Starting phenix.real_space_refine on Tue Jan 14 00:31:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zsz_60435/01_2025/8zsz_60435.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zsz_60435/01_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_60435/01_2025/8zsz_60435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zsz_60435/01_2025/8zsz_60435.map" model { file = "/net/cci-nas-00/data/ceres_data/8zsz_60435/01_2025/8zsz_60435.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zsz_60435/01_2025/8zsz_60435.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.093 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 41 5.16 5 C 3071 2.51 5 N 829 2.21 5 O 805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4754 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2362 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 11, 'TRANS': 303} Chain breaks: 3 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2384 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 11, 'TRANS': 303} Chain breaks: 3 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.43, per 1000 atoms: 0.72 Number of scatterers: 4754 At special positions: 0 Unit cell: (70.655, 58.698, 117.396, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 8 29.99 S 41 16.00 O 805 8.00 N 829 7.00 C 3071 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS B 291 " distance=2.01 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 282 " distance=2.03 Simple disulfide: pdb=" SG CYS B 286 " - pdb=" SG CYS B 311 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 674.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS B 157 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 370 " pdb=" ZN A 602 " pdb="ZN ZN A 602 " - pdb=" NE2 HIS A 43 " pdb="ZN ZN A 602 " - pdb=" NE2 HIS A 251 " pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" NE2 HIS A 373 " pdb="ZN ZN A 603 " - pdb=" NE2 HIS B 148 " pdb="ZN ZN A 603 " - pdb=" NE2 HIS B 146 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS A 157 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 370 " pdb=" ZN B 602 " pdb="ZN ZN B 602 " - pdb=" NE2 HIS B 43 " pdb="ZN ZN B 602 " - pdb=" NE2 HIS B 251 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" NE2 HIS B 373 " pdb="ZN ZN B 603 " - pdb=" NE2 HIS A 148 " pdb="ZN ZN B 603 " - pdb=" NE2 HIS A 146 " 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 68.1% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 5 through 33 Processing helix chain 'A' and resid 35 through 62 removed outlier: 3.514A pdb=" N LEU A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 106 removed outlier: 3.532A pdb=" N GLU A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 134 Processing helix chain 'A' and resid 239 through 273 Processing helix chain 'A' and resid 310 through 315 removed outlier: 4.239A pdb=" N LEU A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 315 " --> pdb=" O CYS A 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 310 through 315' Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.622A pdb=" N THR A 319 " --> pdb=" O TYR A 315 " (cutoff:3.500A) Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 352 through 362 removed outlier: 3.539A pdb=" N LEU A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 411 removed outlier: 3.793A pdb=" N MET A 397 " --> pdb=" O PRO A 393 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 33 Processing helix chain 'B' and resid 35 through 63 removed outlier: 3.512A pdb=" N ARG B 63 " --> pdb=" O ARG B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 106 removed outlier: 3.715A pdb=" N GLU B 78 " --> pdb=" O TRP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 134 Processing helix chain 'B' and resid 239 through 273 Processing helix chain 'B' and resid 310 through 315 removed outlier: 4.238A pdb=" N LEU B 314 " --> pdb=" O PRO B 310 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 315 " --> pdb=" O CYS B 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 310 through 315' Processing helix chain 'B' and resid 315 through 343 removed outlier: 3.622A pdb=" N THR B 319 " --> pdb=" O TYR B 315 " (cutoff:3.500A) Proline residue: B 334 - end of helix Processing helix chain 'B' and resid 352 through 363 removed outlier: 3.539A pdb=" N LEU B 356 " --> pdb=" O ASP B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 411 removed outlier: 3.793A pdb=" N MET B 397 " --> pdb=" O PRO B 393 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 370 through 377 removed outlier: 6.056A pdb=" N GLU A 371 " --> pdb=" O HIS A 387 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N HIS A 387 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA A 414 " --> pdb=" O ILE A 382 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 370 through 377 removed outlier: 6.046A pdb=" N GLU B 371 " --> pdb=" O HIS B 387 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N HIS B 387 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA B 414 " --> pdb=" O ILE B 382 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 1053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 748 1.28 - 1.42: 1281 1.42 - 1.55: 2759 1.55 - 1.68: 2 1.68 - 1.82: 60 Bond restraints: 4850 Sorted by residual: bond pdb=" CA TRP A 375 " pdb=" C TRP A 375 " ideal model delta sigma weight residual 1.521 1.399 0.122 1.24e-02 6.50e+03 9.65e+01 bond pdb=" CA TRP B 375 " pdb=" C TRP B 375 " ideal model delta sigma weight residual 1.521 1.401 0.120 1.24e-02 6.50e+03 9.41e+01 bond pdb=" CA LEU A 372 " pdb=" C LEU A 372 " ideal model delta sigma weight residual 1.524 1.410 0.114 1.23e-02 6.61e+03 8.55e+01 bond pdb=" CA LEU B 372 " pdb=" C LEU B 372 " ideal model delta sigma weight residual 1.524 1.410 0.114 1.23e-02 6.61e+03 8.53e+01 bond pdb=" CA ALA A 54 " pdb=" C ALA A 54 " ideal model delta sigma weight residual 1.522 1.393 0.129 1.40e-02 5.10e+03 8.46e+01 ... (remaining 4845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.72: 6224 3.72 - 7.43: 303 7.43 - 11.15: 66 11.15 - 14.86: 8 14.86 - 18.58: 3 Bond angle restraints: 6604 Sorted by residual: angle pdb=" N VAL B 56 " pdb=" CA VAL B 56 " pdb=" C VAL B 56 " ideal model delta sigma weight residual 110.72 92.14 18.58 1.01e+00 9.80e-01 3.38e+02 angle pdb=" N LYS A 69 " pdb=" CA LYS A 69 " pdb=" C LYS A 69 " ideal model delta sigma weight residual 114.31 98.58 15.73 1.29e+00 6.01e-01 1.49e+02 angle pdb=" N HIS A 43 " pdb=" CA HIS A 43 " pdb=" C HIS A 43 " ideal model delta sigma weight residual 113.01 100.68 12.33 1.20e+00 6.94e-01 1.06e+02 angle pdb=" N VAL A 56 " pdb=" CA VAL A 56 " pdb=" C VAL A 56 " ideal model delta sigma weight residual 111.89 97.80 14.09 1.44e+00 4.82e-01 9.58e+01 angle pdb=" N LYS B 69 " pdb=" CA LYS B 69 " pdb=" C LYS B 69 " ideal model delta sigma weight residual 113.61 99.82 13.79 1.50e+00 4.44e-01 8.46e+01 ... (remaining 6599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 2494 15.99 - 31.99: 249 31.99 - 47.98: 63 47.98 - 63.98: 18 63.98 - 79.97: 9 Dihedral angle restraints: 2833 sinusoidal: 1037 harmonic: 1796 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS B 291 " pdb=" CB CYS B 291 " ideal model delta sinusoidal sigma weight residual -86.00 -162.51 76.51 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CB CYS A 286 " pdb=" SG CYS A 286 " pdb=" SG CYS A 311 " pdb=" CB CYS A 311 " ideal model delta sinusoidal sigma weight residual -86.00 -23.94 -62.06 1 1.00e+01 1.00e-02 5.10e+01 dihedral pdb=" CB CYS B 286 " pdb=" SG CYS B 286 " pdb=" SG CYS B 311 " pdb=" CB CYS B 311 " ideal model delta sinusoidal sigma weight residual -86.00 -23.98 -62.02 1 1.00e+01 1.00e-02 5.10e+01 ... (remaining 2830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 663 0.098 - 0.197: 94 0.197 - 0.295: 24 0.295 - 0.394: 10 0.394 - 0.492: 8 Chirality restraints: 799 Sorted by residual: chirality pdb=" CA TRP B 74 " pdb=" N TRP B 74 " pdb=" C TRP B 74 " pdb=" CB TRP B 74 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" CA HIS A 408 " pdb=" N HIS A 408 " pdb=" C HIS A 408 " pdb=" CB HIS A 408 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.86e+00 chirality pdb=" CA HIS B 408 " pdb=" N HIS B 408 " pdb=" C HIS B 408 " pdb=" CB HIS B 408 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.83e+00 ... (remaining 796 not shown) Planarity restraints: 825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 336 " 0.041 2.00e-02 2.50e+03 8.23e-02 6.77e+01 pdb=" C LEU A 336 " -0.142 2.00e-02 2.50e+03 pdb=" O LEU A 336 " 0.053 2.00e-02 2.50e+03 pdb=" N LYS A 337 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 336 " -0.041 2.00e-02 2.50e+03 8.22e-02 6.76e+01 pdb=" C LEU B 336 " 0.142 2.00e-02 2.50e+03 pdb=" O LEU B 336 " -0.053 2.00e-02 2.50e+03 pdb=" N LYS B 337 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 411 " -0.040 2.00e-02 2.50e+03 7.79e-02 6.07e+01 pdb=" C GLY A 411 " 0.135 2.00e-02 2.50e+03 pdb=" O GLY A 411 " -0.050 2.00e-02 2.50e+03 pdb=" N ILE A 412 " -0.045 2.00e-02 2.50e+03 ... (remaining 822 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.28: 22 2.28 - 2.93: 2485 2.93 - 3.59: 7490 3.59 - 4.24: 10516 4.24 - 4.90: 17643 Nonbonded interactions: 38156 Sorted by model distance: nonbonded pdb=" OE2 GLU B 420 " pdb="ZN ZN B 601 " model vdw 1.624 2.230 nonbonded pdb=" OE2 GLU A 420 " pdb="ZN ZN A 601 " model vdw 1.659 2.230 nonbonded pdb=" OD1 ASP A 255 " pdb="ZN ZN A 602 " model vdw 1.782 2.230 nonbonded pdb=" OD1 ASP B 255 " pdb="ZN ZN B 602 " model vdw 1.792 2.230 nonbonded pdb=" OE1 GLU B 371 " pdb="ZN ZN B 603 " model vdw 1.851 2.230 ... (remaining 38151 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 361 or (resid 362 and (name N or name CA or name \ C or name O or name CB )) or resid 363 through 366 or (resid 367 and (name N or \ name CA or name C or name O or name CB )) or resid 368 through 421 or resid 601 \ through 604)) selection = (chain 'B' and (resid 5 through 353 or (resid 354 and (name N or name CA or name \ C or name O or name CB )) or resid 355 through 360 or (resid 361 through 362 an \ d (name N or name CA or name C or name O or name CB )) or resid 363 through 381 \ or (resid 382 and (name N or name CA or name C or name O or name CB )) or resid \ 383 through 388 or (resid 389 and (name N or name CA or name C or name O or name \ CB )) or resid 390 through 396 or (resid 397 through 398 and (name N or name CA \ or name C or name O or name CB )) or resid 399 through 403 or (resid 404 throug \ h 405 and (name N or name CA or name C or name O or name CB )) or resid 406 thro \ ugh 421 or resid 601 through 604)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.090 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.840 ------------------------------------------------------------------------------- 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 : 0.017 0.129 4850 Z= 1.144 Angle : 1.805 18.578 6604 Z= 1.231 Chirality : 0.094 0.492 799 Planarity : 0.012 0.082 825 Dihedral : 14.915 79.971 1654 Min Nonbonded Distance : 1.624 Molprobity Statistics. All-atom Clashscore : 28.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.63 % Allowed : 5.05 % Favored : 92.32 % Cbeta Deviations : 1.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.35), residues: 614 helix: 0.74 (0.25), residues: 404 sheet: -0.56 (0.85), residues: 44 loop : -1.58 (0.53), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.005 TRP A 375 HIS 0.053 0.007 HIS A 146 PHE 0.027 0.002 PHE B 72 TYR 0.009 0.001 TYR B 396 ARG 0.004 0.000 ARG B 62 *********************** 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 : 0.482 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: 0.1398 time to fit residues: 30.7313 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 : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 370 HIS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 289 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 18 optimal weight: 30.0000 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 HIS ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 ASN A 410 HIS A 413 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.214509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.156319 restraints weight = 5271.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.160528 restraints weight = 3909.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.162823 restraints weight = 3257.431| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4850 Z= 0.290 Angle : 0.715 8.585 6604 Z= 0.383 Chirality : 0.046 0.177 799 Planarity : 0.005 0.048 825 Dihedral : 5.861 56.466 672 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.12 % Favored : 97.72 % Rotamer: Outliers : 4.65 % Allowed : 13.94 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.35), residues: 614 helix: 1.60 (0.24), residues: 404 sheet: -2.13 (0.65), residues: 44 loop : -0.85 (0.58), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 375 HIS 0.037 0.004 HIS A 148 PHE 0.029 0.001 PHE A 421 TYR 0.013 0.002 TYR A 396 ARG 0.005 0.001 ARG B 76 *********************** 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 164 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.6573 (OUTLIER) cc_final: 0.5955 (mp) REVERT: A 287 PHE cc_start: 0.9032 (t80) cc_final: 0.8798 (t80) REVERT: A 289 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7047 (t0) REVERT: A 409 ASN cc_start: 0.8376 (t0) cc_final: 0.8125 (m-40) REVERT: B 75 ILE cc_start: 0.6818 (OUTLIER) cc_final: 0.6314 (mp) REVERT: B 287 PHE cc_start: 0.9068 (t80) cc_final: 0.8813 (t80) REVERT: B 289 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.6977 (t0) REVERT: B 320 LEU cc_start: 0.8536 (mt) cc_final: 0.8278 (mt) outliers start: 23 outliers final: 10 residues processed: 154 average time/residue: 0.1258 time to fit residues: 25.8315 Evaluate side-chains 148 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 7 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.215176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.156339 restraints weight = 5194.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.159964 restraints weight = 3888.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.162864 restraints weight = 3256.512| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4850 Z= 0.247 Angle : 0.624 6.035 6604 Z= 0.334 Chirality : 0.045 0.139 799 Planarity : 0.004 0.034 825 Dihedral : 4.646 22.175 662 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 5.05 % Allowed : 16.97 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.36), residues: 614 helix: 1.83 (0.24), residues: 406 sheet: -1.72 (0.77), residues: 40 loop : -0.62 (0.60), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 74 HIS 0.040 0.003 HIS B 148 PHE 0.020 0.001 PHE A 421 TYR 0.014 0.002 TYR A 396 ARG 0.003 0.000 ARG A 59 *********************** 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 169 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7564 (mmp) cc_final: 0.7047 (mpp) REVERT: A 75 ILE cc_start: 0.6604 (OUTLIER) cc_final: 0.6030 (mp) REVERT: A 115 VAL cc_start: 0.9026 (m) cc_final: 0.8808 (p) REVERT: A 124 LEU cc_start: 0.7848 (tt) cc_final: 0.7642 (tt) REVERT: A 396 TYR cc_start: 0.7826 (t80) cc_final: 0.7565 (t80) REVERT: A 410 HIS cc_start: 0.8181 (m-70) cc_final: 0.7876 (m170) REVERT: B 75 ILE cc_start: 0.6844 (OUTLIER) cc_final: 0.6307 (mp) REVERT: B 115 VAL cc_start: 0.9024 (m) cc_final: 0.8814 (p) REVERT: B 124 LEU cc_start: 0.7861 (tt) cc_final: 0.7645 (tt) REVERT: B 368 GLU cc_start: 0.8407 (pt0) cc_final: 0.7843 (pm20) REVERT: B 404 LYS cc_start: 0.8696 (tppt) cc_final: 0.8399 (mmmm) REVERT: B 409 ASN cc_start: 0.8480 (m-40) cc_final: 0.8208 (m-40) outliers start: 25 outliers final: 16 residues processed: 155 average time/residue: 0.1279 time to fit residues: 26.3682 Evaluate side-chains 143 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 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 385 THR Chi-restraints excluded: chain B residue 415 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 26 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 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 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 = 0.4406 r_free = 0.4406 target = 0.214376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.155519 restraints weight = 5056.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.159456 restraints weight = 3847.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.162068 restraints weight = 3245.051| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4850 Z= 0.238 Angle : 0.619 6.981 6604 Z= 0.327 Chirality : 0.044 0.159 799 Planarity : 0.004 0.033 825 Dihedral : 4.314 21.427 658 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.85 % Allowed : 19.39 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.35), residues: 614 helix: 1.96 (0.25), residues: 406 sheet: -1.48 (0.81), residues: 38 loop : -0.80 (0.56), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 74 HIS 0.043 0.003 HIS B 148 PHE 0.007 0.001 PHE B 94 TYR 0.014 0.001 TYR A 396 ARG 0.003 0.000 ARG A 62 *********************** 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 149 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.6576 (OUTLIER) cc_final: 0.5995 (mp) REVERT: A 115 VAL cc_start: 0.9007 (m) cc_final: 0.8796 (p) REVERT: A 420 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7896 (tt0) REVERT: B 75 ILE cc_start: 0.6737 (OUTLIER) cc_final: 0.6194 (mp) REVERT: B 115 VAL cc_start: 0.9015 (m) cc_final: 0.8804 (p) REVERT: B 368 GLU cc_start: 0.8368 (pt0) cc_final: 0.7939 (pm20) REVERT: B 404 LYS cc_start: 0.8621 (tppt) cc_final: 0.8324 (mmmm) REVERT: B 409 ASN cc_start: 0.8429 (m-40) cc_final: 0.8081 (m-40) REVERT: B 420 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8161 (tt0) outliers start: 24 outliers final: 15 residues processed: 137 average time/residue: 0.1406 time to fit residues: 25.2839 Evaluate side-chains 144 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 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 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 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 Chi-restraints excluded: chain B residue 420 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 0 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.214128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.155417 restraints weight = 5428.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.159147 restraints weight = 4111.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.161780 restraints weight = 3477.816| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4850 Z= 0.267 Angle : 0.598 7.998 6604 Z= 0.321 Chirality : 0.044 0.225 799 Planarity : 0.004 0.032 825 Dihedral : 4.257 20.854 658 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 6.67 % Allowed : 21.21 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.35), residues: 614 helix: 1.88 (0.25), residues: 406 sheet: -1.38 (0.83), residues: 38 loop : -0.79 (0.56), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 375 HIS 0.038 0.003 HIS B 148 PHE 0.009 0.001 PHE B 287 TYR 0.019 0.002 TYR B 396 ARG 0.003 0.000 ARG B 76 *********************** 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 162 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.6822 (OUTLIER) cc_final: 0.6292 (mp) REVERT: A 115 VAL cc_start: 0.9030 (m) cc_final: 0.8821 (p) REVERT: A 289 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.6827 (t0) REVERT: A 312 TRP cc_start: 0.8688 (p-90) cc_final: 0.8120 (p-90) REVERT: A 420 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: B 42 PHE cc_start: 0.7927 (m-80) cc_final: 0.7589 (m-80) REVERT: B 75 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6428 (mp) REVERT: B 289 ASP cc_start: 0.7342 (OUTLIER) cc_final: 0.6809 (t0) REVERT: B 312 TRP cc_start: 0.8646 (p-90) cc_final: 0.8096 (p-90) REVERT: B 368 GLU cc_start: 0.8270 (pt0) cc_final: 0.7951 (pm20) REVERT: B 404 LYS cc_start: 0.8647 (tppt) cc_final: 0.8338 (mmmm) REVERT: B 420 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8121 (tt0) outliers start: 33 outliers final: 19 residues processed: 148 average time/residue: 0.1431 time to fit residues: 27.6447 Evaluate side-chains 149 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 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 51 LEU 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 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 Chi-restraints excluded: chain B residue 420 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 51 optimal weight: 0.0370 chunk 33 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.0970 chunk 38 optimal weight: 0.0970 chunk 37 optimal weight: 0.9990 overall best weight: 0.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 HIS ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.216577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.159483 restraints weight = 5379.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.163568 restraints weight = 4014.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.166072 restraints weight = 3360.601| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4850 Z= 0.194 Angle : 0.560 6.219 6604 Z= 0.301 Chirality : 0.042 0.152 799 Planarity : 0.003 0.030 825 Dihedral : 4.214 23.005 658 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.45 % Allowed : 23.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.35), residues: 614 helix: 2.14 (0.25), residues: 406 sheet: -1.36 (0.83), residues: 38 loop : -0.86 (0.55), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 74 HIS 0.037 0.002 HIS B 148 PHE 0.020 0.001 PHE A 42 TYR 0.023 0.002 TYR A 396 ARG 0.002 0.000 ARG A 59 *********************** 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 161 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 VAL cc_start: 0.8997 (m) cc_final: 0.8793 (p) REVERT: A 312 TRP cc_start: 0.8614 (p-90) cc_final: 0.7952 (p-90) REVERT: A 420 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7657 (tt0) REVERT: B 42 PHE cc_start: 0.7780 (m-80) cc_final: 0.7457 (m-80) REVERT: B 75 ILE cc_start: 0.6629 (OUTLIER) cc_final: 0.6078 (mp) REVERT: B 312 TRP cc_start: 0.8643 (p-90) cc_final: 0.7982 (p-90) REVERT: B 368 GLU cc_start: 0.8131 (pt0) cc_final: 0.7914 (pm20) REVERT: B 404 LYS cc_start: 0.8641 (tppt) cc_final: 0.8356 (mmmm) REVERT: B 420 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8001 (tt0) outliers start: 27 outliers final: 19 residues processed: 144 average time/residue: 0.1405 time to fit residues: 26.5068 Evaluate side-chains 151 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 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 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 268 VAL Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 420 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4417 r_free = 0.4417 target = 0.214884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.157896 restraints weight = 5374.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.161918 restraints weight = 4035.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.164368 restraints weight = 3393.489| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4850 Z= 0.225 Angle : 0.567 7.202 6604 Z= 0.305 Chirality : 0.042 0.142 799 Planarity : 0.004 0.030 825 Dihedral : 4.179 23.584 658 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 6.26 % Allowed : 23.43 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.35), residues: 614 helix: 2.14 (0.24), residues: 406 sheet: -1.30 (0.85), residues: 38 loop : -0.84 (0.55), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 74 HIS 0.034 0.002 HIS B 148 PHE 0.015 0.001 PHE A 42 TYR 0.029 0.002 TYR A 396 ARG 0.002 0.000 ARG B 76 *********************** 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 159 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 TRP cc_start: 0.8622 (p-90) cc_final: 0.8001 (p-90) REVERT: A 420 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7498 (tt0) REVERT: B 42 PHE cc_start: 0.7819 (m-80) cc_final: 0.7513 (m-80) REVERT: B 75 ILE cc_start: 0.6734 (OUTLIER) cc_final: 0.6181 (mp) REVERT: B 312 TRP cc_start: 0.8658 (p-90) cc_final: 0.8030 (p-90) REVERT: B 368 GLU cc_start: 0.8109 (pt0) cc_final: 0.7896 (pm20) REVERT: B 404 LYS cc_start: 0.8646 (tppt) cc_final: 0.8351 (mmmm) REVERT: B 420 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8052 (tt0) outliers start: 31 outliers final: 19 residues processed: 143 average time/residue: 0.1349 time to fit residues: 25.6240 Evaluate side-chains 142 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 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 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 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 Chi-restraints excluded: chain B residue 420 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 58 optimal weight: 0.1980 chunk 26 optimal weight: 0.4980 chunk 29 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.216742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.159896 restraints weight = 5330.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.164041 restraints weight = 3999.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.166021 restraints weight = 3344.075| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4850 Z= 0.209 Angle : 0.584 7.726 6604 Z= 0.310 Chirality : 0.042 0.140 799 Planarity : 0.003 0.024 825 Dihedral : 4.185 29.699 658 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.66 % Allowed : 24.44 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.35), residues: 614 helix: 2.23 (0.25), residues: 406 sheet: -1.29 (0.86), residues: 38 loop : -0.83 (0.54), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 74 HIS 0.011 0.002 HIS B 146 PHE 0.009 0.001 PHE A 421 TYR 0.035 0.002 TYR A 396 ARG 0.002 0.000 ARG B 76 *********************** 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 151 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ARG cc_start: 0.7924 (mtm110) cc_final: 0.7706 (mtm-85) REVERT: A 68 GLN cc_start: 0.7512 (tt0) cc_final: 0.7232 (tt0) REVERT: A 75 ILE cc_start: 0.6523 (OUTLIER) cc_final: 0.5973 (mp) REVERT: A 157 HIS cc_start: 0.5845 (p-80) cc_final: 0.5263 (p-80) REVERT: A 312 TRP cc_start: 0.8632 (p-90) cc_final: 0.8017 (p-90) REVERT: A 420 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7502 (tt0) REVERT: B 75 ILE cc_start: 0.6608 (OUTLIER) cc_final: 0.6041 (mp) REVERT: B 312 TRP cc_start: 0.8655 (p-90) cc_final: 0.8045 (p-90) REVERT: B 404 LYS cc_start: 0.8588 (tppt) cc_final: 0.8356 (mmmm) outliers start: 28 outliers final: 17 residues processed: 139 average time/residue: 0.1483 time to fit residues: 27.1098 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 : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 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 90 THR Chi-restraints excluded: chain B residue 110 MET 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 HIS B 148 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.214088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.156997 restraints weight = 5369.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.161279 restraints weight = 3994.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.163995 restraints weight = 3307.591| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4850 Z= 0.232 Angle : 0.589 8.290 6604 Z= 0.313 Chirality : 0.043 0.151 799 Planarity : 0.003 0.024 825 Dihedral : 4.162 23.908 658 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.65 % Allowed : 24.85 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.34), residues: 614 helix: 1.94 (0.24), residues: 418 sheet: -1.26 (0.85), residues: 38 loop : -1.24 (0.52), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 74 HIS 0.010 0.002 HIS B 148 PHE 0.008 0.001 PHE A 421 TYR 0.025 0.002 TYR A 396 ARG 0.007 0.000 ARG B 62 *********************** 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 152 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6429 (mpp) REVERT: A 68 GLN cc_start: 0.7478 (tt0) cc_final: 0.7177 (tt0) REVERT: A 75 ILE cc_start: 0.6570 (OUTLIER) cc_final: 0.6028 (mp) REVERT: A 289 ASP cc_start: 0.7019 (OUTLIER) cc_final: 0.6716 (t70) REVERT: A 312 TRP cc_start: 0.8659 (p-90) cc_final: 0.8050 (p-90) REVERT: A 324 MET cc_start: 0.7870 (tmm) cc_final: 0.7617 (ttp) REVERT: A 420 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: B 75 ILE cc_start: 0.6646 (OUTLIER) cc_final: 0.6103 (mp) REVERT: B 312 TRP cc_start: 0.8692 (p-90) cc_final: 0.8074 (p-90) REVERT: B 404 LYS cc_start: 0.8446 (tppt) cc_final: 0.8224 (mmmm) outliers start: 23 outliers final: 15 residues processed: 142 average time/residue: 0.1393 time to fit residues: 26.3021 Evaluate side-chains 138 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 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 30 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 49 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 53 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.215737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.159508 restraints weight = 5371.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.163732 restraints weight = 4019.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.166456 restraints weight = 3344.649| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4850 Z= 0.220 Angle : 0.607 8.623 6604 Z= 0.323 Chirality : 0.043 0.140 799 Planarity : 0.004 0.024 825 Dihedral : 4.299 28.511 658 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.44 % Allowed : 25.25 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.34), residues: 614 helix: 1.93 (0.24), residues: 418 sheet: -1.49 (0.81), residues: 42 loop : -1.27 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 74 HIS 0.019 0.002 HIS B 148 PHE 0.007 0.001 PHE A 421 TYR 0.031 0.002 TYR A 396 ARG 0.005 0.000 ARG B 62 ********************** 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 148 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6344 (mpp) REVERT: A 68 GLN cc_start: 0.7403 (tt0) cc_final: 0.7154 (tt0) REVERT: A 75 ILE cc_start: 0.6496 (OUTLIER) cc_final: 0.5933 (mp) REVERT: A 312 TRP cc_start: 0.8782 (p-90) cc_final: 0.8222 (p-90) REVERT: A 410 HIS cc_start: 0.8201 (OUTLIER) cc_final: 0.7425 (t-90) REVERT: A 420 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7452 (tt0) REVERT: B 42 PHE cc_start: 0.7732 (m-80) cc_final: 0.7467 (m-80) REVERT: B 75 ILE cc_start: 0.6592 (OUTLIER) cc_final: 0.6033 (mp) REVERT: B 312 TRP cc_start: 0.8699 (p-90) cc_final: 0.8116 (p-90) REVERT: B 396 TYR cc_start: 0.7419 (t80) cc_final: 0.7204 (t80) outliers start: 22 outliers final: 16 residues processed: 136 average time/residue: 0.1302 time to fit residues: 23.6368 Evaluate side-chains 145 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 410 HIS 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 90 THR Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 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 52 optimal weight: 0.2980 chunk 19 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4434 r_free = 0.4434 target = 0.216477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.157657 restraints weight = 5439.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.162175 restraints weight = 3927.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.164583 restraints weight = 3212.227| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4850 Z= 0.237 Angle : 0.618 8.675 6604 Z= 0.326 Chirality : 0.043 0.142 799 Planarity : 0.004 0.024 825 Dihedral : 4.435 37.303 658 Min Nonbonded Distance : 1.431 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.44 % Allowed : 25.05 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.34), residues: 614 helix: 2.06 (0.24), residues: 406 sheet: -1.38 (0.82), residues: 42 loop : -0.94 (0.53), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 74 HIS 0.017 0.002 HIS A 387 PHE 0.008 0.001 PHE B 94 TYR 0.017 0.001 TYR A 396 ARG 0.004 0.000 ARG A 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1710.12 seconds wall clock time: 31 minutes 17.72 seconds (1877.72 seconds total)