Starting phenix.real_space_refine on Sat May 10 02:39:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zsz_60435/05_2025/8zsz_60435.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zsz_60435/05_2025/8zsz_60435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zsz_60435/05_2025/8zsz_60435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zsz_60435/05_2025/8zsz_60435.map" model { file = "/net/cci-nas-00/data/ceres_data/8zsz_60435/05_2025/8zsz_60435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zsz_60435/05_2025/8zsz_60435.cif" } resolution = 3.59 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= 0.093 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 41 5.16 5 C 3071 2.51 5 N 829 2.21 5 O 805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4754 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2362 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 11, 'TRANS': 303} Chain breaks: 3 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2384 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 11, 'TRANS': 303} Chain breaks: 3 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.36, per 1000 atoms: 0.71 Number of scatterers: 4754 At special positions: 0 Unit cell: (70.655, 58.698, 117.396, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 8 29.99 S 41 16.00 O 805 8.00 N 829 7.00 C 3071 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS B 291 " distance=2.01 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 282 " distance=2.03 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 311 " 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: 1.16 Conformation dependent library (CDL) restraints added in 531.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS B 157 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 370 " pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" NE2 HIS A 43 " pdb="ZN ZN A 602 " - pdb=" NE2 HIS A 251 " pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" NE2 HIS A 373 " pdb="ZN ZN A 603 " - pdb=" NE2 HIS B 148 " pdb="ZN ZN A 603 " - pdb=" NE2 HIS B 146 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS A 157 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 370 " pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" NE2 HIS B 43 " pdb="ZN ZN B 602 " - pdb=" NE2 HIS B 251 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" NE2 HIS B 373 " pdb="ZN ZN B 603 " - pdb=" NE2 HIS A 148 " pdb="ZN ZN B 603 " - pdb=" NE2 HIS A 146 " 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 68.1% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 5 through 33 Processing helix chain 'A' and resid 35 through 62 removed outlier: 3.514A pdb=" N LEU A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 106 removed outlier: 3.532A pdb=" N GLU A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 134 Processing helix chain 'A' and resid 239 through 273 Processing helix chain 'A' and resid 310 through 315 removed outlier: 4.239A pdb=" N LEU A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 315 " --> pdb=" O CYS A 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 310 through 315' Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.622A pdb=" N THR A 319 " --> pdb=" O TYR A 315 " (cutoff:3.500A) Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 352 through 362 removed outlier: 3.539A pdb=" N LEU A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 411 removed outlier: 3.793A pdb=" N MET A 397 " --> pdb=" O PRO A 393 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 33 Processing helix chain 'B' and resid 35 through 63 removed outlier: 3.512A pdb=" N ARG B 63 " --> pdb=" O ARG B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 106 removed outlier: 3.715A pdb=" N GLU B 78 " --> pdb=" O TRP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 134 Processing helix chain 'B' and resid 239 through 273 Processing helix chain 'B' and resid 310 through 315 removed outlier: 4.238A pdb=" N LEU B 314 " --> pdb=" O PRO B 310 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 315 " --> pdb=" O CYS B 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 310 through 315' Processing helix chain 'B' and resid 315 through 343 removed outlier: 3.622A pdb=" N THR B 319 " --> pdb=" O TYR B 315 " (cutoff:3.500A) Proline residue: B 334 - end of helix Processing helix chain 'B' and resid 352 through 363 removed outlier: 3.539A pdb=" N LEU B 356 " --> pdb=" O ASP B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 411 removed outlier: 3.793A pdb=" N MET B 397 " --> pdb=" O PRO B 393 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 370 through 377 removed outlier: 6.056A pdb=" N GLU A 371 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N HIS A 387 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA A 414 " --> pdb=" O ILE A 382 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 370 through 377 removed outlier: 6.046A pdb=" N GLU B 371 " --> pdb=" O HIS B 387 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N HIS B 387 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA B 414 " --> pdb=" O ILE B 382 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 1053 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: 1.44 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 748 1.28 - 1.42: 1281 1.42 - 1.55: 2759 1.55 - 1.68: 2 1.68 - 1.82: 60 Bond restraints: 4850 Sorted by residual: bond pdb=" CA TRP A 375 " pdb=" C TRP A 375 " ideal model delta sigma weight residual 1.521 1.399 0.122 1.24e-02 6.50e+03 9.65e+01 bond pdb=" CA TRP B 375 " pdb=" C TRP B 375 " ideal model delta sigma weight residual 1.521 1.401 0.120 1.24e-02 6.50e+03 9.41e+01 bond pdb=" CA LEU A 372 " pdb=" C LEU A 372 " ideal model delta sigma weight residual 1.524 1.410 0.114 1.23e-02 6.61e+03 8.55e+01 bond pdb=" CA LEU B 372 " pdb=" C LEU B 372 " ideal model delta sigma weight residual 1.524 1.410 0.114 1.23e-02 6.61e+03 8.53e+01 bond pdb=" CA ALA A 54 " pdb=" C ALA A 54 " ideal model delta sigma weight residual 1.522 1.393 0.129 1.40e-02 5.10e+03 8.46e+01 ... (remaining 4845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.72: 6224 3.72 - 7.43: 303 7.43 - 11.15: 66 11.15 - 14.86: 8 14.86 - 18.58: 3 Bond angle restraints: 6604 Sorted by residual: angle pdb=" N VAL B 56 " pdb=" CA VAL B 56 " pdb=" C VAL B 56 " ideal model delta sigma weight residual 110.72 92.14 18.58 1.01e+00 9.80e-01 3.38e+02 angle pdb=" N LYS A 69 " pdb=" CA LYS A 69 " pdb=" C LYS A 69 " ideal model delta sigma weight residual 114.31 98.58 15.73 1.29e+00 6.01e-01 1.49e+02 angle pdb=" N HIS A 43 " pdb=" CA HIS A 43 " pdb=" C HIS A 43 " ideal model delta sigma weight residual 113.01 100.68 12.33 1.20e+00 6.94e-01 1.06e+02 angle pdb=" N VAL A 56 " pdb=" CA VAL A 56 " pdb=" C VAL A 56 " ideal model delta sigma weight residual 111.89 97.80 14.09 1.44e+00 4.82e-01 9.58e+01 angle pdb=" N LYS B 69 " pdb=" CA LYS B 69 " pdb=" C LYS B 69 " ideal model delta sigma weight residual 113.61 99.82 13.79 1.50e+00 4.44e-01 8.46e+01 ... (remaining 6599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 2494 15.99 - 31.99: 249 31.99 - 47.98: 63 47.98 - 63.98: 18 63.98 - 79.97: 9 Dihedral angle restraints: 2833 sinusoidal: 1037 harmonic: 1796 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS B 291 " pdb=" CB CYS B 291 " ideal model delta sinusoidal sigma weight residual -86.00 -162.51 76.51 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CB CYS A 286 " pdb=" SG CYS A 286 " pdb=" SG CYS A 311 " pdb=" CB CYS A 311 " ideal model delta sinusoidal sigma weight residual -86.00 -23.94 -62.06 1 1.00e+01 1.00e-02 5.10e+01 dihedral pdb=" CB CYS B 286 " pdb=" SG CYS B 286 " pdb=" SG CYS B 311 " pdb=" CB CYS B 311 " ideal model delta sinusoidal sigma weight residual -86.00 -23.98 -62.02 1 1.00e+01 1.00e-02 5.10e+01 ... (remaining 2830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 663 0.098 - 0.197: 94 0.197 - 0.295: 24 0.295 - 0.394: 10 0.394 - 0.492: 8 Chirality restraints: 799 Sorted by residual: chirality pdb=" CA TRP B 74 " pdb=" N TRP B 74 " pdb=" C TRP B 74 " pdb=" CB TRP B 74 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" CA HIS A 408 " pdb=" N HIS A 408 " pdb=" C HIS A 408 " pdb=" CB HIS A 408 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.86e+00 chirality pdb=" CA HIS B 408 " pdb=" N HIS B 408 " pdb=" C HIS B 408 " pdb=" CB HIS B 408 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.83e+00 ... (remaining 796 not shown) Planarity restraints: 825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 336 " 0.041 2.00e-02 2.50e+03 8.23e-02 6.77e+01 pdb=" C LEU A 336 " -0.142 2.00e-02 2.50e+03 pdb=" O LEU A 336 " 0.053 2.00e-02 2.50e+03 pdb=" N LYS A 337 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 336 " -0.041 2.00e-02 2.50e+03 8.22e-02 6.76e+01 pdb=" C LEU B 336 " 0.142 2.00e-02 2.50e+03 pdb=" O LEU B 336 " -0.053 2.00e-02 2.50e+03 pdb=" N LYS B 337 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 411 " -0.040 2.00e-02 2.50e+03 7.79e-02 6.07e+01 pdb=" C GLY A 411 " 0.135 2.00e-02 2.50e+03 pdb=" O GLY A 411 " -0.050 2.00e-02 2.50e+03 pdb=" N ILE A 412 " -0.045 2.00e-02 2.50e+03 ... (remaining 822 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.28: 22 2.28 - 2.93: 2485 2.93 - 3.59: 7490 3.59 - 4.24: 10516 4.24 - 4.90: 17643 Nonbonded interactions: 38156 Sorted by model distance: nonbonded pdb=" OE2 GLU B 420 " pdb="ZN ZN B 601 " model vdw 1.624 2.230 nonbonded pdb=" OE2 GLU A 420 " pdb="ZN ZN A 601 " model vdw 1.659 2.230 nonbonded pdb=" OD1 ASP A 255 " pdb="ZN ZN A 602 " model vdw 1.782 2.230 nonbonded pdb=" OD1 ASP B 255 " pdb="ZN ZN B 602 " model vdw 1.792 2.230 nonbonded pdb=" OE1 GLU B 371 " pdb="ZN ZN B 603 " model vdw 1.851 2.230 ... (remaining 38151 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 361 or (resid 362 and (name N or name CA or name \ C or name O or name CB )) or resid 363 through 366 or (resid 367 and (name N or \ name CA or name C or name O or name CB )) or resid 368 through 421 or resid 601 \ through 604)) selection = (chain 'B' and (resid 5 through 353 or (resid 354 and (name N or name CA or name \ C or name O or name CB )) or resid 355 through 360 or (resid 361 through 362 an \ d (name N or name CA or name C or name O or name CB )) or resid 363 through 381 \ or (resid 382 and (name N or name CA or name C or name O or name CB )) or resid \ 383 through 388 or (resid 389 and (name N or name CA or name C or name O or name \ CB )) or resid 390 through 396 or (resid 397 through 398 and (name N or name CA \ or name C or name O or name CB )) or resid 399 through 403 or (resid 404 throug \ h 405 and (name N or name CA or name C or name O or name CB )) or resid 406 thro \ ugh 421 or resid 601 through 604)) } 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: 0.410 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.830 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 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 : 0.027 0.721 4869 Z= 1.422 Angle : 1.806 18.578 6614 Z= 1.230 Chirality : 0.094 0.492 799 Planarity : 0.012 0.082 825 Dihedral : 14.915 79.971 1654 Min Nonbonded Distance : 1.624 Molprobity Statistics. All-atom Clashscore : 28.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.63 % Allowed : 5.05 % Favored : 92.32 % Cbeta Deviations : 1.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.35), residues: 614 helix: 0.74 (0.25), residues: 404 sheet: -0.56 (0.85), residues: 44 loop : -1.58 (0.53), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.005 TRP A 375 HIS 0.053 0.007 HIS A 146 PHE 0.027 0.002 PHE B 72 TYR 0.009 0.001 TYR B 396 ARG 0.004 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.17204 ( 351) hydrogen bonds : angle 7.70688 ( 1053) metal coordination : bond 0.39086 ( 14) SS BOND : bond 0.01058 ( 5) SS BOND : angle 1.89073 ( 10) covalent geometry : bond 0.01718 ( 4850) covalent geometry : angle 1.80542 ( 6604) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8360 (mmt) cc_final: 0.8077 (mmt) REVERT: A 46 SER cc_start: 0.8443 (m) cc_final: 0.8179 (t) REVERT: A 62 ARG cc_start: 0.8217 (mmt180) cc_final: 0.8005 (mtp-110) REVERT: A 287 PHE cc_start: 0.8941 (t80) cc_final: 0.8574 (t80) REVERT: A 289 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.8081 (m-30) REVERT: A 324 MET cc_start: 0.8106 (tmm) cc_final: 0.7676 (tmm) REVERT: A 370 HIS cc_start: 0.6386 (OUTLIER) cc_final: 0.5971 (p90) REVERT: A 409 ASN cc_start: 0.9068 (t0) cc_final: 0.8818 (m-40) REVERT: B 49 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8031 (tp) REVERT: B 287 PHE cc_start: 0.8989 (t80) cc_final: 0.8625 (t80) REVERT: B 289 ASP cc_start: 0.8353 (OUTLIER) cc_final: 0.8093 (m-30) REVERT: B 324 MET cc_start: 0.8139 (tmm) cc_final: 0.7702 (tmm) outliers start: 13 outliers final: 4 residues processed: 169 average time/residue: 0.1366 time to fit residues: 30.2541 Evaluate side-chains 142 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 289 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 18 optimal weight: 30.0000 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN A 410 HIS A 413 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.213945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.156076 restraints weight = 5272.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.160451 restraints weight = 3873.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.162746 restraints weight = 3211.816| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 4869 Z= 0.231 Angle : 0.719 8.557 6614 Z= 0.384 Chirality : 0.046 0.174 799 Planarity : 0.005 0.048 825 Dihedral : 5.864 56.662 672 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.12 % Favored : 97.72 % Rotamer: Outliers : 4.85 % Allowed : 13.74 % Favored : 81.41 % 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: 0.98 (0.35), residues: 614 helix: 1.61 (0.24), residues: 404 sheet: -2.15 (0.65), residues: 44 loop : -0.86 (0.58), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 375 HIS 0.037 0.004 HIS A 148 PHE 0.030 0.002 PHE A 421 TYR 0.012 0.002 TYR A 396 ARG 0.005 0.001 ARG B 76 Details of bonding type rmsd hydrogen bonds : bond 0.06021 ( 351) hydrogen bonds : angle 5.14435 ( 1053) metal coordination : bond 0.06809 ( 14) SS BOND : bond 0.00531 ( 5) SS BOND : angle 1.82336 ( 10) covalent geometry : bond 0.00426 ( 4850) covalent geometry : angle 0.71600 ( 6604) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.6584 (OUTLIER) cc_final: 0.5957 (mp) REVERT: A 287 PHE cc_start: 0.9026 (t80) cc_final: 0.8795 (t80) REVERT: A 289 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7045 (t0) REVERT: A 409 ASN cc_start: 0.8371 (t0) cc_final: 0.8134 (m110) REVERT: B 75 ILE cc_start: 0.6818 (OUTLIER) cc_final: 0.6306 (mp) REVERT: B 287 PHE cc_start: 0.9059 (t80) cc_final: 0.8809 (t80) REVERT: B 289 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.6978 (t0) REVERT: B 320 LEU cc_start: 0.8564 (mt) cc_final: 0.8313 (mt) outliers start: 24 outliers final: 10 residues processed: 156 average time/residue: 0.1313 time to fit residues: 27.4831 Evaluate side-chains 145 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 415 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 7 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS A 410 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.215494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.156034 restraints weight = 5165.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.159922 restraints weight = 3874.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.162798 restraints weight = 3229.298| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 4869 Z= 0.172 Angle : 0.626 5.780 6614 Z= 0.334 Chirality : 0.044 0.133 799 Planarity : 0.004 0.031 825 Dihedral : 4.776 25.144 662 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.25 % Allowed : 16.57 % Favored : 78.18 % 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: 1.40 (0.36), residues: 614 helix: 1.87 (0.24), residues: 404 sheet: -1.65 (0.79), residues: 40 loop : -0.66 (0.60), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 74 HIS 0.032 0.003 HIS B 148 PHE 0.016 0.001 PHE A 421 TYR 0.014 0.002 TYR A 396 ARG 0.003 0.000 ARG A 59 Details of bonding type rmsd hydrogen bonds : bond 0.05219 ( 351) hydrogen bonds : angle 4.83902 ( 1053) metal coordination : bond 0.03148 ( 14) SS BOND : bond 0.00437 ( 5) SS BOND : angle 1.16849 ( 10) covalent geometry : bond 0.00359 ( 4850) covalent geometry : angle 0.62532 ( 6604) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7610 (mmp) cc_final: 0.7041 (mpp) REVERT: A 75 ILE cc_start: 0.6603 (OUTLIER) cc_final: 0.6022 (mp) REVERT: A 115 VAL cc_start: 0.9026 (m) cc_final: 0.8805 (p) REVERT: A 410 HIS cc_start: 0.8186 (m-70) cc_final: 0.7902 (m170) REVERT: B 75 ILE cc_start: 0.6846 (OUTLIER) cc_final: 0.6320 (mp) REVERT: B 115 VAL cc_start: 0.9036 (m) cc_final: 0.8822 (p) REVERT: B 404 LYS cc_start: 0.8727 (tppt) cc_final: 0.8435 (mmmm) REVERT: B 409 ASN cc_start: 0.8478 (m-40) cc_final: 0.8227 (m-40) outliers start: 26 outliers final: 18 residues processed: 149 average time/residue: 0.1279 time to fit residues: 25.2246 Evaluate side-chains 144 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 26 optimal weight: 0.8980 chunk 18 optimal weight: 40.0000 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.215401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.155879 restraints weight = 5061.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.159708 restraints weight = 3820.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.162359 restraints weight = 3222.617| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4869 Z= 0.162 Angle : 0.631 7.065 6614 Z= 0.334 Chirality : 0.043 0.139 799 Planarity : 0.004 0.029 825 Dihedral : 4.478 21.942 658 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.45 % Allowed : 18.38 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.48 (0.36), residues: 614 helix: 1.91 (0.24), residues: 406 sheet: -1.25 (0.85), residues: 38 loop : -0.75 (0.58), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 74 HIS 0.032 0.003 HIS A 148 PHE 0.007 0.001 PHE A 421 TYR 0.019 0.001 TYR A 396 ARG 0.003 0.000 ARG A 59 Details of bonding type rmsd hydrogen bonds : bond 0.04895 ( 351) hydrogen bonds : angle 4.71357 ( 1053) metal coordination : bond 0.02626 ( 14) SS BOND : bond 0.00326 ( 5) SS BOND : angle 3.08683 ( 10) covalent geometry : bond 0.00348 ( 4850) covalent geometry : angle 0.62030 ( 6604) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.6571 (OUTLIER) cc_final: 0.6007 (mp) REVERT: A 115 VAL cc_start: 0.9007 (m) cc_final: 0.8793 (p) REVERT: A 420 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.8018 (tt0) REVERT: B 42 PHE cc_start: 0.7875 (m-80) cc_final: 0.7506 (m-80) REVERT: B 75 ILE cc_start: 0.6770 (OUTLIER) cc_final: 0.6219 (mp) REVERT: B 115 VAL cc_start: 0.9010 (m) cc_final: 0.8801 (p) REVERT: B 368 GLU cc_start: 0.8386 (pt0) cc_final: 0.7945 (pm20) REVERT: B 404 LYS cc_start: 0.8662 (tppt) cc_final: 0.8372 (mmmm) REVERT: B 409 ASN cc_start: 0.8470 (m-40) cc_final: 0.8097 (m-40) outliers start: 27 outliers final: 18 residues processed: 137 average time/residue: 0.1359 time to fit residues: 24.8258 Evaluate side-chains 144 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 371 GLU Chi-restraints excluded: chain B residue 415 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS A 410 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.213579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.155233 restraints weight = 5433.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.158854 restraints weight = 4101.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.160519 restraints weight = 3453.207| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 4869 Z= 0.180 Angle : 0.611 6.144 6614 Z= 0.329 Chirality : 0.044 0.130 799 Planarity : 0.004 0.026 825 Dihedral : 4.422 23.082 658 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 7.47 % Allowed : 19.39 % Favored : 73.13 % 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: 1.50 (0.35), residues: 614 helix: 1.93 (0.24), residues: 406 sheet: -1.12 (0.88), residues: 38 loop : -0.75 (0.57), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 375 HIS 0.028 0.003 HIS A 148 PHE 0.009 0.001 PHE B 287 TYR 0.019 0.002 TYR B 396 ARG 0.003 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 351) hydrogen bonds : angle 4.60401 ( 1053) metal coordination : bond 0.03689 ( 14) SS BOND : bond 0.00366 ( 5) SS BOND : angle 2.08595 ( 10) covalent geometry : bond 0.00386 ( 4850) covalent geometry : angle 0.60566 ( 6604) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.6822 (OUTLIER) cc_final: 0.6305 (mp) REVERT: A 115 VAL cc_start: 0.9034 (m) cc_final: 0.8825 (p) REVERT: A 289 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.6817 (t0) REVERT: A 312 TRP cc_start: 0.8699 (p-90) cc_final: 0.8148 (p-90) REVERT: A 420 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7596 (tt0) REVERT: B 42 PHE cc_start: 0.7866 (m-80) cc_final: 0.7517 (m-80) REVERT: B 75 ILE cc_start: 0.7019 (OUTLIER) cc_final: 0.6552 (mp) REVERT: B 289 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.6801 (t0) REVERT: B 312 TRP cc_start: 0.8669 (p-90) cc_final: 0.8121 (p-90) REVERT: B 368 GLU cc_start: 0.8214 (pt0) cc_final: 0.7917 (pm20) REVERT: B 404 LYS cc_start: 0.8566 (tppt) cc_final: 0.8292 (mmmm) outliers start: 37 outliers final: 21 residues processed: 151 average time/residue: 0.1402 time to fit residues: 27.7647 Evaluate side-chains 153 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 51 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 37 optimal weight: 0.0670 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.214145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.156583 restraints weight = 5342.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.160559 restraints weight = 3948.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.163306 restraints weight = 3284.403| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 4869 Z= 0.147 Angle : 0.578 5.870 6614 Z= 0.312 Chirality : 0.043 0.136 799 Planarity : 0.004 0.034 825 Dihedral : 4.393 23.690 658 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.66 % Allowed : 22.42 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.65 (0.35), residues: 614 helix: 2.05 (0.25), residues: 406 sheet: -0.95 (0.90), residues: 38 loop : -0.77 (0.56), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 74 HIS 0.040 0.003 HIS A 148 PHE 0.021 0.001 PHE A 42 TYR 0.015 0.002 TYR A 396 ARG 0.002 0.000 ARG A 59 Details of bonding type rmsd hydrogen bonds : bond 0.04528 ( 351) hydrogen bonds : angle 4.56110 ( 1053) metal coordination : bond 0.02716 ( 14) SS BOND : bond 0.00249 ( 5) SS BOND : angle 0.54022 ( 10) covalent geometry : bond 0.00308 ( 4850) covalent geometry : angle 0.57794 ( 6604) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7844 (m-80) cc_final: 0.7623 (m-80) REVERT: A 75 ILE cc_start: 0.6583 (OUTLIER) cc_final: 0.6029 (mp) REVERT: A 115 VAL cc_start: 0.8983 (m) cc_final: 0.8783 (p) REVERT: A 289 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6800 (t70) REVERT: A 312 TRP cc_start: 0.8620 (p-90) cc_final: 0.8246 (p-90) REVERT: A 420 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7628 (tt0) REVERT: B 42 PHE cc_start: 0.7859 (m-80) cc_final: 0.7521 (m-80) REVERT: B 75 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6294 (mp) REVERT: B 289 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.6778 (t70) REVERT: B 312 TRP cc_start: 0.8656 (p-90) cc_final: 0.8006 (p-90) REVERT: B 404 LYS cc_start: 0.8606 (tppt) cc_final: 0.8292 (mmmm) outliers start: 28 outliers final: 19 residues processed: 146 average time/residue: 0.1266 time to fit residues: 24.5685 Evaluate side-chains 153 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 0.0980 chunk 48 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.215430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.155559 restraints weight = 5351.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.159879 restraints weight = 3897.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.162212 restraints weight = 3219.719| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 4869 Z= 0.163 Angle : 0.594 7.133 6614 Z= 0.318 Chirality : 0.043 0.137 799 Planarity : 0.004 0.032 825 Dihedral : 4.426 27.849 658 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 7.07 % Allowed : 22.42 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.72 (0.35), residues: 614 helix: 2.09 (0.24), residues: 406 sheet: -0.98 (0.92), residues: 38 loop : -0.66 (0.56), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 375 HIS 0.038 0.003 HIS A 148 PHE 0.013 0.001 PHE A 42 TYR 0.024 0.002 TYR A 396 ARG 0.002 0.000 ARG B 76 Details of bonding type rmsd hydrogen bonds : bond 0.04553 ( 351) hydrogen bonds : angle 4.56721 ( 1053) metal coordination : bond 0.03292 ( 14) SS BOND : bond 0.00323 ( 5) SS BOND : angle 0.79383 ( 10) covalent geometry : bond 0.00352 ( 4850) covalent geometry : angle 0.59358 ( 6604) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.7934 (m-80) cc_final: 0.7732 (m-80) REVERT: A 75 ILE cc_start: 0.6736 (OUTLIER) cc_final: 0.6198 (mp) REVERT: A 115 VAL cc_start: 0.9005 (m) cc_final: 0.8805 (p) REVERT: A 289 ASP cc_start: 0.7073 (OUTLIER) cc_final: 0.6757 (t70) REVERT: A 312 TRP cc_start: 0.8673 (p-90) cc_final: 0.8337 (p-90) REVERT: A 420 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7509 (tt0) REVERT: B 42 PHE cc_start: 0.7874 (m-80) cc_final: 0.7557 (m-80) REVERT: B 75 ILE cc_start: 0.6766 (OUTLIER) cc_final: 0.6240 (mp) REVERT: B 312 TRP cc_start: 0.8703 (p-90) cc_final: 0.8071 (p-90) REVERT: B 404 LYS cc_start: 0.8622 (tppt) cc_final: 0.8335 (mmmm) outliers start: 35 outliers final: 23 residues processed: 147 average time/residue: 0.1291 time to fit residues: 25.1837 Evaluate side-chains 152 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.213649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.156926 restraints weight = 5356.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.161020 restraints weight = 3986.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.163282 restraints weight = 3328.292| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4869 Z= 0.161 Angle : 0.609 7.535 6614 Z= 0.326 Chirality : 0.043 0.163 799 Planarity : 0.004 0.025 825 Dihedral : 4.515 34.091 658 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 6.26 % Allowed : 23.23 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: 1.46 (0.35), residues: 614 helix: 1.92 (0.25), residues: 418 sheet: -1.20 (0.88), residues: 42 loop : -1.06 (0.55), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 375 HIS 0.016 0.002 HIS A 148 PHE 0.012 0.001 PHE A 42 TYR 0.041 0.002 TYR A 396 ARG 0.003 0.000 ARG B 76 Details of bonding type rmsd hydrogen bonds : bond 0.04485 ( 351) hydrogen bonds : angle 4.56644 ( 1053) metal coordination : bond 0.03034 ( 14) SS BOND : bond 0.00211 ( 5) SS BOND : angle 0.89082 ( 10) covalent geometry : bond 0.00349 ( 4850) covalent geometry : angle 0.60836 ( 6604) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.6697 (OUTLIER) cc_final: 0.6160 (mp) REVERT: A 289 ASP cc_start: 0.6934 (OUTLIER) cc_final: 0.6695 (t70) REVERT: A 312 TRP cc_start: 0.8624 (p-90) cc_final: 0.8273 (p-90) REVERT: A 324 MET cc_start: 0.7900 (tmm) cc_final: 0.7628 (ttp) REVERT: A 420 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: B 42 PHE cc_start: 0.7841 (m-80) cc_final: 0.7554 (m-80) REVERT: B 62 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7297 (mmp80) REVERT: B 75 ILE cc_start: 0.6755 (OUTLIER) cc_final: 0.6242 (mp) REVERT: B 312 TRP cc_start: 0.8620 (p-90) cc_final: 0.8007 (p-90) REVERT: B 404 LYS cc_start: 0.8604 (tppt) cc_final: 0.8317 (mmmm) outliers start: 31 outliers final: 21 residues processed: 139 average time/residue: 0.1432 time to fit residues: 25.9066 Evaluate side-chains 150 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 50 optimal weight: 0.0370 chunk 17 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 55 optimal weight: 0.0870 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.216271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.160734 restraints weight = 5435.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.164859 restraints weight = 4006.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.167675 restraints weight = 3313.600| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4869 Z= 0.144 Angle : 0.606 8.302 6614 Z= 0.316 Chirality : 0.042 0.149 799 Planarity : 0.003 0.025 825 Dihedral : 4.352 29.377 658 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.43 % Allowed : 25.66 % Favored : 70.91 % 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: 1.62 (0.35), residues: 614 helix: 2.05 (0.25), residues: 418 sheet: -0.95 (0.94), residues: 38 loop : -1.08 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 312 HIS 0.016 0.002 HIS A 148 PHE 0.009 0.001 PHE A 42 TYR 0.033 0.002 TYR A 396 ARG 0.003 0.000 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 351) hydrogen bonds : angle 4.52924 ( 1053) metal coordination : bond 0.02577 ( 14) SS BOND : bond 0.00295 ( 5) SS BOND : angle 0.71903 ( 10) covalent geometry : bond 0.00307 ( 4850) covalent geometry : angle 0.60576 ( 6604) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.6951 (OUTLIER) cc_final: 0.6289 (mpp) REVERT: A 75 ILE cc_start: 0.6473 (OUTLIER) cc_final: 0.5919 (mp) REVERT: A 312 TRP cc_start: 0.8633 (p-90) cc_final: 0.8363 (p-90) REVERT: A 368 GLU cc_start: 0.7490 (tt0) cc_final: 0.7064 (pt0) REVERT: A 420 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7598 (tt0) REVERT: B 75 ILE cc_start: 0.6560 (OUTLIER) cc_final: 0.6011 (mp) REVERT: B 312 TRP cc_start: 0.8682 (p-90) cc_final: 0.8101 (p-90) REVERT: B 404 LYS cc_start: 0.8539 (tppt) cc_final: 0.8242 (mmmm) outliers start: 17 outliers final: 11 residues processed: 132 average time/residue: 0.1473 time to fit residues: 25.3548 Evaluate side-chains 134 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 30 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 18 optimal weight: 40.0000 chunk 49 optimal weight: 50.0000 chunk 8 optimal weight: 0.3980 chunk 59 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.213897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.156243 restraints weight = 5225.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.160209 restraints weight = 3855.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.162788 restraints weight = 3199.761| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4869 Z= 0.174 Angle : 0.624 8.450 6614 Z= 0.332 Chirality : 0.044 0.149 799 Planarity : 0.004 0.025 825 Dihedral : 4.348 28.384 658 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.44 % Allowed : 25.05 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.33 (0.34), residues: 614 helix: 1.84 (0.24), residues: 418 sheet: -1.22 (0.88), residues: 42 loop : -1.15 (0.53), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 74 HIS 0.013 0.002 HIS A 148 PHE 0.008 0.001 PHE B 94 TYR 0.017 0.001 TYR A 396 ARG 0.006 0.001 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 351) hydrogen bonds : angle 4.54637 ( 1053) metal coordination : bond 0.02654 ( 14) SS BOND : bond 0.00250 ( 5) SS BOND : angle 0.67331 ( 10) covalent geometry : bond 0.00398 ( 4850) covalent geometry : angle 0.62435 ( 6604) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.6749 (OUTLIER) cc_final: 0.6250 (mp) REVERT: A 97 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7701 (tp) REVERT: A 367 GLU cc_start: 0.6490 (pm20) cc_final: 0.6188 (pm20) REVERT: A 368 GLU cc_start: 0.7479 (tt0) cc_final: 0.7077 (pt0) REVERT: A 420 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: B 42 PHE cc_start: 0.7674 (m-80) cc_final: 0.7372 (m-80) REVERT: B 75 ILE cc_start: 0.6845 (OUTLIER) cc_final: 0.6365 (mp) REVERT: B 312 TRP cc_start: 0.8848 (p-90) cc_final: 0.8556 (p-90) REVERT: B 404 LYS cc_start: 0.8559 (tppt) cc_final: 0.8284 (mmmm) outliers start: 22 outliers final: 17 residues processed: 135 average time/residue: 0.1458 time to fit residues: 25.6566 Evaluate side-chains 143 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.214809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.167876 restraints weight = 5348.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.168905 restraints weight = 5179.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.171151 restraints weight = 4937.972| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4869 Z= 0.161 Angle : 0.634 8.721 6614 Z= 0.334 Chirality : 0.043 0.150 799 Planarity : 0.004 0.025 825 Dihedral : 4.339 27.317 658 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.24 % Allowed : 26.06 % Favored : 69.70 % 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: 1.33 (0.34), residues: 614 helix: 1.84 (0.24), residues: 418 sheet: -1.15 (0.88), residues: 42 loop : -1.20 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 74 HIS 0.009 0.002 HIS A 148 PHE 0.007 0.001 PHE B 94 TYR 0.009 0.001 TYR A 396 ARG 0.006 0.001 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.04471 ( 351) hydrogen bonds : angle 4.53246 ( 1053) metal coordination : bond 0.02137 ( 14) SS BOND : bond 0.00224 ( 5) SS BOND : angle 0.62524 ( 10) covalent geometry : bond 0.00368 ( 4850) covalent geometry : angle 0.63361 ( 6604) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1728.80 seconds wall clock time: 30 minutes 54.29 seconds (1854.29 seconds total)