Starting phenix.real_space_refine on Wed Sep 17 05:03:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zsz_60435/09_2025/8zsz_60435.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zsz_60435/09_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_60435/09_2025/8zsz_60435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zsz_60435/09_2025/8zsz_60435.map" model { file = "/net/cci-nas-00/data/ceres_data/8zsz_60435/09_2025/8zsz_60435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zsz_60435/09_2025/8zsz_60435.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'GLU:plan': 6, 'ASP:plan': 3, 'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 2} 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: {'GLU:plan': 7, 'ASP:plan': 2, 'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1} 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: 1.41, per 1000 atoms: 0.30 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: 0.46 Conformation dependent library (CDL) restraints added in 199.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.18 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: 0.77 Time building geometry restraints manager: 0.60 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 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 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.390 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.500 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG B 62 TYR 0.009 0.001 TYR B 396 PHE 0.027 0.002 PHE B 72 TRP 0.062 0.005 TRP A 375 HIS 0.053 0.007 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.01718 ( 4850) covalent geometry : angle 1.80542 ( 6604) SS BOND : bond 0.01058 ( 5) SS BOND : angle 1.89073 ( 10) hydrogen bonds : bond 0.17204 ( 351) hydrogen bonds : angle 7.70688 ( 1053) metal coordination : bond 0.39086 ( 14) *********************** 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 : 0.183 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: 0.0643 time to fit residues: 14.3261 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 : 0.220 ------------------------------------------------------------------------------- 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 54 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 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 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 265 ASN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.215194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.156947 restraints weight = 5337.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.161259 restraints weight = 3933.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.164132 restraints weight = 3260.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.165620 restraints weight = 2908.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.167168 restraints weight = 2710.427| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 4869 Z= 0.224 Angle : 0.716 8.829 6614 Z= 0.384 Chirality : 0.046 0.181 799 Planarity : 0.005 0.048 825 Dihedral : 5.828 56.619 672 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.12 % Favored : 97.72 % Rotamer: Outliers : 5.05 % Allowed : 13.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.35), residues: 614 helix: 1.61 (0.24), residues: 404 sheet: -2.18 (0.66), residues: 44 loop : -0.85 (0.58), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 76 TYR 0.013 0.002 TYR A 396 PHE 0.030 0.001 PHE A 421 TRP 0.010 0.001 TRP B 375 HIS 0.043 0.004 HIS A 148 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 4850) covalent geometry : angle 0.71281 ( 6604) SS BOND : bond 0.00606 ( 5) SS BOND : angle 1.84157 ( 10) hydrogen bonds : bond 0.06027 ( 351) hydrogen bonds : angle 5.16907 ( 1053) metal coordination : bond 0.05815 ( 14) *********************** 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: 25 poor density : 141 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.6522 (OUTLIER) cc_final: 0.5894 (mp) REVERT: A 287 PHE cc_start: 0.8975 (t80) cc_final: 0.8761 (t80) REVERT: A 289 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7042 (t0) REVERT: A 409 ASN cc_start: 0.8315 (t0) cc_final: 0.8112 (m-40) REVERT: A 420 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8307 (mt-10) REVERT: B 75 ILE cc_start: 0.6715 (OUTLIER) cc_final: 0.6193 (mp) REVERT: B 287 PHE cc_start: 0.9021 (t80) cc_final: 0.8787 (t80) REVERT: B 289 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.6970 (t0) REVERT: B 320 LEU cc_start: 0.8525 (mt) cc_final: 0.8282 (mt) outliers start: 25 outliers final: 10 residues processed: 156 average time/residue: 0.0557 time to fit residues: 11.9065 Evaluate side-chains 147 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 110 MET 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 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 36 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 148 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 = 0.216068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.154451 restraints weight = 5068.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.158582 restraints weight = 3711.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.160972 restraints weight = 3069.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.162835 restraints weight = 2745.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.164360 restraints weight = 2545.652| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 4869 Z= 0.186 Angle : 0.630 5.961 6614 Z= 0.337 Chirality : 0.044 0.131 799 Planarity : 0.004 0.038 825 Dihedral : 4.774 24.508 662 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 5.25 % Allowed : 16.97 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.36), residues: 614 helix: 1.81 (0.24), residues: 406 sheet: -1.71 (0.79), residues: 40 loop : -0.67 (0.60), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 59 TYR 0.013 0.002 TYR A 396 PHE 0.019 0.001 PHE A 421 TRP 0.009 0.001 TRP B 74 HIS 0.039 0.003 HIS B 148 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 4850) covalent geometry : angle 0.62933 ( 6604) SS BOND : bond 0.00439 ( 5) SS BOND : angle 1.15250 ( 10) hydrogen bonds : bond 0.05277 ( 351) hydrogen bonds : angle 4.84136 ( 1053) metal coordination : bond 0.04505 ( 14) *********************** 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 166 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.6629 (OUTLIER) cc_final: 0.6060 (mp) REVERT: A 115 VAL cc_start: 0.9022 (m) cc_final: 0.8804 (p) REVERT: A 124 LEU cc_start: 0.7859 (tt) cc_final: 0.7643 (tt) REVERT: A 410 HIS cc_start: 0.8172 (m-70) cc_final: 0.7894 (m170) REVERT: B 75 ILE cc_start: 0.6904 (OUTLIER) cc_final: 0.6390 (mp) REVERT: B 115 VAL cc_start: 0.9040 (m) cc_final: 0.8831 (p) REVERT: B 124 LEU cc_start: 0.7869 (tt) cc_final: 0.7648 (tt) REVERT: B 404 LYS cc_start: 0.8703 (tppt) cc_final: 0.8424 (mmmm) REVERT: B 409 ASN cc_start: 0.8477 (m-40) cc_final: 0.8220 (m-40) outliers start: 26 outliers final: 18 residues processed: 151 average time/residue: 0.0625 time to fit residues: 12.6288 Evaluate side-chains 142 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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 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 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 49 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 148 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 = 0.4411 r_free = 0.4411 target = 0.214737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.155359 restraints weight = 5086.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.159192 restraints weight = 3910.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.161847 restraints weight = 3293.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.162912 restraints weight = 2960.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.164526 restraints weight = 2787.959| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 4869 Z= 0.174 Angle : 0.630 6.851 6614 Z= 0.334 Chirality : 0.044 0.158 799 Planarity : 0.004 0.033 825 Dihedral : 4.446 21.300 658 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 6.06 % Allowed : 17.58 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.35), residues: 614 helix: 1.92 (0.25), residues: 406 sheet: -1.30 (0.85), residues: 38 loop : -0.80 (0.57), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 59 TYR 0.023 0.001 TYR A 396 PHE 0.009 0.001 PHE A 421 TRP 0.007 0.001 TRP B 74 HIS 0.038 0.003 HIS B 148 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 4850) covalent geometry : angle 0.61961 ( 6604) SS BOND : bond 0.00711 ( 5) SS BOND : angle 3.00226 ( 10) hydrogen bonds : bond 0.04955 ( 351) hydrogen bonds : angle 4.73665 ( 1053) metal coordination : bond 0.03752 ( 14) *********************** 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 158 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7826 (tt) REVERT: A 75 ILE cc_start: 0.6646 (OUTLIER) cc_final: 0.6073 (mp) REVERT: A 115 VAL cc_start: 0.9007 (m) cc_final: 0.8792 (p) REVERT: A 289 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.6910 (t0) REVERT: B 75 ILE cc_start: 0.6803 (OUTLIER) cc_final: 0.6270 (mp) REVERT: B 115 VAL cc_start: 0.9009 (m) cc_final: 0.8793 (p) REVERT: B 368 GLU cc_start: 0.8406 (pt0) cc_final: 0.7944 (pm20) REVERT: B 404 LYS cc_start: 0.8632 (tppt) cc_final: 0.8327 (mmmm) REVERT: B 409 ASN cc_start: 0.8462 (m-40) cc_final: 0.8081 (m-40) outliers start: 30 outliers final: 18 residues processed: 142 average time/residue: 0.0618 time to fit residues: 11.7274 Evaluate side-chains 141 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU 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 289 ASP 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 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 245 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 385 THR 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 27 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 155 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS B 413 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.214876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.157125 restraints weight = 5304.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.160864 restraints weight = 3976.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.163507 restraints weight = 3356.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.164895 restraints weight = 3006.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.166188 restraints weight = 2810.035| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 4869 Z= 0.166 Angle : 0.610 7.978 6614 Z= 0.323 Chirality : 0.044 0.233 799 Planarity : 0.004 0.032 825 Dihedral : 4.404 21.270 658 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 7.47 % Allowed : 18.79 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.35), residues: 614 helix: 2.01 (0.25), residues: 406 sheet: -1.11 (0.87), residues: 38 loop : -0.87 (0.55), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 59 TYR 0.022 0.002 TYR A 396 PHE 0.011 0.001 PHE B 42 TRP 0.005 0.001 TRP B 74 HIS 0.039 0.003 HIS B 148 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 4850) covalent geometry : angle 0.60566 ( 6604) SS BOND : bond 0.00265 ( 5) SS BOND : angle 2.04909 ( 10) hydrogen bonds : bond 0.04742 ( 351) hydrogen bonds : angle 4.64924 ( 1053) metal coordination : bond 0.03413 ( 14) *********************** 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 166 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.6683 (OUTLIER) cc_final: 0.6130 (mp) REVERT: A 115 VAL cc_start: 0.8987 (m) cc_final: 0.8783 (p) REVERT: A 289 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.6788 (t0) REVERT: A 312 TRP cc_start: 0.8604 (p-90) cc_final: 0.8052 (p-90) REVERT: A 420 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7643 (tt0) REVERT: B 75 ILE cc_start: 0.6912 (OUTLIER) cc_final: 0.6412 (mp) REVERT: B 289 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.6780 (t0) REVERT: B 312 TRP cc_start: 0.8573 (p-90) cc_final: 0.8036 (p-90) REVERT: B 368 GLU cc_start: 0.8192 (pt0) cc_final: 0.7991 (pm20) REVERT: B 404 LYS cc_start: 0.8620 (tppt) cc_final: 0.8357 (mmmm) outliers start: 37 outliers final: 20 residues processed: 147 average time/residue: 0.0661 time to fit residues: 12.8533 Evaluate side-chains 147 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 36 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 28 optimal weight: 0.0270 chunk 4 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 408 HIS A 413 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.215643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.157898 restraints weight = 5399.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.162288 restraints weight = 4017.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.164122 restraints weight = 3336.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.166495 restraints weight = 3016.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.167087 restraints weight = 2805.249| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.4037 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= 0.153 Angle : 0.580 6.829 6614 Z= 0.311 Chirality : 0.043 0.148 799 Planarity : 0.004 0.032 825 Dihedral : 4.405 23.730 658 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.45 % Allowed : 23.23 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.35), residues: 614 helix: 2.16 (0.25), residues: 406 sheet: -0.90 (0.93), residues: 38 loop : -0.93 (0.53), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 59 TYR 0.015 0.001 TYR B 396 PHE 0.010 0.001 PHE B 42 TRP 0.004 0.001 TRP A 312 HIS 0.038 0.003 HIS A 148 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 4850) covalent geometry : angle 0.58007 ( 6604) SS BOND : bond 0.00239 ( 5) SS BOND : angle 0.55670 ( 10) hydrogen bonds : bond 0.04455 ( 351) hydrogen bonds : angle 4.58392 ( 1053) metal coordination : bond 0.03680 ( 14) *********************** 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 158 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 VAL cc_start: 0.8986 (m) cc_final: 0.8784 (p) REVERT: A 289 ASP cc_start: 0.7133 (OUTLIER) cc_final: 0.6795 (t70) REVERT: A 312 TRP cc_start: 0.8548 (p-90) cc_final: 0.8188 (p-90) REVERT: A 420 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7482 (tt0) REVERT: B 42 PHE cc_start: 0.7734 (m-80) cc_final: 0.7411 (m-80) REVERT: B 75 ILE cc_start: 0.6742 (OUTLIER) cc_final: 0.6213 (mp) REVERT: B 289 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6746 (t70) REVERT: B 312 TRP cc_start: 0.8588 (p-90) cc_final: 0.7958 (p-90) REVERT: B 404 LYS cc_start: 0.8652 (tppt) cc_final: 0.8374 (mmmm) outliers start: 27 outliers final: 20 residues processed: 144 average time/residue: 0.0642 time to fit residues: 12.2877 Evaluate side-chains 151 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 110 MET 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 385 THR Chi-restraints excluded: chain A residue 408 HIS 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 51 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 47 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 408 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.212917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.160336 restraints weight = 5311.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.161158 restraints weight = 5337.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.163133 restraints weight = 4173.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.163348 restraints weight = 3347.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.163585 restraints weight = 3200.246| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.302 4869 Z= 0.212 Angle : 0.575 6.629 6614 Z= 0.309 Chirality : 0.042 0.140 799 Planarity : 0.004 0.030 825 Dihedral : 4.337 24.753 658 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 6.26 % Allowed : 22.02 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.35), residues: 614 helix: 2.19 (0.25), residues: 406 sheet: -0.99 (0.92), residues: 38 loop : -0.92 (0.53), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 76 TYR 0.020 0.002 TYR B 396 PHE 0.008 0.001 PHE B 42 TRP 0.004 0.001 TRP B 74 HIS 0.036 0.003 HIS A 148 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 4850) covalent geometry : angle 0.57455 ( 6604) SS BOND : bond 0.00298 ( 5) SS BOND : angle 0.73391 ( 10) hydrogen bonds : bond 0.04442 ( 351) hydrogen bonds : angle 4.58525 ( 1053) metal coordination : bond 0.08621 ( 14) *********************** 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 162 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8482 (p-90) cc_final: 0.8154 (p-90) REVERT: A 368 GLU cc_start: 0.7545 (pt0) cc_final: 0.7322 (pt0) REVERT: A 420 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7543 (tt0) REVERT: B 75 ILE cc_start: 0.6782 (OUTLIER) cc_final: 0.6255 (mp) REVERT: B 289 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6656 (t70) REVERT: B 312 TRP cc_start: 0.8562 (p-90) cc_final: 0.7973 (p-90) REVERT: B 404 LYS cc_start: 0.8630 (tppt) cc_final: 0.8377 (mmmm) outliers start: 31 outliers final: 20 residues processed: 146 average time/residue: 0.0589 time to fit residues: 11.3533 Evaluate side-chains 150 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET 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 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 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 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 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 35 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 44 optimal weight: 0.0040 chunk 12 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 39 optimal weight: 0.2980 chunk 42 optimal weight: 2.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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 = 0.4432 r_free = 0.4432 target = 0.216216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.159745 restraints weight = 5476.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.164047 restraints weight = 4021.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.166280 restraints weight = 3330.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.168547 restraints weight = 2977.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.169267 restraints weight = 2761.399| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.4377 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= 0.145 Angle : 0.582 7.815 6614 Z= 0.311 Chirality : 0.042 0.140 799 Planarity : 0.004 0.024 825 Dihedral : 4.380 32.750 658 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 5.25 % Allowed : 23.84 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.35), residues: 614 helix: 2.26 (0.25), residues: 406 sheet: -1.18 (0.92), residues: 38 loop : -0.93 (0.52), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.048 0.002 TYR A 396 PHE 0.009 0.001 PHE B 42 TRP 0.005 0.001 TRP B 375 HIS 0.016 0.002 HIS A 148 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4850) covalent geometry : angle 0.58126 ( 6604) SS BOND : bond 0.00325 ( 5) SS BOND : angle 0.74145 ( 10) hydrogen bonds : bond 0.04299 ( 351) hydrogen bonds : angle 4.57012 ( 1053) metal coordination : bond 0.02512 ( 14) *********************** 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 152 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.7461 (tt0) cc_final: 0.7230 (tt0) REVERT: A 75 ILE cc_start: 0.6454 (OUTLIER) cc_final: 0.5888 (mp) REVERT: A 106 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8073 (mt-10) REVERT: A 312 TRP cc_start: 0.8553 (p-90) cc_final: 0.7955 (p-90) REVERT: A 420 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: B 42 PHE cc_start: 0.7709 (m-80) cc_final: 0.7368 (m-80) REVERT: B 75 ILE cc_start: 0.6662 (OUTLIER) cc_final: 0.6133 (mp) REVERT: B 97 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7587 (tp) REVERT: B 289 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6756 (t70) REVERT: B 312 TRP cc_start: 0.8635 (p-90) cc_final: 0.8048 (p-90) REVERT: B 404 LYS cc_start: 0.8654 (tppt) cc_final: 0.8392 (mmmm) outliers start: 26 outliers final: 15 residues processed: 139 average time/residue: 0.0610 time to fit residues: 11.3049 Evaluate side-chains 141 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 110 MET 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 67 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 97 LEU 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 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 34 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 43 optimal weight: 0.4980 chunk 4 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 50 optimal weight: 0.0870 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.215762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.159303 restraints weight = 5265.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.163812 restraints weight = 3726.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.166529 restraints weight = 3019.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.168705 restraints weight = 2652.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.169509 restraints weight = 2444.037| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.468 4869 Z= 0.265 Angle : 0.587 8.351 6614 Z= 0.307 Chirality : 0.042 0.148 799 Planarity : 0.003 0.024 825 Dihedral : 4.258 27.578 658 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.44 % Allowed : 24.24 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.35), residues: 614 helix: 2.28 (0.24), residues: 406 sheet: -1.48 (0.92), residues: 38 loop : -0.94 (0.52), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 62 TYR 0.030 0.002 TYR A 396 PHE 0.009 0.001 PHE A 421 TRP 0.011 0.001 TRP B 375 HIS 0.015 0.002 HIS A 148 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4850) covalent geometry : angle 0.58690 ( 6604) SS BOND : bond 0.00261 ( 5) SS BOND : angle 0.80595 ( 10) hydrogen bonds : bond 0.04161 ( 351) hydrogen bonds : angle 4.45154 ( 1053) metal coordination : bond 0.12758 ( 14) *********************** 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 149 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.7421 (tt0) cc_final: 0.7031 (tt0) REVERT: A 75 ILE cc_start: 0.6430 (OUTLIER) cc_final: 0.5873 (mp) REVERT: A 106 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8078 (mt-10) REVERT: A 312 TRP cc_start: 0.8620 (p-90) cc_final: 0.8071 (p-90) REVERT: A 420 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7496 (tt0) REVERT: B 75 ILE cc_start: 0.6533 (OUTLIER) cc_final: 0.5980 (mp) REVERT: B 97 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7646 (tp) REVERT: B 312 TRP cc_start: 0.8623 (p-90) cc_final: 0.8067 (p-90) REVERT: B 404 LYS cc_start: 0.8603 (tppt) cc_final: 0.8364 (mmmm) outliers start: 22 outliers final: 15 residues processed: 138 average time/residue: 0.0659 time to fit residues: 11.8431 Evaluate side-chains 139 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 148 HIS 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 67 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 97 LEU 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 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 56 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 49 optimal weight: 50.0000 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 ASN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.212356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.155349 restraints weight = 5233.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.159581 restraints weight = 3764.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.162423 restraints weight = 3082.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.163551 restraints weight = 2729.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.165166 restraints weight = 2556.766| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.954 4869 Z= 0.487 Angle : 0.630 8.836 6614 Z= 0.334 Chirality : 0.044 0.152 799 Planarity : 0.004 0.024 825 Dihedral : 4.283 26.780 658 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.04 % Allowed : 25.25 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.35), residues: 614 helix: 2.11 (0.24), residues: 406 sheet: -1.90 (0.85), residues: 42 loop : -0.94 (0.53), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 62 TYR 0.025 0.002 TYR A 396 PHE 0.017 0.001 PHE A 42 TRP 0.012 0.001 TRP B 375 HIS 0.016 0.002 HIS A 148 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 4850) covalent geometry : angle 0.62954 ( 6604) SS BOND : bond 0.00305 ( 5) SS BOND : angle 0.86865 ( 10) hydrogen bonds : bond 0.04511 ( 351) hydrogen bonds : angle 4.48049 ( 1053) metal coordination : bond 0.25616 ( 14) ********************** 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 145 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6380 (mpp) REVERT: A 68 GLN cc_start: 0.7504 (tt0) cc_final: 0.7134 (tt0) REVERT: A 75 ILE cc_start: 0.6746 (OUTLIER) cc_final: 0.6239 (mp) REVERT: A 106 GLU cc_start: 0.8222 (mt-10) cc_final: 0.8019 (mt-10) REVERT: A 312 TRP cc_start: 0.8649 (p-90) cc_final: 0.8389 (p-90) REVERT: A 324 MET cc_start: 0.7846 (tmm) cc_final: 0.7644 (ttp) REVERT: A 420 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: B 42 PHE cc_start: 0.7773 (m-80) cc_final: 0.7467 (m-80) REVERT: B 75 ILE cc_start: 0.6839 (OUTLIER) cc_final: 0.6341 (mp) REVERT: B 312 TRP cc_start: 0.8725 (p-90) cc_final: 0.8155 (p-90) REVERT: B 324 MET cc_start: 0.7883 (tmm) cc_final: 0.7673 (ttp) outliers start: 20 outliers final: 13 residues processed: 133 average time/residue: 0.0565 time to fit residues: 10.1247 Evaluate side-chains 138 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET 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 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 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 314 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 385 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 29 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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 = 0.4406 r_free = 0.4406 target = 0.213166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.158294 restraints weight = 5512.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.162547 restraints weight = 4083.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.164779 restraints weight = 3370.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.167046 restraints weight = 3009.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.168001 restraints weight = 2783.765| |-----------------------------------------------------------------------------| r_work (final): 0.3934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4869 Z= 0.166 Angle : 0.661 8.773 6614 Z= 0.347 Chirality : 0.044 0.140 799 Planarity : 0.004 0.025 825 Dihedral : 4.492 36.029 658 Min Nonbonded Distance : 1.492 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.64 % Allowed : 25.86 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.35), residues: 614 helix: 2.10 (0.24), residues: 406 sheet: -1.84 (0.86), residues: 42 loop : -0.97 (0.52), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 62 TYR 0.015 0.001 TYR A 396 PHE 0.009 0.001 PHE A 421 TRP 0.010 0.001 TRP B 375 HIS 0.014 0.002 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 4850) covalent geometry : angle 0.66148 ( 6604) SS BOND : bond 0.00220 ( 5) SS BOND : angle 0.60665 ( 10) hydrogen bonds : bond 0.04406 ( 351) hydrogen bonds : angle 4.52905 ( 1053) metal coordination : bond 0.02581 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1004.20 seconds wall clock time: 18 minutes 2.41 seconds (1082.41 seconds total)