0.7900 (tptt) REVERT: B 189 ILE cc_start: 0.8733 (mm) cc_final: 0.8413 (mm) REVERT: B 197 TYR cc_start: 0.6928 (m-80) cc_final: 0.6636 (m-80) REVERT: B 211 ASP cc_start: 0.7896 (t0) cc_final: 0.7503 (t0) REVERT: B 217 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8072 (mm) REVERT: B 252 THR cc_start: 0.8183 (t) cc_final: 0.7859 (m) outliers start: 34 outliers final: 21 residues processed: 229 average time/residue: 0.3304 time to fit residues: 96.5192 Evaluate side-chains 226 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 217 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 44 optimal weight: 0.8980 chunk 11 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.161525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.129589 restraints weight = 12495.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.135071 restraints weight = 7192.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.138892 restraints weight = 4790.437| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6714 Z= 0.181 Angle : 0.718 7.950 9140 Z= 0.368 Chirality : 0.047 0.178 1003 Planarity : 0.005 0.054 1175 Dihedral : 6.961 80.499 930 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 5.01 % Allowed : 22.98 % Favored : 72.01 % 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: -3.39 (0.27), residues: 815 helix: -0.81 (1.43), residues: 16 sheet: -2.22 (0.35), residues: 198 loop : -2.49 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP B 174 HIS 0.014 0.003 HIS A 519 PHE 0.058 0.002 PHE A 275 TYR 0.017 0.001 TYR B 32 ARG 0.005 0.001 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 112) hydrogen bonds : angle 7.21093 ( 264) SS BOND : bond 0.00542 ( 11) SS BOND : angle 1.07252 ( 22) covalent geometry : bond 0.00386 ( 6703) covalent geometry : angle 0.71707 ( 9118) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.6967 (mmp80) cc_final: 0.6295 (mtp85) REVERT: A 52 GLN cc_start: 0.7344 (tm130) cc_final: 0.7045 (tp40) REVERT: A 86 PHE cc_start: 0.8575 (t80) cc_final: 0.8229 (t80) REVERT: A 170 TYR cc_start: 0.8776 (t80) cc_final: 0.8402 (t80) REVERT: A 177 MET cc_start: 0.6470 (mmt) cc_final: 0.6160 (mmt) REVERT: A 313 TYR cc_start: 0.6257 (m-80) cc_final: 0.5645 (m-80) REVERT: A 328 ARG cc_start: 0.6810 (ttm110) cc_final: 0.6379 (ttm110) REVERT: A 337 PRO cc_start: 0.8067 (Cg_exo) cc_final: 0.7304 (Cg_endo) REVERT: A 340 GLU cc_start: 0.8150 (mp0) cc_final: 0.7833 (mp0) REVERT: A 357 ARG cc_start: 0.7725 (ttp80) cc_final: 0.7116 (ttp80) REVERT: A 360 ASN cc_start: 0.8546 (p0) cc_final: 0.8301 (p0) REVERT: A 377 PHE cc_start: 0.7232 (t80) cc_final: 0.6942 (t80) REVERT: A 386 LYS cc_start: 0.8415 (ttpp) cc_final: 0.8190 (ptmm) REVERT: A 387 LEU cc_start: 0.8627 (mt) cc_final: 0.8338 (mt) REVERT: A 396 TYR cc_start: 0.6925 (m-80) cc_final: 0.6464 (m-10) REVERT: A 408 ARG cc_start: 0.7850 (ttp-170) cc_final: 0.7474 (ttp-170) REVERT: A 442 ASP cc_start: 0.8254 (p0) cc_final: 0.7831 (p0) REVERT: A 452 LEU cc_start: 0.7618 (mp) cc_final: 0.6995 (tt) REVERT: A 490 PHE cc_start: 0.8188 (t80) cc_final: 0.7971 (t80) REVERT: A 501 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.7366 (t80) REVERT: A 588 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8689 (p) REVERT: A 673 SER cc_start: 0.8462 (t) cc_final: 0.8020 (m) REVERT: B 29 PHE cc_start: 0.8192 (m-80) cc_final: 0.7539 (m-80) REVERT: B 38 ARG cc_start: 0.7371 (ttp80) cc_final: 0.7093 (ttp80) REVERT: B 45 PRO cc_start: 0.8728 (Cg_endo) cc_final: 0.8513 (Cg_exo) REVERT: B 64 LYS cc_start: 0.8346 (tptt) cc_final: 0.7979 (tptt) REVERT: B 160 CYS cc_start: 0.4922 (t) cc_final: 0.4677 (t) REVERT: B 189 ILE cc_start: 0.8758 (mm) cc_final: 0.8448 (mm) REVERT: B 197 TYR cc_start: 0.7237 (m-80) cc_final: 0.7021 (m-80) REVERT: B 211 ASP cc_start: 0.8007 (t0) cc_final: 0.7599 (t0) REVERT: B 217 LEU cc_start: 0.8529 (tt) cc_final: 0.8213 (mm) REVERT: B 234 CYS cc_start: 0.5088 (p) cc_final: 0.4510 (p) REVERT: B 252 THR cc_start: 0.8077 (t) cc_final: 0.7788 (m) outliers start: 36 outliers final: 30 residues processed: 220 average time/residue: 0.3382 time to fit residues: 96.4908 Evaluate side-chains 228 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 208 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 50 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 0.0770 chunk 10 optimal weight: 0.0870 chunk 62 optimal weight: 8.9990 chunk 20 optimal weight: 0.0980 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 overall best weight: 0.2516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 321 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 564 GLN A 690 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.167315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.135800 restraints weight = 12541.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.141376 restraints weight = 7275.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.145311 restraints weight = 4824.969| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6714 Z= 0.122 Angle : 0.720 8.676 9140 Z= 0.364 Chirality : 0.047 0.203 1003 Planarity : 0.005 0.057 1175 Dihedral : 6.898 80.653 930 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 4.74 % Allowed : 23.12 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.24 (0.28), residues: 815 helix: -0.63 (1.51), residues: 16 sheet: -2.05 (0.35), residues: 207 loop : -2.40 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 174 HIS 0.009 0.002 HIS A 519 PHE 0.042 0.002 PHE A 275 TYR 0.015 0.001 TYR B 32 ARG 0.006 0.001 ARG A 493 Details of bonding type rmsd hydrogen bonds : bond 0.02974 ( 112) hydrogen bonds : angle 6.73193 ( 264) SS BOND : bond 0.00373 ( 11) SS BOND : angle 2.36905 ( 22) covalent geometry : bond 0.00273 ( 6703) covalent geometry : angle 0.71104 ( 9118) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7124 (mmp80) cc_final: 0.6216 (mmm-85) REVERT: A 52 GLN cc_start: 0.7391 (tm130) cc_final: 0.7093 (tp40) REVERT: A 86 PHE cc_start: 0.8373 (t80) cc_final: 0.8080 (t80) REVERT: A 92 PHE cc_start: 0.6453 (t80) cc_final: 0.6193 (t80) REVERT: A 177 MET cc_start: 0.6358 (mmt) cc_final: 0.6062 (mmt) REVERT: A 229 LEU cc_start: 0.8371 (tp) cc_final: 0.8058 (mp) REVERT: A 308 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8139 (p) REVERT: A 313 TYR cc_start: 0.5924 (m-80) cc_final: 0.5340 (m-80) REVERT: A 340 GLU cc_start: 0.8087 (mp0) cc_final: 0.7564 (mp0) REVERT: A 355 ARG cc_start: 0.7833 (mtp85) cc_final: 0.7475 (mtp85) REVERT: A 357 ARG cc_start: 0.7450 (ttp80) cc_final: 0.7055 (ttp80) REVERT: A 359 SER cc_start: 0.8193 (m) cc_final: 0.7772 (t) REVERT: A 360 ASN cc_start: 0.8397 (p0) cc_final: 0.8147 (p0) REVERT: A 387 LEU cc_start: 0.8516 (mt) cc_final: 0.8283 (mt) REVERT: A 396 TYR cc_start: 0.7062 (m-80) cc_final: 0.6574 (m-10) REVERT: A 422 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.8022 (t0) REVERT: A 442 ASP cc_start: 0.8299 (p0) cc_final: 0.7781 (p0) REVERT: A 490 PHE cc_start: 0.8192 (t80) cc_final: 0.7945 (t80) REVERT: A 501 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.7277 (t80) REVERT: A 547 LYS cc_start: 0.7473 (mmmt) cc_final: 0.7114 (mmmt) REVERT: A 673 SER cc_start: 0.8239 (t) cc_final: 0.7843 (m) REVERT: B 29 PHE cc_start: 0.8127 (m-80) cc_final: 0.7529 (m-80) REVERT: B 38 ARG cc_start: 0.7216 (ttp80) cc_final: 0.6996 (ttp80) REVERT: B 64 LYS cc_start: 0.8249 (tptt) cc_final: 0.7888 (tptt) REVERT: B 189 ILE cc_start: 0.8683 (mm) cc_final: 0.8354 (mm) REVERT: B 197 TYR cc_start: 0.6940 (m-80) cc_final: 0.6605 (m-80) REVERT: B 211 ASP cc_start: 0.7918 (t0) cc_final: 0.7549 (t0) REVERT: B 217 LEU cc_start: 0.8493 (tt) cc_final: 0.8155 (mm) REVERT: B 234 CYS cc_start: 0.4810 (p) cc_final: 0.4424 (p) REVERT: B 252 THR cc_start: 0.8172 (t) cc_final: 0.7916 (m) outliers start: 34 outliers final: 23 residues processed: 221 average time/residue: 0.2444 time to fit residues: 69.5610 Evaluate side-chains 223 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 185 TRP Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 208 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 690 GLN B 3 GLN B 250 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.152815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.122088 restraints weight = 12942.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.127296 restraints weight = 7535.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.130846 restraints weight = 5048.895| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.6691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 6714 Z= 0.376 Angle : 0.927 11.523 9140 Z= 0.488 Chirality : 0.055 0.294 1003 Planarity : 0.006 0.053 1175 Dihedral : 7.985 83.643 930 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 28.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 15.58 % Favored : 84.29 % Rotamer: Outliers : 5.99 % Allowed : 23.68 % Favored : 70.33 % 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: -3.46 (0.27), residues: 815 helix: -1.86 (1.09), residues: 17 sheet: -2.73 (0.35), residues: 182 loop : -2.34 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.005 TRP B 174 HIS 0.004 0.001 HIS A 49 PHE 0.067 0.003 PHE A 275 TYR 0.023 0.002 TYR A 37 ARG 0.009 0.001 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.05204 ( 112) hydrogen bonds : angle 8.04507 ( 264) SS BOND : bond 0.01531 ( 11) SS BOND : angle 3.52644 ( 22) covalent geometry : bond 0.00759 ( 6703) covalent geometry : angle 0.91143 ( 9118) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 219 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7525 (tm130) cc_final: 0.7284 (tm-30) REVERT: A 55 PHE cc_start: 0.7542 (m-80) cc_final: 0.7047 (m-80) REVERT: A 84 LEU cc_start: 0.8772 (mt) cc_final: 0.8513 (mp) REVERT: A 86 PHE cc_start: 0.8862 (t80) cc_final: 0.8539 (t80) REVERT: A 177 MET cc_start: 0.7061 (mmt) cc_final: 0.6719 (mmt) REVERT: A 328 ARG cc_start: 0.6749 (ttm110) cc_final: 0.6210 (ttm110) REVERT: A 340 GLU cc_start: 0.8204 (mp0) cc_final: 0.7760 (mp0) REVERT: A 343 ASN cc_start: 0.8310 (t0) cc_final: 0.7862 (p0) REVERT: A 360 ASN cc_start: 0.8661 (p0) cc_final: 0.8401 (p0) REVERT: A 393 THR cc_start: 0.8570 (p) cc_final: 0.8284 (p) REVERT: A 396 TYR cc_start: 0.7268 (m-80) cc_final: 0.5961 (m-80) REVERT: A 408 ARG cc_start: 0.8038 (ttp-170) cc_final: 0.7754 (ttp-170) REVERT: A 424 LYS cc_start: 0.8454 (tptt) cc_final: 0.8218 (tptp) REVERT: A 442 ASP cc_start: 0.8064 (p0) cc_final: 0.7751 (p0) REVERT: A 465 GLU cc_start: 0.8039 (pt0) cc_final: 0.7807 (pt0) REVERT: A 501 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7524 (t80) REVERT: A 562 PHE cc_start: 0.6800 (t80) cc_final: 0.6348 (t80) REVERT: A 673 SER cc_start: 0.8852 (t) cc_final: 0.8339 (m) REVERT: B 29 PHE cc_start: 0.8220 (m-80) cc_final: 0.7572 (m-80) REVERT: B 43 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8345 (pttm) REVERT: B 64 LYS cc_start: 0.8538 (tptt) cc_final: 0.8155 (tptt) REVERT: B 158 LEU cc_start: 0.7813 (mm) cc_final: 0.7484 (mp) REVERT: B 165 PHE cc_start: 0.7854 (t80) cc_final: 0.7612 (t80) REVERT: B 189 ILE cc_start: 0.8822 (mm) cc_final: 0.8488 (mm) REVERT: B 198 TYR cc_start: 0.8043 (m-80) cc_final: 0.7758 (m-10) REVERT: B 211 ASP cc_start: 0.8098 (t0) cc_final: 0.7492 (t0) REVERT: B 252 THR cc_start: 0.8106 (t) cc_final: 0.7872 (m) outliers start: 43 outliers final: 30 residues processed: 240 average time/residue: 0.3680 time to fit residues: 114.3569 Evaluate side-chains 239 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 185 TRP Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 217 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 72 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 48 optimal weight: 0.1980 chunk 63 optimal weight: 0.8980 chunk 79 optimal weight: 0.0870 chunk 14 optimal weight: 3.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 580 GLN A 675 GLN A 690 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.158653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.126731 restraints weight = 12590.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.132246 restraints weight = 7326.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.136037 restraints weight = 4873.243| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.6668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6714 Z= 0.170 Angle : 0.852 11.585 9140 Z= 0.432 Chirality : 0.050 0.248 1003 Planarity : 0.007 0.105 1175 Dihedral : 7.392 83.006 928 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.15 % Favored : 87.73 % Rotamer: Outliers : 4.18 % Allowed : 27.99 % Favored : 67.83 % Cbeta Deviations : 0.13 % 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: -3.34 (0.28), residues: 815 helix: -2.09 (1.03), residues: 17 sheet: -2.36 (0.34), residues: 218 loop : -2.30 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP B 174 HIS 0.018 0.003 HIS A 519 PHE 0.049 0.002 PHE A 275 TYR 0.024 0.002 TYR B 170 ARG 0.007 0.001 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.03459 ( 112) hydrogen bonds : angle 7.27764 ( 264) SS BOND : bond 0.00456 ( 11) SS BOND : angle 2.51043 ( 22) covalent geometry : bond 0.00374 ( 6703) covalent geometry : angle 0.84432 ( 9118) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.6947 (m-80) cc_final: 0.6445 (m-80) REVERT: A 86 PHE cc_start: 0.8715 (t80) cc_final: 0.8470 (t80) REVERT: A 108 THR cc_start: 0.7495 (m) cc_final: 0.7276 (p) REVERT: A 177 MET cc_start: 0.6880 (mmt) cc_final: 0.6533 (mmt) REVERT: A 207 PRO cc_start: 0.8378 (Cg_exo) cc_final: 0.7708 (Cg_endo) REVERT: A 229 LEU cc_start: 0.8344 (tp) cc_final: 0.8099 (mm) REVERT: A 313 TYR cc_start: 0.6584 (m-80) cc_final: 0.5917 (m-80) REVERT: A 328 ARG cc_start: 0.6312 (ttm110) cc_final: 0.5952 (ttm110) REVERT: A 337 PRO cc_start: 0.8240 (Cg_exo) cc_final: 0.7170 (Cg_endo) REVERT: A 340 GLU cc_start: 0.8197 (mp0) cc_final: 0.7673 (mp0) REVERT: A 360 ASN cc_start: 0.8588 (p0) cc_final: 0.8280 (p0) REVERT: A 396 TYR cc_start: 0.7133 (m-80) cc_final: 0.6907 (m-10) REVERT: A 408 ARG cc_start: 0.7876 (ttp-170) cc_final: 0.7564 (ttp-170) REVERT: A 424 LYS cc_start: 0.8232 (tptt) cc_final: 0.7943 (tptp) REVERT: A 442 ASP cc_start: 0.8261 (p0) cc_final: 0.7893 (p0) REVERT: A 465 GLU cc_start: 0.7892 (pt0) cc_final: 0.7504 (pt0) REVERT: A 501 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.7501 (t80) REVERT: A 547 LYS cc_start: 0.7477 (mmmt) cc_final: 0.7070 (mmmt) REVERT: A 642 VAL cc_start: 0.8654 (p) cc_final: 0.8446 (t) REVERT: A 643 PHE cc_start: 0.6539 (t80) cc_final: 0.6331 (t80) REVERT: A 673 SER cc_start: 0.8547 (t) cc_final: 0.7955 (m) REVERT: B 29 PHE cc_start: 0.8088 (m-80) cc_final: 0.7529 (m-80) REVERT: B 38 ARG cc_start: 0.7121 (ttp80) cc_final: 0.6707 (ttp80) REVERT: B 64 LYS cc_start: 0.8307 (tptt) cc_final: 0.7947 (tptt) REVERT: B 96 VAL cc_start: 0.8861 (t) cc_final: 0.7601 (p) REVERT: B 189 ILE cc_start: 0.8683 (mm) cc_final: 0.8094 (mm) REVERT: B 211 ASP cc_start: 0.7938 (t0) cc_final: 0.7468 (t0) REVERT: B 217 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8244 (mm) REVERT: B 252 THR cc_start: 0.8068 (t) cc_final: 0.7817 (m) outliers start: 30 outliers final: 25 residues processed: 224 average time/residue: 0.3663 time to fit residues: 105.2563 Evaluate side-chains 233 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 185 TRP Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 234 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 80 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 690 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.162584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.130932 restraints weight = 12643.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.136415 restraints weight = 7424.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.140206 restraints weight = 4963.397| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.6833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6714 Z= 0.195 Angle : 0.861 10.488 9140 Z= 0.441 Chirality : 0.051 0.285 1003 Planarity : 0.007 0.093 1175 Dihedral : 7.445 82.833 928 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.48 % Favored : 85.52 % Rotamer: Outliers : 3.76 % Allowed : 28.83 % Favored : 67.41 % 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: -3.31 (0.28), residues: 815 helix: -1.99 (1.04), residues: 17 sheet: -2.26 (0.35), residues: 215 loop : -2.32 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.004 TRP B 174 HIS 0.008 0.002 HIS A 519 PHE 0.053 0.003 PHE A 275 TYR 0.022 0.002 TYR B 170 ARG 0.008 0.001 ARG A 493 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 112) hydrogen bonds : angle 7.28383 ( 264) SS BOND : bond 0.00530 ( 11) SS BOND : angle 2.61220 ( 22) covalent geometry : bond 0.00423 ( 6703) covalent geometry : angle 0.85236 ( 9118) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7511 (tp40) cc_final: 0.7115 (tp40) REVERT: A 55 PHE cc_start: 0.7094 (m-80) cc_final: 0.6497 (m-80) REVERT: A 86 PHE cc_start: 0.8675 (t80) cc_final: 0.8468 (t80) REVERT: A 177 MET cc_start: 0.6961 (mmt) cc_final: 0.6623 (mmt) REVERT: A 229 LEU cc_start: 0.8367 (tp) cc_final: 0.8098 (mm) REVERT: A 233 ILE cc_start: 0.6484 (OUTLIER) cc_final: 0.6235 (mt) REVERT: A 313 TYR cc_start: 0.6544 (m-80) cc_final: 0.5897 (m-80) REVERT: A 328 ARG cc_start: 0.6338 (ttm110) cc_final: 0.5976 (ttm110) REVERT: A 337 PRO cc_start: 0.8231 (Cg_exo) cc_final: 0.7244 (Cg_endo) REVERT: A 340 GLU cc_start: 0.8042 (mp0) cc_final: 0.7598 (mp0) REVERT: A 360 ASN cc_start: 0.8583 (p0) cc_final: 0.8334 (p0) REVERT: A 408 ARG cc_start: 0.7877 (ttp-170) cc_final: 0.7561 (ttp-170) REVERT: A 424 LYS cc_start: 0.8237 (tptt) cc_final: 0.7965 (tptp) REVERT: A 442 ASP cc_start: 0.8233 (p0) cc_final: 0.7868 (p0) REVERT: A 465 GLU cc_start: 0.7897 (pt0) cc_final: 0.7562 (pt0) REVERT: A 501 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.7540 (t80) REVERT: A 643 PHE cc_start: 0.6708 (t80) cc_final: 0.6465 (t80) REVERT: A 673 SER cc_start: 0.8597 (t) cc_final: 0.8003 (m) REVERT: B 29 PHE cc_start: 0.8085 (m-80) cc_final: 0.7525 (m-80) REVERT: B 64 LYS cc_start: 0.8255 (tptt) cc_final: 0.7938 (tptt) REVERT: B 82 MET cc_start: 0.8502 (mtt) cc_final: 0.8209 (ttt) REVERT: B 189 ILE cc_start: 0.8645 (mm) cc_final: 0.8367 (mm) REVERT: B 197 TYR cc_start: 0.7473 (m-80) cc_final: 0.7195 (m-80) REVERT: B 211 ASP cc_start: 0.8031 (t0) cc_final: 0.7596 (t0) REVERT: B 217 LEU cc_start: 0.8519 (tt) cc_final: 0.8241 (mm) REVERT: B 252 THR cc_start: 0.8120 (t) cc_final: 0.7816 (m) outliers start: 27 outliers final: 23 residues processed: 223 average time/residue: 0.2456 time to fit residues: 70.3037 Evaluate side-chains 229 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 185 TRP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 234 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 58 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 46 optimal weight: 0.1980 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 675 GLN A 690 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.159890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.128332 restraints weight = 12740.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.133874 restraints weight = 7365.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.137632 restraints weight = 4898.091| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.6860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6714 Z= 0.153 Angle : 0.846 9.972 9140 Z= 0.431 Chirality : 0.050 0.265 1003 Planarity : 0.006 0.083 1175 Dihedral : 7.222 82.806 928 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.25 % Favored : 86.75 % Rotamer: Outliers : 4.46 % Allowed : 28.97 % Favored : 66.57 % 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: -3.12 (0.28), residues: 815 helix: -1.98 (1.06), residues: 17 sheet: -2.00 (0.38), residues: 195 loop : -2.25 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.108 0.004 TRP B 174 HIS 0.005 0.001 HIS A 519 PHE 0.047 0.002 PHE A 275 TYR 0.017 0.001 TYR A 91 ARG 0.008 0.001 ARG A 493 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 112) hydrogen bonds : angle 7.06148 ( 264) SS BOND : bond 0.00406 ( 11) SS BOND : angle 2.41016 ( 22) covalent geometry : bond 0.00346 ( 6703) covalent geometry : angle 0.83904 ( 9118) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3833.25 seconds wall clock time: 72 minutes 24.49 seconds (4344.49 seconds total)