Starting phenix.real_space_refine on Thu Jul 2 12:26:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ext_28662/07_2026/8ext_28662.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ext_28662/07_2026/8ext_28662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ext_28662/07_2026/8ext_28662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ext_28662/07_2026/8ext_28662.map" model { file = "/net/cci-nas-00/data/ceres_data/8ext_28662/07_2026/8ext_28662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ext_28662/07_2026/8ext_28662.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ext_28662/07_2026/8ext_28662.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ext_28662/07_2026/8ext_28662.cif" } resolution = 4.6 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= 0.000 sd= 0.003 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 2 6.06 5 S 38 5.16 5 C 5806 2.51 5 N 1460 2.21 5 O 1540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8846 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4422 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 520} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 2.52, per 1000 atoms: 0.28 Number of scatterers: 8846 At special positions: 0 Unit cell: (88.395, 92.655, 116.085, 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 2 29.99 S 38 16.00 O 1540 8.00 N 1460 7.00 C 5806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 396.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 201 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 205 " pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 201 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 205 " 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 60.0% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 1 through 31 Processing helix chain 'A' and resid 36 through 48 removed outlier: 4.044A pdb=" N TYR A 40 " --> pdb=" O TYR A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 99 through 134 removed outlier: 3.846A pdb=" N ASP A 103 " --> pdb=" O TRP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 152 removed outlier: 5.172A pdb=" N LYS A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 193 through 208 Processing helix chain 'A' and resid 209 through 225 Processing helix chain 'A' and resid 228 through 252 Processing helix chain 'A' and resid 257 through 271 Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 307 through 328 removed outlier: 3.808A pdb=" N LEU A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 391 through 402 Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 438 through 449 Processing helix chain 'A' and resid 450 through 461 removed outlier: 3.530A pdb=" N THR A 454 " --> pdb=" O PRO A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 497 Processing helix chain 'A' and resid 502 through 513 removed outlier: 3.617A pdb=" N SER A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 579 Processing helix chain 'B' and resid 2 through 31 Processing helix chain 'B' and resid 36 through 48 removed outlier: 4.044A pdb=" N TYR B 40 " --> pdb=" O TYR B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 99 through 134 removed outlier: 3.846A pdb=" N ASP B 103 " --> pdb=" O TRP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 152 removed outlier: 5.173A pdb=" N LYS B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 189 Processing helix chain 'B' and resid 193 through 208 Processing helix chain 'B' and resid 209 through 225 Processing helix chain 'B' and resid 228 through 252 Processing helix chain 'B' and resid 257 through 271 Processing helix chain 'B' and resid 289 through 300 Processing helix chain 'B' and resid 307 through 328 removed outlier: 3.808A pdb=" N LEU B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 387 through 390 Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 429 through 436 Processing helix chain 'B' and resid 438 through 449 Processing helix chain 'B' and resid 450 through 461 removed outlier: 3.530A pdb=" N THR B 454 " --> pdb=" O PRO B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 497 Processing helix chain 'B' and resid 502 through 513 removed outlier: 3.616A pdb=" N SER B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 513 " --> pdb=" O LEU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 579 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 164 removed outlier: 6.645A pdb=" N VAL A 160 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE A 182 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ARG A 162 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.615A pdb=" N ASP A 346 " --> pdb=" O TYR A 373 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE A 375 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN A 348 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLY A 530 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLY A 539 " --> pdb=" O GLY A 528 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLY A 528 " --> pdb=" O GLY A 539 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE A 541 " --> pdb=" O LYS A 526 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS A 526 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY A 543 " --> pdb=" O TYR A 524 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR A 524 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL A 545 " --> pdb=" O GLU A 522 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU A 522 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR A 521 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS A 517 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU A 523 " --> pdb=" O ILE A 515 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 164 removed outlier: 6.645A pdb=" N VAL B 160 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE B 182 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG B 162 " --> pdb=" O ILE B 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 346 through 350 removed outlier: 6.615A pdb=" N ASP B 346 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE B 375 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN B 348 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY B 530 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY B 539 " --> pdb=" O GLY B 528 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLY B 528 " --> pdb=" O GLY B 539 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE B 541 " --> pdb=" O LYS B 526 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS B 526 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY B 543 " --> pdb=" O TYR B 524 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TYR B 524 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL B 545 " --> pdb=" O GLU B 522 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU B 522 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR B 521 " --> pdb=" O LYS B 517 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LYS B 517 " --> pdb=" O TYR B 521 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU B 523 " --> pdb=" O ILE B 515 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1461 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: 1.11 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1815 1.31 - 1.44: 2726 1.44 - 1.58: 4399 1.58 - 1.71: 38 1.71 - 1.84: 68 Bond restraints: 9046 Sorted by residual: bond pdb=" CB HIS A 282 " pdb=" CG HIS A 282 " ideal model delta sigma weight residual 1.497 1.335 0.162 1.40e-02 5.10e+03 1.34e+02 bond pdb=" CB HIS B 282 " pdb=" CG HIS B 282 " ideal model delta sigma weight residual 1.497 1.335 0.162 1.40e-02 5.10e+03 1.34e+02 bond pdb=" CB HIS B 153 " pdb=" CG HIS B 153 " ideal model delta sigma weight residual 1.497 1.349 0.148 1.40e-02 5.10e+03 1.11e+02 bond pdb=" CB HIS A 153 " pdb=" CG HIS A 153 " ideal model delta sigma weight residual 1.497 1.349 0.148 1.40e-02 5.10e+03 1.11e+02 bond pdb=" CB PHE A 220 " pdb=" CG PHE A 220 " ideal model delta sigma weight residual 1.502 1.312 0.190 2.30e-02 1.89e+03 6.83e+01 ... (remaining 9041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.92: 12014 5.92 - 11.84: 144 11.84 - 17.77: 6 17.77 - 23.69: 2 23.69 - 29.61: 6 Bond angle restraints: 12172 Sorted by residual: angle pdb=" O ASP B 346 " pdb=" C ASP B 346 " pdb=" N TYR B 347 " ideal model delta sigma weight residual 122.79 148.72 -25.93 1.14e+00 7.69e-01 5.17e+02 angle pdb=" O ASP A 346 " pdb=" C ASP A 346 " pdb=" N TYR A 347 " ideal model delta sigma weight residual 122.79 148.72 -25.93 1.14e+00 7.69e-01 5.17e+02 angle pdb=" CA ASP A 346 " pdb=" C ASP A 346 " pdb=" N TYR A 347 " ideal model delta sigma weight residual 115.27 85.66 29.61 1.34e+00 5.57e-01 4.88e+02 angle pdb=" CA ASP B 346 " pdb=" C ASP B 346 " pdb=" N TYR B 347 " ideal model delta sigma weight residual 115.27 85.66 29.61 1.34e+00 5.57e-01 4.88e+02 angle pdb=" O ILE A 51 " pdb=" C ILE A 51 " pdb=" N PRO A 52 " ideal model delta sigma weight residual 121.10 136.04 -14.94 1.14e+00 7.69e-01 1.72e+02 ... (remaining 12167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.03: 5016 14.03 - 28.05: 308 28.05 - 42.08: 70 42.08 - 56.10: 28 56.10 - 70.13: 10 Dihedral angle restraints: 5432 sinusoidal: 2256 harmonic: 3176 Sorted by residual: dihedral pdb=" C LEU B 18 " pdb=" N LEU B 18 " pdb=" CA LEU B 18 " pdb=" CB LEU B 18 " ideal model delta harmonic sigma weight residual -122.60 -112.59 -10.01 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" C LEU A 18 " pdb=" N LEU A 18 " pdb=" CA LEU A 18 " pdb=" CB LEU A 18 " ideal model delta harmonic sigma weight residual -122.60 -112.59 -10.01 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" C ASN B 406 " pdb=" N ASN B 406 " pdb=" CA ASN B 406 " pdb=" CB ASN B 406 " ideal model delta harmonic sigma weight residual -122.60 -132.21 9.61 0 2.50e+00 1.60e-01 1.48e+01 ... (remaining 5429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 716 0.085 - 0.171: 414 0.171 - 0.256: 156 0.256 - 0.341: 36 0.341 - 0.426: 14 Chirality restraints: 1336 Sorted by residual: chirality pdb=" CA TYR A 178 " pdb=" N TYR A 178 " pdb=" C TYR A 178 " pdb=" CB TYR A 178 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.54e+00 chirality pdb=" CA TYR B 178 " pdb=" N TYR B 178 " pdb=" C TYR B 178 " pdb=" CB TYR B 178 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CA PHE B 151 " pdb=" N PHE B 151 " pdb=" C PHE B 151 " pdb=" CB PHE B 151 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 1333 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 346 " 0.022 2.00e-02 2.50e+03 7.33e-02 5.37e+01 pdb=" C ASP A 346 " -0.125 2.00e-02 2.50e+03 pdb=" O ASP A 346 " 0.058 2.00e-02 2.50e+03 pdb=" N TYR A 347 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 346 " -0.022 2.00e-02 2.50e+03 7.33e-02 5.37e+01 pdb=" C ASP B 346 " 0.125 2.00e-02 2.50e+03 pdb=" O ASP B 346 " -0.058 2.00e-02 2.50e+03 pdb=" N TYR B 347 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 51 " 0.024 2.00e-02 2.50e+03 6.08e-02 3.70e+01 pdb=" C ILE A 51 " -0.105 2.00e-02 2.50e+03 pdb=" O ILE A 51 " 0.044 2.00e-02 2.50e+03 pdb=" N PRO A 52 " 0.036 2.00e-02 2.50e+03 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 174 2.59 - 3.17: 9050 3.17 - 3.75: 15210 3.75 - 4.32: 22367 4.32 - 4.90: 32315 Nonbonded interactions: 79116 Sorted by model distance: nonbonded pdb=" OE2 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.014 2.230 nonbonded pdb=" OE2 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.014 2.230 nonbonded pdb=" OE1 GLU A 242 " pdb="ZN ZN A 701 " model vdw 2.021 2.230 nonbonded pdb=" OE1 GLU B 242 " pdb="ZN ZN B 701 " model vdw 2.022 2.230 nonbonded pdb=" O MET A 33 " pdb=" CD1 LEU B 311 " model vdw 2.281 3.460 ... (remaining 79111 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' } Set refine NCS operators NCS operators will be refined. 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: 0.600 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: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.620 Find NCS groups from input model: 0.040 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4531 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 : 0.026 0.190 9050 Z= 1.544 Angle : 2.042 29.611 12172 Z= 1.432 Chirality : 0.123 0.426 1336 Planarity : 0.010 0.073 1488 Dihedral : 10.968 70.129 3384 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.76 % Allowed : 5.33 % Favored : 93.90 % Rotamer: Outliers : 2.03 % Allowed : 1.01 % Favored : 96.96 % 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 are not related in a simple way. whole: -0.66 (0.24), residues: 1050 helix: -0.09 (0.19), residues: 550 sheet: -0.87 (0.47), residues: 118 loop : -0.57 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 384 TYR 0.056 0.010 TYR B 203 PHE 0.045 0.006 PHE B 151 TRP 0.055 0.011 TRP B 540 HIS 0.014 0.003 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.02633 / 1.54 ( 9046) covalent geometry : angle 2.04192 / 1.43 (12172) hydrogen bonds : bond 0.20237 / 13.34 ( 495) hydrogen bonds : angle 8.18963 / 5.86 ( 1461) metal coordination : bond 0.12888 / 6.47 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.8475 (mt) cc_final: 0.8015 (mm) REVERT: A 20 LEU cc_start: 0.8877 (mt) cc_final: 0.8628 (mt) REVERT: A 37 LYS cc_start: 0.8324 (mttt) cc_final: 0.8005 (mttt) REVERT: A 119 PHE cc_start: 0.7232 (m-10) cc_final: 0.7000 (m-80) REVERT: A 260 THR cc_start: 0.7838 (t) cc_final: 0.7605 (t) REVERT: A 314 ILE cc_start: 0.8847 (mt) cc_final: 0.8631 (mt) REVERT: A 341 LYS cc_start: 0.6199 (OUTLIER) cc_final: 0.5324 (tppt) outliers start: 10 outliers final: 4 residues processed: 167 average time/residue: 0.0709 time to fit residues: 14.7427 Evaluate side-chains 101 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.0980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.0010 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0270 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 0.0980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 overall best weight: 0.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 HIS ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN A 487 GLN A 538 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.160594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.113335 restraints weight = 12557.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.118012 restraints weight = 8236.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.121285 restraints weight = 6019.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.123800 restraints weight = 4697.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.125744 restraints weight = 3813.188| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9050 Z= 0.172 Angle : 0.741 7.973 12172 Z= 0.402 Chirality : 0.047 0.269 1336 Planarity : 0.005 0.046 1488 Dihedral : 5.379 21.049 1156 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.20 % Allowed : 2.03 % Favored : 97.77 % 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 are not related in a simple way. whole: 0.35 (0.25), residues: 1050 helix: 0.86 (0.20), residues: 584 sheet: -0.42 (0.48), residues: 120 loop : -0.42 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 28 TYR 0.037 0.002 TYR B 203 PHE 0.025 0.003 PHE B 248 TRP 0.018 0.002 TRP A 39 HIS 0.014 0.002 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 ( 9046) covalent geometry : angle 0.74111 / 0.40 (12172) hydrogen bonds : bond 0.06497 / 4.23 ( 495) hydrogen bonds : angle 6.00978 / 4.27 ( 1461) metal coordination : bond 0.00769 / 0.39 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ILE cc_start: 0.9254 (mt) cc_final: 0.8921 (mt) REVERT: A 18 LEU cc_start: 0.9472 (mt) cc_final: 0.9078 (mt) REVERT: A 20 LEU cc_start: 0.9521 (mt) cc_final: 0.9317 (mt) REVERT: A 37 LYS cc_start: 0.8567 (mttt) cc_final: 0.7750 (mmtm) REVERT: A 181 LEU cc_start: 0.8199 (mp) cc_final: 0.7741 (mp) REVERT: A 202 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8377 (mm-30) REVERT: A 209 ARG cc_start: 0.8030 (mtt180) cc_final: 0.7650 (mtt180) REVERT: A 214 LEU cc_start: 0.9639 (tp) cc_final: 0.9399 (tp) REVERT: A 218 ASN cc_start: 0.9170 (m110) cc_final: 0.8820 (m110) REVERT: A 221 SER cc_start: 0.8788 (m) cc_final: 0.8481 (p) REVERT: A 235 ARG cc_start: 0.8135 (mmt180) cc_final: 0.7878 (mmm160) REVERT: A 240 ASP cc_start: 0.8551 (p0) cc_final: 0.7958 (p0) REVERT: A 241 ASN cc_start: 0.9138 (m-40) cc_final: 0.8909 (m110) REVERT: A 244 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8623 (mt-10) REVERT: A 266 MET cc_start: 0.8009 (tmm) cc_final: 0.7725 (tmm) REVERT: A 292 LYS cc_start: 0.8677 (mptt) cc_final: 0.8367 (mttt) REVERT: A 294 ARG cc_start: 0.7836 (mtp180) cc_final: 0.7430 (mtp180) REVERT: A 330 MET cc_start: 0.3022 (ppp) cc_final: 0.2772 (ppp) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.0636 time to fit residues: 10.9340 Evaluate side-chains 110 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 22 optimal weight: 3.9990 chunk 50 optimal weight: 0.2980 chunk 32 optimal weight: 0.0040 chunk 66 optimal weight: 6.9990 chunk 82 optimal weight: 0.0980 chunk 53 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 62 optimal weight: 3.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 ASN ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN A 497 GLN ** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.156356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.113533 restraints weight = 12777.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.118038 restraints weight = 8319.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.121104 restraints weight = 5937.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.123420 restraints weight = 4503.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.124991 restraints weight = 3580.193| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9050 Z= 0.137 Angle : 0.625 7.302 12172 Z= 0.342 Chirality : 0.042 0.156 1336 Planarity : 0.004 0.045 1488 Dihedral : 4.975 18.736 1156 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.61 % Allowed : 2.03 % Favored : 97.36 % 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 are not related in a simple way. whole: 0.67 (0.26), residues: 1050 helix: 1.06 (0.20), residues: 594 sheet: -0.21 (0.49), residues: 122 loop : -0.24 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 235 TYR 0.035 0.002 TYR B 203 PHE 0.013 0.002 PHE A 16 TRP 0.010 0.001 TRP A 39 HIS 0.024 0.002 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 ( 9046) covalent geometry : angle 0.62460 / 0.34 (12172) hydrogen bonds : bond 0.04987 / 3.24 ( 495) hydrogen bonds : angle 5.62169 / 4.00 ( 1461) metal coordination : bond 0.00098 / 0.05 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 18 LEU cc_start: 0.9445 (mt) cc_final: 0.8944 (mt) REVERT: B 22 PHE cc_start: 0.9223 (m-80) cc_final: 0.8830 (m-80) REVERT: B 37 LYS cc_start: 0.8568 (mttt) cc_final: 0.7760 (mmtm) REVERT: B 202 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8405 (mm-30) REVERT: B 209 ARG cc_start: 0.8011 (mtt180) cc_final: 0.7704 (mtt180) REVERT: B 212 LEU cc_start: 0.9406 (tp) cc_final: 0.9200 (tp) REVERT: B 214 LEU cc_start: 0.9666 (tp) cc_final: 0.9446 (tp) REVERT: B 215 ILE cc_start: 0.9108 (pt) cc_final: 0.8874 (pt) REVERT: B 216 ILE cc_start: 0.9565 (mt) cc_final: 0.9261 (mt) REVERT: B 218 ASN cc_start: 0.9239 (m110) cc_final: 0.8937 (m110) REVERT: B 240 ASP cc_start: 0.8405 (p0) cc_final: 0.7789 (p0) REVERT: B 244 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8447 (mt-10) REVERT: B 266 MET cc_start: 0.7722 (tmm) cc_final: 0.7355 (tmm) REVERT: B 287 LYS cc_start: 0.2962 (tppp) cc_final: 0.2274 (tptm) REVERT: B 292 LYS cc_start: 0.8622 (mptt) cc_final: 0.8338 (mttt) REVERT: B 319 PHE cc_start: 0.9156 (t80) cc_final: 0.8720 (t80) outliers start: 3 outliers final: 0 residues processed: 124 average time/residue: 0.0538 time to fit residues: 8.7541 Evaluate side-chains 100 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 0.0040 chunk 79 optimal weight: 0.0870 chunk 64 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 14 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.4370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.160357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.116493 restraints weight = 12360.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.120780 restraints weight = 8255.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.123977 restraints weight = 6131.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.126230 restraints weight = 4727.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.127905 restraints weight = 3848.732| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6144 moved from start: 0.6156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9050 Z= 0.119 Angle : 0.583 6.903 12172 Z= 0.317 Chirality : 0.042 0.172 1336 Planarity : 0.004 0.038 1488 Dihedral : 4.716 17.189 1156 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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 are not related in a simple way. whole: 0.86 (0.26), residues: 1050 helix: 1.31 (0.21), residues: 598 sheet: -0.40 (0.49), residues: 122 loop : -0.28 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 293 TYR 0.032 0.001 TYR A 203 PHE 0.012 0.001 PHE B 187 TRP 0.010 0.001 TRP B 39 HIS 0.009 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 ( 9046) covalent geometry : angle 0.58341 / 0.32 (12172) hydrogen bonds : bond 0.04536 / 2.90 ( 495) hydrogen bonds : angle 5.44512 / 3.87 ( 1461) metal coordination : bond 0.00152 / 0.08 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 18 LEU cc_start: 0.9464 (mt) cc_final: 0.9243 (mt) REVERT: B 22 PHE cc_start: 0.9095 (m-80) cc_final: 0.8827 (m-80) REVERT: B 37 LYS cc_start: 0.8555 (mttt) cc_final: 0.7718 (mmtm) REVERT: B 105 ILE cc_start: 0.8782 (mt) cc_final: 0.8507 (mm) REVERT: B 181 LEU cc_start: 0.8005 (mp) cc_final: 0.7644 (mp) REVERT: B 187 PHE cc_start: 0.7605 (m-80) cc_final: 0.7147 (m-80) REVERT: B 202 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8647 (mm-30) REVERT: B 209 ARG cc_start: 0.8245 (mtt180) cc_final: 0.7703 (mtt180) REVERT: B 214 LEU cc_start: 0.9606 (tp) cc_final: 0.9403 (tp) REVERT: B 215 ILE cc_start: 0.9081 (pt) cc_final: 0.8826 (pt) REVERT: B 216 ILE cc_start: 0.9511 (mt) cc_final: 0.9118 (mt) REVERT: B 230 VAL cc_start: 0.8458 (m) cc_final: 0.8257 (m) REVERT: B 240 ASP cc_start: 0.8298 (p0) cc_final: 0.8053 (p0) REVERT: B 244 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8261 (mt-10) REVERT: B 292 LYS cc_start: 0.8703 (mptt) cc_final: 0.8390 (mttt) REVERT: B 319 PHE cc_start: 0.8931 (t80) cc_final: 0.8662 (t80) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0533 time to fit residues: 8.8792 Evaluate side-chains 102 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 7 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 39 optimal weight: 0.0870 chunk 50 optimal weight: 0.0020 chunk 91 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 104 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 overall best weight: 0.5166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 205 HIS B 239 HIS B 241 ASN ** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.150828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.107670 restraints weight = 12724.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.111586 restraints weight = 8648.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.114344 restraints weight = 6384.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.116356 restraints weight = 5012.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.117815 restraints weight = 4105.157| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 moved from start: 0.6684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.147 9050 Z= 0.146 Angle : 0.606 8.207 12172 Z= 0.327 Chirality : 0.043 0.160 1336 Planarity : 0.004 0.040 1488 Dihedral : 4.642 16.472 1156 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.20 % Allowed : 0.61 % Favored : 99.19 % 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 are not related in a simple way. whole: 0.91 (0.26), residues: 1050 helix: 1.30 (0.21), residues: 602 sheet: -0.20 (0.49), residues: 120 loop : -0.23 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 23 TYR 0.024 0.002 TYR B 130 PHE 0.011 0.001 PHE A 187 TRP 0.014 0.001 TRP A 475 HIS 0.011 0.002 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 ( 9046) covalent geometry : angle 0.60585 / 0.33 (12172) hydrogen bonds : bond 0.04524 / 2.85 ( 495) hydrogen bonds : angle 5.42476 / 3.85 ( 1461) metal coordination : bond 0.10409 / 5.08 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 PHE cc_start: 0.8847 (t80) cc_final: 0.8604 (t80) REVERT: B 18 LEU cc_start: 0.9535 (mt) cc_final: 0.9264 (mt) REVERT: B 20 LEU cc_start: 0.9569 (mt) cc_final: 0.9360 (mt) REVERT: B 22 PHE cc_start: 0.9285 (m-80) cc_final: 0.8997 (m-80) REVERT: B 37 LYS cc_start: 0.8538 (mttt) cc_final: 0.7632 (mmtm) REVERT: B 105 ILE cc_start: 0.8844 (mt) cc_final: 0.8616 (mm) REVERT: B 171 ILE cc_start: 0.8628 (mt) cc_final: 0.8314 (tp) REVERT: B 187 PHE cc_start: 0.7775 (m-80) cc_final: 0.7409 (m-80) REVERT: B 215 ILE cc_start: 0.9137 (pt) cc_final: 0.8863 (pt) REVERT: B 218 ASN cc_start: 0.8983 (m110) cc_final: 0.8697 (m110) REVERT: B 240 ASP cc_start: 0.8341 (p0) cc_final: 0.8127 (p0) REVERT: B 244 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8517 (mt-10) REVERT: B 292 LYS cc_start: 0.8613 (mptt) cc_final: 0.8333 (mttt) REVERT: B 319 PHE cc_start: 0.9047 (t80) cc_final: 0.8784 (t80) REVERT: B 330 MET cc_start: 0.2122 (ppp) cc_final: 0.1770 (ppp) REVERT: B 494 MET cc_start: 0.7905 (ttp) cc_final: 0.7625 (mtp) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.0518 time to fit residues: 8.8105 Evaluate side-chains 99 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 82 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 95 optimal weight: 0.0870 chunk 91 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 21 optimal weight: 0.0370 chunk 57 optimal weight: 0.8980 chunk 35 optimal weight: 0.0670 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.151910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.108159 restraints weight = 12949.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.112256 restraints weight = 8768.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.115110 restraints weight = 6514.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.117236 restraints weight = 5121.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.118791 restraints weight = 4195.834| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6153 moved from start: 0.7136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9050 Z= 0.118 Angle : 0.602 9.622 12172 Z= 0.322 Chirality : 0.043 0.183 1336 Planarity : 0.004 0.040 1488 Dihedral : 4.449 15.996 1156 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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 are not related in a simple way. whole: 0.95 (0.26), residues: 1050 helix: 1.39 (0.21), residues: 604 sheet: -0.25 (0.50), residues: 120 loop : -0.31 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 384 TYR 0.020 0.001 TYR B 441 PHE 0.022 0.001 PHE A 442 TRP 0.006 0.001 TRP B 475 HIS 0.006 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 ( 9046) covalent geometry : angle 0.60214 / 0.32 (12172) hydrogen bonds : bond 0.04364 / 2.75 ( 495) hydrogen bonds : angle 5.23848 / 3.71 ( 1461) metal coordination : bond 0.00271 / 0.14 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.8785 (t80) cc_final: 0.8491 (t80) REVERT: A 18 LEU cc_start: 0.9533 (mt) cc_final: 0.9304 (mt) REVERT: A 20 LEU cc_start: 0.9544 (mt) cc_final: 0.9274 (mt) REVERT: A 22 PHE cc_start: 0.9366 (m-80) cc_final: 0.9085 (m-80) REVERT: A 37 LYS cc_start: 0.8508 (mttt) cc_final: 0.7578 (mmtm) REVERT: A 181 LEU cc_start: 0.8143 (mp) cc_final: 0.7919 (mp) REVERT: A 214 LEU cc_start: 0.9647 (tp) cc_final: 0.9434 (tp) REVERT: A 215 ILE cc_start: 0.9106 (pt) cc_final: 0.8861 (pt) REVERT: A 218 ASN cc_start: 0.9010 (m110) cc_final: 0.8699 (m110) REVERT: A 244 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8529 (mt-10) REVERT: A 287 LYS cc_start: 0.0823 (tptm) cc_final: 0.0229 (tptt) REVERT: A 292 LYS cc_start: 0.8718 (mptt) cc_final: 0.7708 (tttp) REVERT: A 294 ARG cc_start: 0.7629 (mtp180) cc_final: 0.6808 (mtp180) REVERT: A 319 PHE cc_start: 0.8993 (t80) cc_final: 0.8777 (t80) REVERT: A 412 MET cc_start: 0.1460 (ptm) cc_final: 0.1139 (ptm) REVERT: A 435 GLN cc_start: 0.5242 (tm-30) cc_final: 0.4614 (pt0) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.0543 time to fit residues: 8.1872 Evaluate side-chains 104 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 32 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 87 optimal weight: 0.0570 chunk 44 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 82 optimal weight: 0.3980 chunk 49 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 HIS ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.152550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.108601 restraints weight = 12901.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.112540 restraints weight = 8624.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.115371 restraints weight = 6373.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.117051 restraints weight = 5029.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.118754 restraints weight = 4185.079| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 moved from start: 0.7374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9050 Z= 0.117 Angle : 0.594 10.250 12172 Z= 0.319 Chirality : 0.043 0.174 1336 Planarity : 0.004 0.040 1488 Dihedral : 4.350 17.692 1156 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % 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 are not related in a simple way. whole: 0.97 (0.26), residues: 1050 helix: 1.45 (0.21), residues: 600 sheet: -0.15 (0.51), residues: 120 loop : -0.42 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 235 TYR 0.022 0.001 TYR A 130 PHE 0.025 0.001 PHE B 12 TRP 0.005 0.001 TRP B 39 HIS 0.008 0.001 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 ( 9046) covalent geometry : angle 0.59375 / 0.32 (12172) hydrogen bonds : bond 0.04201 / 2.64 ( 495) hydrogen bonds : angle 5.28112 / 3.72 ( 1461) metal coordination : bond 0.00050 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.8894 (t80) cc_final: 0.8636 (t80) REVERT: A 20 LEU cc_start: 0.9559 (mt) cc_final: 0.9315 (mt) REVERT: A 22 PHE cc_start: 0.9341 (m-80) cc_final: 0.9112 (m-80) REVERT: A 37 LYS cc_start: 0.8286 (mttt) cc_final: 0.7375 (mmtm) REVERT: A 214 LEU cc_start: 0.9667 (tp) cc_final: 0.9450 (tp) REVERT: A 215 ILE cc_start: 0.9182 (pt) cc_final: 0.8906 (pt) REVERT: A 216 ILE cc_start: 0.9605 (mt) cc_final: 0.9298 (mt) REVERT: A 218 ASN cc_start: 0.9022 (m110) cc_final: 0.8740 (m110) REVERT: A 244 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8409 (mt-10) REVERT: A 287 LYS cc_start: 0.0634 (tptm) cc_final: 0.0353 (tptt) REVERT: A 292 LYS cc_start: 0.8694 (mptt) cc_final: 0.8469 (mptt) REVERT: A 294 ARG cc_start: 0.7531 (mtp180) cc_final: 0.6623 (mtp180) REVERT: A 314 ILE cc_start: 0.9522 (mm) cc_final: 0.9238 (pt) REVERT: A 319 PHE cc_start: 0.9080 (t80) cc_final: 0.8842 (t80) REVERT: A 412 MET cc_start: 0.1403 (ptm) cc_final: 0.1163 (ptm) REVERT: A 434 MET cc_start: 0.3728 (tmm) cc_final: 0.2578 (ptm) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.0511 time to fit residues: 7.6610 Evaluate side-chains 98 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 77 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 52 optimal weight: 7.9990 chunk 22 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.151217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.106714 restraints weight = 13060.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.110826 restraints weight = 8821.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.113750 restraints weight = 6494.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.115813 restraints weight = 5074.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.117262 restraints weight = 4164.350| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 moved from start: 0.7620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9050 Z= 0.118 Angle : 0.606 8.517 12172 Z= 0.326 Chirality : 0.043 0.193 1336 Planarity : 0.003 0.041 1488 Dihedral : 4.319 17.235 1156 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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 are not related in a simple way. whole: 0.90 (0.26), residues: 1050 helix: 1.38 (0.21), residues: 600 sheet: -0.06 (0.53), residues: 114 loop : -0.48 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 402 TYR 0.016 0.001 TYR A 203 PHE 0.028 0.002 PHE A 119 TRP 0.006 0.001 TRP A 39 HIS 0.005 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 ( 9046) covalent geometry : angle 0.60613 / 0.33 (12172) hydrogen bonds : bond 0.04237 / 2.64 ( 495) hydrogen bonds : angle 5.29362 / 3.72 ( 1461) metal coordination : bond 0.00064 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.8856 (t80) cc_final: 0.8561 (t80) REVERT: A 20 LEU cc_start: 0.9533 (mt) cc_final: 0.9267 (mt) REVERT: A 22 PHE cc_start: 0.9311 (m-80) cc_final: 0.9080 (m-80) REVERT: A 37 LYS cc_start: 0.8330 (mttt) cc_final: 0.7402 (mmtm) REVERT: A 39 TRP cc_start: 0.8561 (m100) cc_final: 0.8065 (m100) REVERT: A 214 LEU cc_start: 0.9642 (tp) cc_final: 0.9420 (tp) REVERT: A 215 ILE cc_start: 0.9214 (pt) cc_final: 0.8934 (pt) REVERT: A 218 ASN cc_start: 0.9125 (m110) cc_final: 0.8782 (m110) REVERT: A 229 LEU cc_start: 0.9442 (tp) cc_final: 0.8935 (pp) REVERT: A 244 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8504 (mt-10) REVERT: A 266 MET cc_start: 0.7468 (ttt) cc_final: 0.6970 (mtp) REVERT: A 287 LYS cc_start: 0.0581 (tptm) cc_final: 0.0304 (tptm) REVERT: A 292 LYS cc_start: 0.8798 (mptt) cc_final: 0.8542 (mttt) REVERT: A 294 ARG cc_start: 0.7589 (mtp180) cc_final: 0.6622 (mtp180) REVERT: A 314 ILE cc_start: 0.9507 (mm) cc_final: 0.9219 (pt) REVERT: A 412 MET cc_start: 0.1329 (ptm) cc_final: 0.1088 (ptm) REVERT: A 434 MET cc_start: 0.3785 (tmm) cc_final: 0.2625 (ptm) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.0562 time to fit residues: 8.1689 Evaluate side-chains 98 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 0.0970 chunk 99 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.151437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.107609 restraints weight = 13125.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.111580 restraints weight = 8836.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.114423 restraints weight = 6507.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.116462 restraints weight = 5055.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.117776 restraints weight = 4147.456| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.7813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9050 Z= 0.119 Angle : 0.617 10.333 12172 Z= 0.329 Chirality : 0.043 0.171 1336 Planarity : 0.003 0.040 1488 Dihedral : 4.284 17.110 1156 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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 are not related in a simple way. whole: 0.85 (0.26), residues: 1050 helix: 1.31 (0.21), residues: 598 sheet: 0.02 (0.54), residues: 114 loop : -0.48 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 384 TYR 0.016 0.001 TYR B 203 PHE 0.015 0.001 PHE B 12 TRP 0.011 0.001 TRP B 475 HIS 0.006 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 ( 9046) covalent geometry : angle 0.61708 / 0.33 (12172) hydrogen bonds : bond 0.04213 / 2.63 ( 495) hydrogen bonds : angle 5.33997 / 3.77 ( 1461) metal coordination : bond 0.00065 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5217 (ptt) cc_final: 0.3351 (pmm) REVERT: B 13 CYS cc_start: 0.9405 (p) cc_final: 0.9133 (m) REVERT: B 16 PHE cc_start: 0.8866 (t80) cc_final: 0.8579 (t80) REVERT: B 18 LEU cc_start: 0.9590 (mt) cc_final: 0.9381 (mt) REVERT: B 20 LEU cc_start: 0.9550 (mt) cc_final: 0.9296 (mt) REVERT: B 22 PHE cc_start: 0.9333 (m-80) cc_final: 0.9056 (m-80) REVERT: B 39 TRP cc_start: 0.8605 (m100) cc_final: 0.8120 (m100) REVERT: B 215 ILE cc_start: 0.9241 (pt) cc_final: 0.8936 (pt) REVERT: B 216 ILE cc_start: 0.9560 (mt) cc_final: 0.9212 (mt) REVERT: B 218 ASN cc_start: 0.9117 (m110) cc_final: 0.8868 (m110) REVERT: B 266 MET cc_start: 0.7406 (ttt) cc_final: 0.6867 (mtp) REVERT: B 287 LYS cc_start: 0.0476 (tptm) cc_final: 0.0192 (tptm) REVERT: B 292 LYS cc_start: 0.8801 (mptt) cc_final: 0.8546 (mttt) REVERT: B 294 ARG cc_start: 0.7532 (mtp180) cc_final: 0.6585 (mtp180) REVERT: B 314 ILE cc_start: 0.9524 (mm) cc_final: 0.9258 (pt) REVERT: B 412 MET cc_start: 0.0990 (ptm) cc_final: 0.0770 (ptm) REVERT: B 434 MET cc_start: 0.3799 (tmm) cc_final: 0.2649 (ptm) REVERT: B 494 MET cc_start: 0.7732 (ptm) cc_final: 0.7332 (ptm) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.0532 time to fit residues: 7.6080 Evaluate side-chains 95 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 66 optimal weight: 2.9990 chunk 79 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 0.0370 chunk 88 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 0.0770 chunk 85 optimal weight: 0.0270 chunk 46 optimal weight: 0.0040 chunk 103 optimal weight: 7.9990 overall best weight: 0.1286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.153547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.109631 restraints weight = 12991.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.113676 restraints weight = 8784.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.116487 restraints weight = 6473.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.118245 restraints weight = 5080.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.119822 restraints weight = 4244.354| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.8144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9050 Z= 0.121 Angle : 0.628 8.623 12172 Z= 0.332 Chirality : 0.044 0.173 1336 Planarity : 0.003 0.040 1488 Dihedral : 4.207 18.439 1156 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 are not related in a simple way. whole: 0.91 (0.26), residues: 1050 helix: 1.43 (0.21), residues: 596 sheet: -0.16 (0.52), residues: 114 loop : -0.52 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 235 TYR 0.013 0.001 TYR B 203 PHE 0.016 0.001 PHE A 12 TRP 0.019 0.001 TRP B 475 HIS 0.013 0.002 HIS A 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 ( 9046) covalent geometry : angle 0.62769 / 0.33 (12172) hydrogen bonds : bond 0.04069 / 2.57 ( 495) hydrogen bonds : angle 5.33208 / 3.77 ( 1461) metal coordination : bond 0.00007 / 0.00 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5312 (ptt) cc_final: 0.3563 (pmm) REVERT: B 13 CYS cc_start: 0.9355 (p) cc_final: 0.9097 (m) REVERT: B 16 PHE cc_start: 0.8826 (t80) cc_final: 0.8527 (t80) REVERT: B 18 LEU cc_start: 0.9558 (mt) cc_final: 0.9350 (mt) REVERT: B 20 LEU cc_start: 0.9533 (mt) cc_final: 0.9236 (mt) REVERT: B 22 PHE cc_start: 0.9278 (m-80) cc_final: 0.9005 (m-80) REVERT: B 39 TRP cc_start: 0.8570 (m100) cc_final: 0.8154 (m100) REVERT: B 215 ILE cc_start: 0.9245 (pt) cc_final: 0.8931 (pt) REVERT: B 216 ILE cc_start: 0.9574 (mt) cc_final: 0.9142 (mt) REVERT: B 218 ASN cc_start: 0.9068 (m110) cc_final: 0.8814 (m110) REVERT: B 247 ARG cc_start: 0.9040 (ttm170) cc_final: 0.8461 (mmt90) REVERT: B 266 MET cc_start: 0.7372 (ttt) cc_final: 0.6857 (mtp) REVERT: B 292 LYS cc_start: 0.8808 (mptt) cc_final: 0.8597 (mttm) REVERT: B 294 ARG cc_start: 0.7510 (mtp180) cc_final: 0.6546 (mtp180) REVERT: B 314 ILE cc_start: 0.9508 (mm) cc_final: 0.9240 (pt) REVERT: B 412 MET cc_start: 0.1032 (ptm) cc_final: 0.0708 (ptm) REVERT: B 434 MET cc_start: 0.3544 (tmm) cc_final: 0.2432 (ptm) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.0583 time to fit residues: 8.4780 Evaluate side-chains 89 residues out of total 496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.0870 chunk 38 optimal weight: 0.0570 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 0.0870 chunk 68 optimal weight: 0.0030 chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 31 optimal weight: 0.0270 chunk 3 optimal weight: 4.9990 chunk 102 optimal weight: 0.0570 chunk 73 optimal weight: 0.9980 overall best weight: 0.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.154738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.111082 restraints weight = 13122.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.115488 restraints weight = 8574.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.118492 restraints weight = 6142.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.120528 restraints weight = 4733.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.122104 restraints weight = 3853.830| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.8445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9050 Z= 0.120 Angle : 0.629 11.572 12172 Z= 0.332 Chirality : 0.044 0.221 1336 Planarity : 0.003 0.040 1488 Dihedral : 4.100 17.300 1156 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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 are not related in a simple way. whole: 0.88 (0.26), residues: 1050 helix: 1.40 (0.21), residues: 598 sheet: -0.21 (0.51), residues: 114 loop : -0.49 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 247 TYR 0.022 0.001 TYR A 203 PHE 0.034 0.002 PHE A 220 TRP 0.021 0.001 TRP A 475 HIS 0.006 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 ( 9046) covalent geometry : angle 0.62874 / 0.33 (12172) hydrogen bonds : bond 0.04174 / 2.60 ( 495) hydrogen bonds : angle 5.32147 / 3.76 ( 1461) metal coordination : bond 0.00020 / 0.01 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1157.38 seconds wall clock time: 20 minutes 54.33 seconds (1254.33 seconds total)