Starting phenix.real_space_refine on Fri Sep 11 07:39:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z2d_14462/09_2026/7z2d_14462.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2d_14462/09_2026/7z2d_14462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z2d_14462/09_2026/7z2d_14462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2d_14462/09_2026/7z2d_14462.map" model { file = "/net/cci-nas-00/data/ceres_data/7z2d_14462/09_2026/7z2d_14462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2d_14462/09_2026/7z2d_14462.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7z2d_14462/09_2026/7z2d_14462.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z2d_14462/09_2026/7z2d_14462.cif" } resolution = 3.38 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= 0.021 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 P 35 5.49 5 S 13 5.16 5 C 5452 2.51 5 N 1432 2.21 5 O 1659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8591 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4450 Classifications: {'peptide': 547} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 508} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3393 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 381} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 720 Classifications: {'DNA': 34, 'RNA': 2} Modifications used: {'5*END': 1, 'rna3p': 2} Link IDs: {'rna3p': 35} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan': 1, ' DA%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'T27': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.59, per 1000 atoms: 0.19 Number of scatterers: 8591 At special positions: 0 Unit cell: (97, 109.61, 100.88, 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) S 13 16.00 P 35 15.00 O 1659 8.00 N 1432 7.00 C 5452 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: 0.84 Conformation dependent library (CDL) restraints added in 272.3 milliseconds 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1804 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 38.0% alpha, 13.0% beta 9 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 33 through 44 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 112 through 117 removed outlier: 3.622A pdb=" N TYR A 115 " --> pdb=" O GLY A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.688A pdb=" N THR A 128 " --> pdb=" O ARG A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix removed outlier: 3.741A pdb=" N GLN A 174 " --> pdb=" O PRO A 170 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 175 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.869A pdb=" N ARG A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N THR A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 201 " --> pdb=" O GLN A 197 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.937A pdb=" N LYS A 223 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 276 through 281 removed outlier: 3.787A pdb=" N LYS A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 296 through 311 removed outlier: 3.637A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 383 removed outlier: 3.568A pdb=" N GLN A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 403 Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.702A pdb=" N ASP A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.928A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.894A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'B' and resid 27 through 43 removed outlier: 3.793A pdb=" N LEU B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 84 Processing helix chain 'B' and resid 84 through 91 removed outlier: 4.149A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU B 89 " --> pdb=" O GLN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 121 through 125 removed outlier: 3.552A pdb=" N ARG B 125 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 154 through 175 removed outlier: 3.893A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 213 Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 277 through 283 removed outlier: 3.581A pdb=" N LEU B 282 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 354 removed outlier: 7.643A pdb=" N LYS A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN A 343 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR A 351 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR A 339 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS A 353 " --> pdb=" O TRP A 337 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP A 337 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 329 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 362 Processing sheet with id=AA4, first strand: chain 'A' and resid 464 through 470 Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AA6, first strand: chain 'B' and resid 60 through 65 removed outlier: 4.431A pdb=" N LYS B 65 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LYS B 70 " --> pdb=" O LYS B 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 179 through 183 Processing sheet with id=AA8, first strand: chain 'B' and resid 347 through 354 removed outlier: 8.273A pdb=" N ASN B 348 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLN B 343 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLN B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN B 340 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU B 328 " --> pdb=" O GLN B 340 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) 288 hydrogen bonds defined for protein. 783 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 1.39 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1342 1.27 - 1.40: 2187 1.40 - 1.54: 5116 1.54 - 1.67: 220 1.67 - 1.81: 25 Bond restraints: 8890 Sorted by residual: bond pdb=" O3' DC E 3 " pdb=" P OMC E 4 " ideal model delta sigma weight residual 1.607 1.700 -0.093 1.20e-02 6.94e+03 5.96e+01 bond pdb=" C20 T27 A 601 " pdb=" C22 T27 A 601 " ideal model delta sigma weight residual 1.419 1.525 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C13 T27 A 601 " pdb=" C19 T27 A 601 " ideal model delta sigma weight residual 1.422 1.524 -0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" C11 T27 A 601 " pdb=" N1 T27 A 601 " ideal model delta sigma weight residual 1.351 1.453 -0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C12 T27 A 601 " pdb=" N4 T27 A 601 " ideal model delta sigma weight residual 1.372 1.455 -0.083 2.00e-02 2.50e+03 1.74e+01 ... (remaining 8885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 12123 2.98 - 5.95: 99 5.95 - 8.93: 7 8.93 - 11.91: 1 11.91 - 14.88: 1 Bond angle restraints: 12231 Sorted by residual: angle pdb=" C2 T27 A 601 " pdb=" C1 T27 A 601 " pdb=" C7 T27 A 601 " ideal model delta sigma weight residual 120.40 105.52 14.88 3.00e+00 1.11e-01 2.46e+01 angle pdb=" N3 DT E 0 " pdb=" C4 DT E 0 " pdb=" O4 DT E 0 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT E 18 " pdb=" C4 DT E 18 " pdb=" O4 DT E 18 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT E -1 " pdb=" C4 DT E -1 " pdb=" O4 DT E -1 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT E 17 " pdb=" C4 DT E 17 " pdb=" O4 DT E 17 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (remaining 12226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4482 17.84 - 35.68: 569 35.68 - 53.52: 111 53.52 - 71.36: 36 71.36 - 89.20: 9 Dihedral angle restraints: 5207 sinusoidal: 2409 harmonic: 2798 Sorted by residual: dihedral pdb=" CA PRO B 4 " pdb=" CB PRO B 4 " pdb=" CG PRO B 4 " pdb=" CD PRO B 4 " ideal model delta sinusoidal sigma weight residual 38.00 115.32 -77.32 1 2.00e+01 2.50e-03 1.87e+01 dihedral pdb=" CA GLU A 224 " pdb=" C GLU A 224 " pdb=" N PRO A 225 " pdb=" CA PRO A 225 " ideal model delta harmonic sigma weight residual 180.00 160.54 19.46 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ILE A 309 " pdb=" C ILE A 309 " pdb=" N LEU A 310 " pdb=" CA LEU A 310 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 5204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1176 0.076 - 0.152: 148 0.152 - 0.229: 3 0.229 - 0.305: 1 0.305 - 0.381: 1 Chirality restraints: 1329 Sorted by residual: chirality pdb=" C4' DA E 25 " pdb=" C5' DA E 25 " pdb=" O4' DA E 25 " pdb=" C3' DA E 25 " both_signs ideal model delta sigma weight residual False -2.53 -2.15 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C3' DT E 8 " pdb=" C4' DT E 8 " pdb=" O3' DT E 8 " pdb=" C2' DT E 8 " both_signs ideal model delta sigma weight residual False -2.73 -2.47 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C3' DA E 26 " pdb=" C4' DA E 26 " pdb=" O3' DA E 26 " pdb=" C2' DA E 26 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1326 not shown) Planarity restraints: 1421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 420 " 0.046 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO A 421 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 421 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 421 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 18 " -0.038 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO A 19 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 19 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 19 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 467 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO A 468 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 468 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 468 " -0.026 5.00e-02 4.00e+02 ... (remaining 1418 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 454 2.73 - 3.27: 7951 3.27 - 3.81: 13893 3.81 - 4.36: 16752 4.36 - 4.90: 28425 Nonbonded interactions: 67475 Sorted by model distance: nonbonded pdb=" NH2 ARG B 356 " pdb=" O ALA B 360 " model vdw 2.187 3.120 nonbonded pdb=" OH TYR B 354 " pdb=" OE2 GLU B 378 " model vdw 2.196 3.040 nonbonded pdb=" NZ LYS B 73 " pdb=" OH TYR B 146 " model vdw 2.216 3.120 nonbonded pdb=" NZ LYS B 366 " pdb=" OE2 GLU B 370 " model vdw 2.221 3.120 nonbonded pdb=" OE2 GLU A 328 " pdb=" OH TYR A 342 " model vdw 2.229 3.040 ... (remaining 67470 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 9.040 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 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 : 0.004 0.106 8890 Z= 0.255 Angle : 0.665 14.883 12231 Z= 0.378 Chirality : 0.046 0.381 1329 Planarity : 0.005 0.070 1421 Dihedral : 16.324 89.196 3403 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.02 (0.28), residues: 951 helix: 1.36 (0.32), residues: 307 sheet: 0.11 (0.42), residues: 157 loop : -0.97 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 83 TYR 0.013 0.001 TYR A 319 PHE 0.010 0.001 PHE B 130 TRP 0.019 0.001 TRP A 402 HIS 0.006 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.26 ( 8890) covalent geometry : angle 0.66486 / 0.38 (12231) hydrogen bonds : bond 0.13935 / 8.57 ( 312) hydrogen bonds : angle 5.84384 / 4.14 ( 831) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.279 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.0887 time to fit residues: 14.9431 Evaluate side-chains 96 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 40.0000 chunk 53 optimal weight: 40.0000 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 332 GLN B 182 GLN B 207 GLN B 367 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.218619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.183614 restraints weight = 9594.378| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 1.83 r_work: 0.3850 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8890 Z= 0.177 Angle : 0.605 6.517 12231 Z= 0.319 Chirality : 0.045 0.167 1329 Planarity : 0.005 0.062 1421 Dihedral : 14.449 82.211 1376 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.93 % Allowed : 6.52 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.28 (0.28), residues: 951 helix: 1.05 (0.30), residues: 320 sheet: -0.40 (0.40), residues: 170 loop : -0.96 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 83 TYR 0.017 0.002 TYR B 144 PHE 0.013 0.001 PHE B 130 TRP 0.018 0.002 TRP A 402 HIS 0.004 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 8890) covalent geometry : angle 0.60493 / 0.32 (12231) hydrogen bonds : bond 0.04588 / 2.89 ( 312) hydrogen bonds : angle 4.36328 / 3.05 ( 831) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.248 Fit side-chains REVERT: A 516 GLU cc_start: 0.6623 (tp30) cc_final: 0.5547 (pm20) outliers start: 8 outliers final: 6 residues processed: 113 average time/residue: 0.0901 time to fit residues: 14.2006 Evaluate side-chains 102 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 131 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 26 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN A 334 GLN B 54 ASN B 367 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.212476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.175356 restraints weight = 9586.131| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 2.00 r_work: 0.3751 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8890 Z= 0.184 Angle : 0.600 5.887 12231 Z= 0.318 Chirality : 0.044 0.149 1329 Planarity : 0.005 0.058 1421 Dihedral : 14.705 82.849 1376 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.63 % Allowed : 10.13 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.43 (0.28), residues: 951 helix: 0.92 (0.30), residues: 322 sheet: -0.50 (0.39), residues: 168 loop : -1.04 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 277 TYR 0.020 0.002 TYR B 144 PHE 0.012 0.002 PHE B 130 TRP 0.019 0.002 TRP A 402 HIS 0.004 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 ( 8890) covalent geometry : angle 0.60032 / 0.32 (12231) hydrogen bonds : bond 0.04302 / 2.74 ( 312) hydrogen bonds : angle 4.40216 / 3.09 ( 831) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.187 Fit side-chains REVERT: A 47 ILE cc_start: 0.7557 (mm) cc_final: 0.7355 (mm) REVERT: A 516 GLU cc_start: 0.6598 (tp30) cc_final: 0.5527 (pm20) outliers start: 14 outliers final: 9 residues processed: 107 average time/residue: 0.0798 time to fit residues: 11.8940 Evaluate side-chains 105 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 0.3980 chunk 89 optimal weight: 8.9990 chunk 3 optimal weight: 30.0000 chunk 17 optimal weight: 6.9990 chunk 96 optimal weight: 50.0000 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN A 334 GLN B 367 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.210783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.173330 restraints weight = 9735.744| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 2.21 r_work: 0.3698 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8890 Z= 0.174 Angle : 0.588 6.280 12231 Z= 0.311 Chirality : 0.043 0.149 1329 Planarity : 0.005 0.055 1421 Dihedral : 14.816 82.732 1376 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.40 % Allowed : 12.81 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.50 (0.28), residues: 951 helix: 0.96 (0.30), residues: 322 sheet: -0.80 (0.38), residues: 176 loop : -1.04 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 358 TYR 0.020 0.002 TYR A 319 PHE 0.011 0.002 PHE A 346 TRP 0.019 0.002 TRP A 402 HIS 0.004 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 8890) covalent geometry : angle 0.58836 / 0.31 (12231) hydrogen bonds : bond 0.04033 / 2.57 ( 312) hydrogen bonds : angle 4.34878 / 3.05 ( 831) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.283 Fit side-chains REVERT: A 516 GLU cc_start: 0.6683 (tp30) cc_final: 0.5647 (pm20) outliers start: 12 outliers final: 10 residues processed: 111 average time/residue: 0.0913 time to fit residues: 14.0715 Evaluate side-chains 105 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 30.0000 chunk 45 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 2 optimal weight: 0.0970 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 96 optimal weight: 50.0000 chunk 30 optimal weight: 10.0000 overall best weight: 5.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 367 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.211017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.174255 restraints weight = 9759.402| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.10 r_work: 0.3691 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8890 Z= 0.200 Angle : 0.615 6.745 12231 Z= 0.325 Chirality : 0.044 0.154 1329 Planarity : 0.006 0.055 1421 Dihedral : 14.942 82.817 1376 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.98 % Allowed : 13.85 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.64 (0.28), residues: 951 helix: 0.82 (0.30), residues: 322 sheet: -0.85 (0.38), residues: 176 loop : -1.11 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 358 TYR 0.020 0.002 TYR B 144 PHE 0.013 0.002 PHE B 130 TRP 0.020 0.002 TRP A 402 HIS 0.006 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 ( 8890) covalent geometry : angle 0.61479 / 0.32 (12231) hydrogen bonds : bond 0.04216 / 2.72 ( 312) hydrogen bonds : angle 4.43883 / 3.13 ( 831) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.319 Fit side-chains REVERT: A 47 ILE cc_start: 0.7578 (mm) cc_final: 0.7069 (mt) REVERT: A 516 GLU cc_start: 0.6680 (tp30) cc_final: 0.5645 (pm20) outliers start: 17 outliers final: 13 residues processed: 115 average time/residue: 0.0804 time to fit residues: 13.1551 Evaluate side-chains 109 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 73 optimal weight: 7.9990 chunk 62 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 97 optimal weight: 40.0000 chunk 57 optimal weight: 9.9990 chunk 87 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 242 GLN B 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.211329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.174538 restraints weight = 9662.265| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.08 r_work: 0.3738 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8890 Z= 0.186 Angle : 0.607 7.458 12231 Z= 0.320 Chirality : 0.044 0.150 1329 Planarity : 0.005 0.055 1421 Dihedral : 14.925 82.811 1376 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.86 % Allowed : 15.72 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.63 (0.28), residues: 951 helix: 0.87 (0.30), residues: 322 sheet: -0.89 (0.38), residues: 176 loop : -1.13 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 358 TYR 0.018 0.002 TYR B 144 PHE 0.011 0.002 PHE B 130 TRP 0.020 0.002 TRP A 402 HIS 0.005 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 ( 8890) covalent geometry : angle 0.60737 / 0.32 (12231) hydrogen bonds : bond 0.04077 / 2.64 ( 312) hydrogen bonds : angle 4.41728 / 3.11 ( 831) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.210 Fit side-chains REVERT: A 47 ILE cc_start: 0.7618 (mm) cc_final: 0.7160 (mt) REVERT: A 516 GLU cc_start: 0.6656 (tp30) cc_final: 0.5651 (pm20) outliers start: 16 outliers final: 13 residues processed: 113 average time/residue: 0.0880 time to fit residues: 13.8992 Evaluate side-chains 106 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 27 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 96 optimal weight: 50.0000 chunk 67 optimal weight: 1.9990 chunk 60 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 80 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 367 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.211282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.174100 restraints weight = 9810.427| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.04 r_work: 0.3717 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8890 Z= 0.190 Angle : 0.610 7.023 12231 Z= 0.322 Chirality : 0.044 0.153 1329 Planarity : 0.006 0.055 1421 Dihedral : 14.885 82.794 1376 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.21 % Allowed : 16.07 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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 (0.28), residues: 951 helix: 0.86 (0.30), residues: 322 sheet: -0.94 (0.38), residues: 176 loop : -1.15 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 358 TYR 0.023 0.002 TYR A 319 PHE 0.011 0.002 PHE B 130 TRP 0.020 0.002 TRP A 402 HIS 0.006 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 ( 8890) covalent geometry : angle 0.61039 / 0.32 (12231) hydrogen bonds : bond 0.04099 / 2.65 ( 312) hydrogen bonds : angle 4.43490 / 3.11 ( 831) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.314 Fit side-chains REVERT: A 47 ILE cc_start: 0.7620 (mm) cc_final: 0.7170 (mt) REVERT: A 514 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6413 (pt0) REVERT: A 516 GLU cc_start: 0.6653 (tp30) cc_final: 0.5652 (pm20) REVERT: B 181 TYR cc_start: 0.7753 (t80) cc_final: 0.7408 (t80) outliers start: 19 outliers final: 16 residues processed: 117 average time/residue: 0.0960 time to fit residues: 15.8072 Evaluate side-chains 110 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 73 optimal weight: 0.3980 chunk 76 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 GLN B 207 GLN B 367 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.212636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.174833 restraints weight = 9626.440| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.05 r_work: 0.3783 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8890 Z= 0.145 Angle : 0.582 7.506 12231 Z= 0.307 Chirality : 0.043 0.145 1329 Planarity : 0.005 0.054 1421 Dihedral : 14.784 81.834 1376 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.75 % Allowed : 17.23 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.49 (0.28), residues: 951 helix: 1.04 (0.30), residues: 322 sheet: -0.81 (0.39), residues: 176 loop : -1.10 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 284 TYR 0.014 0.001 TYR A 144 PHE 0.010 0.001 PHE A 227 TRP 0.020 0.001 TRP A 402 HIS 0.004 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 8890) covalent geometry : angle 0.58197 / 0.31 (12231) hydrogen bonds : bond 0.03688 / 2.37 ( 312) hydrogen bonds : angle 4.30719 / 3.01 ( 831) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.314 Fit side-chains REVERT: A 47 ILE cc_start: 0.7571 (mm) cc_final: 0.7121 (mt) REVERT: A 516 GLU cc_start: 0.6624 (tp30) cc_final: 0.5634 (pm20) REVERT: B 181 TYR cc_start: 0.7688 (t80) cc_final: 0.7374 (t80) outliers start: 15 outliers final: 15 residues processed: 112 average time/residue: 0.0932 time to fit residues: 14.7415 Evaluate side-chains 110 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 97 optimal weight: 40.0000 chunk 93 optimal weight: 0.2980 chunk 25 optimal weight: 9.9990 chunk 2 optimal weight: 30.0000 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 207 GLN B 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.212586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.174656 restraints weight = 9660.317| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.01 r_work: 0.3769 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8890 Z= 0.147 Angle : 0.579 7.790 12231 Z= 0.305 Chirality : 0.043 0.145 1329 Planarity : 0.005 0.054 1421 Dihedral : 14.733 81.099 1376 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.75 % Allowed : 17.11 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.48 (0.28), residues: 951 helix: 1.12 (0.30), residues: 320 sheet: -0.85 (0.38), residues: 178 loop : -1.12 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 358 TYR 0.014 0.001 TYR B 144 PHE 0.010 0.001 PHE A 227 TRP 0.020 0.001 TRP A 402 HIS 0.004 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 8890) covalent geometry : angle 0.57894 / 0.30 (12231) hydrogen bonds : bond 0.03649 / 2.34 ( 312) hydrogen bonds : angle 4.27219 / 2.99 ( 831) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.326 Fit side-chains REVERT: A 47 ILE cc_start: 0.7565 (mm) cc_final: 0.7106 (mt) REVERT: A 516 GLU cc_start: 0.6609 (tp30) cc_final: 0.5634 (pm20) REVERT: B 181 TYR cc_start: 0.7678 (t80) cc_final: 0.7391 (t80) REVERT: B 242 GLN cc_start: 0.6668 (mm110) cc_final: 0.6468 (mm-40) outliers start: 15 outliers final: 14 residues processed: 114 average time/residue: 0.0927 time to fit residues: 15.0625 Evaluate side-chains 111 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 69 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 48 optimal weight: 0.1980 chunk 64 optimal weight: 7.9990 chunk 96 optimal weight: 50.0000 chunk 19 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 overall best weight: 5.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 367 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.210540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.173816 restraints weight = 9719.849| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.04 r_work: 0.3730 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8890 Z= 0.206 Angle : 0.638 7.791 12231 Z= 0.336 Chirality : 0.045 0.155 1329 Planarity : 0.006 0.054 1421 Dihedral : 14.867 82.081 1376 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 1.51 % Allowed : 17.46 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.68 (0.28), residues: 951 helix: 0.88 (0.30), residues: 322 sheet: -0.89 (0.39), residues: 176 loop : -1.22 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 358 TYR 0.020 0.002 TYR B 144 PHE 0.013 0.002 PHE B 130 TRP 0.017 0.002 TRP A 402 HIS 0.005 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 ( 8890) covalent geometry : angle 0.63769 / 0.34 (12231) hydrogen bonds : bond 0.04153 / 2.71 ( 312) hydrogen bonds : angle 4.45715 / 3.13 ( 831) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.362 Fit side-chains REVERT: A 47 ILE cc_start: 0.7640 (mm) cc_final: 0.7197 (mt) REVERT: A 516 GLU cc_start: 0.6652 (tp30) cc_final: 0.5633 (pm20) REVERT: B 181 TYR cc_start: 0.7709 (t80) cc_final: 0.7388 (t80) outliers start: 13 outliers final: 13 residues processed: 108 average time/residue: 0.0959 time to fit residues: 14.3284 Evaluate side-chains 107 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 12 optimal weight: 20.0000 chunk 44 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 20.0000 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 242 GLN B 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.212744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.176226 restraints weight = 9664.574| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.04 r_work: 0.3779 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8890 Z= 0.138 Angle : 0.582 7.849 12231 Z= 0.306 Chirality : 0.042 0.143 1329 Planarity : 0.005 0.053 1421 Dihedral : 14.780 80.891 1376 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.75 % Allowed : 17.69 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.50 (0.28), residues: 951 helix: 1.08 (0.30), residues: 322 sheet: -0.84 (0.38), residues: 176 loop : -1.13 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 358 TYR 0.014 0.001 TYR A 115 PHE 0.009 0.001 PHE A 77 TRP 0.021 0.001 TRP A 402 HIS 0.004 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 8890) covalent geometry : angle 0.58195 / 0.31 (12231) hydrogen bonds : bond 0.03586 / 2.30 ( 312) hydrogen bonds : angle 4.28229 / 2.99 ( 831) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1750.53 seconds wall clock time: 30 minutes 49.49 seconds (1849.49 seconds total)