Starting phenix.real_space_refine on Tue Aug 4 22:49:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i1z_52577/08_2026/9i1z_52577.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i1z_52577/08_2026/9i1z_52577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9i1z_52577/08_2026/9i1z_52577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i1z_52577/08_2026/9i1z_52577.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i1z_52577/08_2026/9i1z_52577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i1z_52577/08_2026/9i1z_52577.map" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.036 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 S 25 5.16 5 C 4657 2.51 5 N 1165 2.21 5 O 1278 1.98 5 H 10 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7135 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3562 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 458, 3553 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 438} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 458, 3553 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 438} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 3634 Chain: "C" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3549 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 3 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: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'NH3': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER B 131 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 131 " occ=0.50 Time building chain proxies: 2.27, per 1000 atoms: 0.32 Number of scatterers: 7135 At special positions: 0 Unit cell: (97.2084, 88.9704, 116.98, 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 25 16.00 O 1278 8.00 N 1165 7.00 C 4657 6.00 H 10 1.00 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: 0.59 Conformation dependent library (CDL) restraints added in 575.8 milliseconds 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 3 sheets defined 58.9% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'B' and resid 38 through 49 removed outlier: 3.594A pdb=" N ASN B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 60 through 65 removed outlier: 4.060A pdb=" N TYR B 65 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 97 Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 114 through 126 Processing helix chain 'B' and resid 126 through 144 removed outlier: 3.619A pdb=" N VAL B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 161 Processing helix chain 'B' and resid 162 through 176 removed outlier: 3.809A pdb=" N CYS B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR B 176 " --> pdb=" O ILE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 209 removed outlier: 3.521A pdb=" N LEU B 182 " --> pdb=" O LYS B 178 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN B 208 " --> pdb=" O VAL B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 239 removed outlier: 3.570A pdb=" N TYR B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 252 removed outlier: 3.673A pdb=" N THR B 249 " --> pdb=" O ASN B 246 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLU B 250 " --> pdb=" O TYR B 247 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE B 252 " --> pdb=" O THR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 285 removed outlier: 3.600A pdb=" N MET B 267 " --> pdb=" O ILE B 263 " (cutoff:3.500A) Proline residue: B 268 - end of helix Processing helix chain 'B' and resid 286 through 293 Processing helix chain 'B' and resid 295 through 304 Processing helix chain 'B' and resid 305 through 309 removed outlier: 3.941A pdb=" N PHE B 308 " --> pdb=" O PHE B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 341 removed outlier: 3.557A pdb=" N LEU B 314 " --> pdb=" O TRP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 374 removed outlier: 3.697A pdb=" N ILE B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 removed outlier: 3.617A pdb=" N ASN B 383 " --> pdb=" O GLN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 404 removed outlier: 3.794A pdb=" N TRP B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN B 400 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 439 removed outlier: 4.125A pdb=" N ILE B 422 " --> pdb=" O VAL B 418 " (cutoff:3.500A) Proline residue: B 435 - end of helix Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 453 through 460 Processing helix chain 'B' and resid 471 through 483 removed outlier: 4.188A pdb=" N ILE B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.712A pdb=" N ALA C 174 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 199 removed outlier: 3.784A pdb=" N TRP C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA C 199 " --> pdb=" O LEU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 206 removed outlier: 4.091A pdb=" N ILE C 205 " --> pdb=" O ALA C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 222 removed outlier: 3.948A pdb=" N THR C 222 " --> pdb=" O TRP C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 246 Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 287 through 302 Processing helix chain 'C' and resid 325 through 342 Processing helix chain 'C' and resid 350 through 354 Processing helix chain 'C' and resid 356 through 372 removed outlier: 3.674A pdb=" N SER C 372 " --> pdb=" O THR C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 395 removed outlier: 3.633A pdb=" N ILE C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER C 395 " --> pdb=" O SER C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 427 Processing helix chain 'C' and resid 441 through 445 Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 450 through 461 removed outlier: 3.626A pdb=" N GLN C 455 " --> pdb=" O LEU C 451 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU C 456 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET C 457 " --> pdb=" O LEU C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 474 Processing helix chain 'C' and resid 505 through 508 removed outlier: 3.503A pdb=" N MET C 508 " --> pdb=" O SER C 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 505 through 508' Processing helix chain 'C' and resid 509 through 514 Processing helix chain 'C' and resid 519 through 534 Processing helix chain 'C' and resid 534 through 540 Processing sheet with id=AA1, first strand: chain 'C' and resid 225 through 227 removed outlier: 3.800A pdb=" N PHE C 467 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 466 " --> pdb=" O TRP C 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 307 through 308 Processing sheet with id=AA3, first strand: chain 'C' and resid 541 through 544 removed outlier: 6.756A pdb=" N LEU C 624 " --> pdb=" O LEU C 597 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 1020 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: 1.12 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 10 1.05 - 1.24: 962 1.24 - 1.43: 2122 1.43 - 1.62: 4174 1.62 - 1.81: 36 Bond restraints: 7304 Sorted by residual: bond pdb=" N GLN B 601 " pdb=" H3 GLN B 601 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N GLN B 601 " pdb=" H2 GLN B 601 " ideal model delta sigma weight residual 0.890 0.959 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" N GLN B 601 " pdb=" CA GLN B 601 " ideal model delta sigma weight residual 1.491 1.457 0.034 2.10e-02 2.27e+03 2.59e+00 bond pdb=" N GLN B 601 " pdb=" H1 GLN B 601 " ideal model delta sigma weight residual 0.890 0.860 0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" CG1 ILE B 135 " pdb=" CD1 ILE B 135 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.33e+00 ... (remaining 7299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.51: 9941 11.51 - 23.02: 0 23.02 - 34.53: 1 34.53 - 46.04: 0 46.04 - 57.55: 1 Bond angle restraints: 9943 Sorted by residual: angle pdb=" H1 GLN B 601 " pdb=" N GLN B 601 " pdb=" H2 GLN B 601 " ideal model delta sigma weight residual 109.47 51.92 57.55 3.00e+00 1.11e-01 3.68e+02 angle pdb=" H1 GLN B 601 " pdb=" N GLN B 601 " pdb=" H3 GLN B 601 " ideal model delta sigma weight residual 109.47 136.36 -26.89 3.00e+00 1.11e-01 8.03e+01 angle pdb=" N ALA B 347 " pdb=" CA ALA B 347 " pdb=" C ALA B 347 " ideal model delta sigma weight residual 114.56 109.58 4.98 1.27e+00 6.20e-01 1.54e+01 angle pdb=" N ILE B 135 " pdb=" CA ILE B 135 " pdb=" CB ILE B 135 " ideal model delta sigma weight residual 110.54 115.31 -4.77 1.36e+00 5.41e-01 1.23e+01 angle pdb=" CA ILE B 135 " pdb=" CB ILE B 135 " pdb=" CG1 ILE B 135 " ideal model delta sigma weight residual 110.40 116.27 -5.87 1.70e+00 3.46e-01 1.19e+01 ... (remaining 9938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 3607 16.94 - 33.88: 487 33.88 - 50.82: 148 50.82 - 67.76: 27 67.76 - 84.70: 8 Dihedral angle restraints: 4277 sinusoidal: 1643 harmonic: 2634 Sorted by residual: dihedral pdb=" CA LEU B 125 " pdb=" C LEU B 125 " pdb=" N ILE B 126 " pdb=" CA ILE B 126 " ideal model delta harmonic sigma weight residual -180.00 -162.11 -17.89 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA TYR B 176 " pdb=" C TYR B 176 " pdb=" N VAL B 177 " pdb=" CA VAL B 177 " ideal model delta harmonic sigma weight residual 180.00 163.63 16.37 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA GLN C 455 " pdb=" CB GLN C 455 " pdb=" CG GLN C 455 " pdb=" CD GLN C 455 " ideal model delta sinusoidal sigma weight residual -180.00 -120.10 -59.90 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 761 0.029 - 0.058: 267 0.058 - 0.087: 77 0.087 - 0.116: 32 0.116 - 0.145: 3 Chirality restraints: 1140 Sorted by residual: chirality pdb=" CB ILE B 135 " pdb=" CA ILE B 135 " pdb=" CG1 ILE B 135 " pdb=" CG2 ILE B 135 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA TYR B 482 " pdb=" N TYR B 482 " pdb=" C TYR B 482 " pdb=" CB TYR B 482 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA ILE C 303 " pdb=" N ILE C 303 " pdb=" C ILE C 303 " pdb=" CB ILE C 303 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.48e-01 ... (remaining 1137 not shown) Planarity restraints: 1242 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 176 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.73e+00 pdb=" N PRO C 177 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 177 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 177 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 340 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.34e+00 pdb=" CD GLN C 340 " -0.020 2.00e-02 2.50e+03 pdb=" OE1 GLN C 340 " 0.008 2.00e-02 2.50e+03 pdb=" NE2 GLN C 340 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 58 " -0.019 5.00e-02 4.00e+02 2.81e-02 1.26e+00 pdb=" N PRO B 59 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 59 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 59 " -0.016 5.00e-02 4.00e+02 ... (remaining 1239 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.61: 66 2.61 - 3.11: 5779 3.11 - 3.61: 8871 3.61 - 4.10: 11539 4.10 - 4.60: 18509 Nonbonded interactions: 44764 Sorted by model distance: nonbonded pdb=" H2 GLN B 601 " pdb=" HA GLN B 601 " model vdw 2.117 1.816 nonbonded pdb=" HB2 GLN B 601 " pdb=" HG3 GLN B 601 " model vdw 2.146 1.952 nonbonded pdb=" H1 GLN B 601 " pdb=" HA GLN B 601 " model vdw 2.193 1.816 nonbonded pdb=" O ASN B 49 " pdb=" H2 GLN B 601 " model vdw 2.290 2.450 nonbonded pdb=" O SER B 240 " pdb=" H2 GLN B 601 " model vdw 2.322 2.450 ... (remaining 44759 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=0.50 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: 1.600 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: 0.100 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.860 Find NCS groups from input model: 0.050 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 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 : 0.002 0.045 7294 Z= 0.089 Angle : 0.440 5.875 9921 Z= 0.243 Chirality : 0.035 0.145 1140 Planarity : 0.003 0.033 1242 Dihedral : 17.203 84.698 2584 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 38.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.93 % Allowed : 29.06 % Favored : 67.02 % 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: 0.32 (0.30), residues: 904 helix: 1.45 (0.26), residues: 482 sheet: -1.93 (0.66), residues: 64 loop : -1.08 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 626 TYR 0.016 0.001 TYR B 482 PHE 0.013 0.001 PHE B 117 TRP 0.015 0.001 TRP C 431 HIS 0.001 0.000 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.09 ( 7294) covalent geometry : angle 0.44023 / 0.24 ( 9921) hydrogen bonds : bond 0.14624 / 10.09 ( 360) hydrogen bonds : angle 6.39930 / 4.42 ( 1020) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.159 Fit side-chains REVERT: B 111 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.7061 (t80) REVERT: B 126 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7824 (tp) REVERT: B 361 SER cc_start: 0.8929 (t) cc_final: 0.8495 (p) REVERT: C 202 VAL cc_start: 0.7236 (OUTLIER) cc_final: 0.6371 (t) REVERT: C 242 LEU cc_start: 0.7935 (pp) cc_final: 0.7722 (pp) REVERT: C 277 ASP cc_start: 0.7614 (t0) cc_final: 0.7381 (t0) REVERT: C 339 LEU cc_start: 0.5844 (OUTLIER) cc_final: 0.5617 (tt) REVERT: C 539 HIS cc_start: 0.7783 (OUTLIER) cc_final: 0.7077 (t-90) outliers start: 29 outliers final: 22 residues processed: 114 average time/residue: 0.0767 time to fit residues: 11.9410 Evaluate side-chains 118 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 91 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 396 SER Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 320 PHE Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 539 HIS Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 623 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.0270 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.261228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.216275 restraints weight = 18198.022| |-----------------------------------------------------------------------------| r_work (start): 0.4417 rms_B_bonded: 5.97 r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4417 r_free = 0.4417 target_work(ls_wunit_k1) = 0.216 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4416 r_free = 0.4416 target_work(ls_wunit_k1) = 0.216 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.4416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.0622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7294 Z= 0.125 Angle : 0.461 5.196 9921 Z= 0.245 Chirality : 0.037 0.137 1140 Planarity : 0.003 0.030 1242 Dihedral : 6.550 57.842 1032 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 39.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.89 % Allowed : 26.44 % Favored : 67.67 % 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: 0.24 (0.29), residues: 904 helix: 1.48 (0.25), residues: 485 sheet: -1.95 (0.66), residues: 64 loop : -1.29 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 626 TYR 0.019 0.001 TYR B 482 PHE 0.015 0.001 PHE B 424 TRP 0.015 0.001 TRP C 431 HIS 0.001 0.000 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 7294) covalent geometry : angle 0.46057 / 0.25 ( 9921) hydrogen bonds : bond 0.03916 / 2.60 ( 360) hydrogen bonds : angle 4.63094 / 3.19 ( 1020) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 88 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: B 111 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.6865 (t80) REVERT: B 361 SER cc_start: 0.8746 (t) cc_final: 0.8318 (p) REVERT: C 204 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7086 (mm) REVERT: C 242 LEU cc_start: 0.8184 (pp) cc_final: 0.7965 (pp) REVERT: C 539 HIS cc_start: 0.7716 (OUTLIER) cc_final: 0.7120 (t-90) REVERT: C 604 ARG cc_start: 0.5576 (mmt180) cc_final: 0.4976 (mtt-85) outliers start: 45 outliers final: 30 residues processed: 120 average time/residue: 0.0761 time to fit residues: 12.7341 Evaluate side-chains 118 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 539 HIS Chi-restraints excluded: chain C residue 555 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 82 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.254079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.206858 restraints weight = 17276.840| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 6.05 r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4325 r_free = 0.4325 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4325 r_free = 0.4325 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 7294 Z= 0.239 Angle : 0.616 6.446 9921 Z= 0.324 Chirality : 0.042 0.154 1140 Planarity : 0.004 0.030 1242 Dihedral : 5.923 57.990 997 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 40.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 7.20 % Allowed : 26.31 % Favored : 66.49 % 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: -0.59 (0.28), residues: 904 helix: 0.58 (0.24), residues: 493 sheet: -2.13 (0.64), residues: 64 loop : -1.38 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 626 TYR 0.025 0.003 TYR B 482 PHE 0.021 0.002 PHE B 424 TRP 0.021 0.002 TRP C 431 HIS 0.004 0.001 HIS B 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.24 ( 7294) covalent geometry : angle 0.61560 / 0.32 ( 9921) hydrogen bonds : bond 0.04782 / 3.14 ( 360) hydrogen bonds : angle 4.93973 / 3.44 ( 1020) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 86 time to evaluate : 0.206 Fit side-chains REVERT: B 111 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6751 (t80) REVERT: B 361 SER cc_start: 0.8769 (t) cc_final: 0.8383 (p) REVERT: C 172 LYS cc_start: 0.5895 (OUTLIER) cc_final: 0.5263 (tppt) REVERT: C 262 LEU cc_start: 0.7892 (tt) cc_final: 0.7674 (tt) REVERT: C 295 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7058 (tp) REVERT: C 539 HIS cc_start: 0.7937 (OUTLIER) cc_final: 0.7429 (t-90) outliers start: 55 outliers final: 36 residues processed: 124 average time/residue: 0.0729 time to fit residues: 12.6527 Evaluate side-chains 122 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 82 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 539 HIS Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 623 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 78 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 30.0000 chunk 49 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.260842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.215458 restraints weight = 19061.959| |-----------------------------------------------------------------------------| r_work (start): 0.4409 rms_B_bonded: 6.13 r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4409 r_free = 0.4409 target_work(ls_wunit_k1) = 0.215 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4409 r_free = 0.4409 target_work(ls_wunit_k1) = 0.215 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.4409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7294 Z= 0.100 Angle : 0.435 4.969 9921 Z= 0.232 Chirality : 0.036 0.149 1140 Planarity : 0.003 0.024 1242 Dihedral : 5.586 58.139 997 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 40.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.76 % Allowed : 28.40 % Favored : 65.84 % 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: -0.01 (0.29), residues: 904 helix: 1.19 (0.25), residues: 488 sheet: -2.00 (0.67), residues: 64 loop : -1.31 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 626 TYR 0.017 0.001 TYR B 482 PHE 0.015 0.001 PHE B 117 TRP 0.013 0.001 TRP C 431 HIS 0.002 0.000 HIS C 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 7294) covalent geometry : angle 0.43534 / 0.23 ( 9921) hydrogen bonds : bond 0.03424 / 2.25 ( 360) hydrogen bonds : angle 4.31740 / 3.00 ( 1020) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 92 time to evaluate : 0.180 Fit side-chains REVERT: B 111 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.6720 (t80) REVERT: B 218 PHE cc_start: 0.6831 (OUTLIER) cc_final: 0.6522 (t80) REVERT: C 172 LYS cc_start: 0.5911 (OUTLIER) cc_final: 0.5406 (tppt) REVERT: C 191 TRP cc_start: 0.7065 (m100) cc_final: 0.5629 (m-10) REVERT: C 204 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7241 (mm) REVERT: C 539 HIS cc_start: 0.7803 (OUTLIER) cc_final: 0.7315 (t-90) outliers start: 44 outliers final: 35 residues processed: 123 average time/residue: 0.0745 time to fit residues: 12.8274 Evaluate side-chains 126 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 86 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 184 TRP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 320 PHE Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 539 HIS Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 565 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 72 optimal weight: 0.0870 chunk 76 optimal weight: 20.0000 chunk 34 optimal weight: 0.0370 chunk 57 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 40.0000 chunk 27 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 overall best weight: 2.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.256185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.203697 restraints weight = 17085.110| |-----------------------------------------------------------------------------| r_work (start): 0.4292 rms_B_bonded: 8.26 r_work: 0.3832 rms_B_bonded: 7.93 restraints_weight: 2.0000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3857 r_free = 0.3857 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3857 r_free = 0.3857 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (15 function evaluations) r_final: 0.3857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7294 Z= 0.181 Angle : 0.535 5.858 9921 Z= 0.280 Chirality : 0.039 0.145 1140 Planarity : 0.003 0.027 1242 Dihedral : 5.777 57.971 997 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 41.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 7.72 % Allowed : 26.18 % Favored : 66.10 % 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: -0.34 (0.29), residues: 904 helix: 0.84 (0.24), residues: 493 sheet: -2.15 (0.65), residues: 64 loop : -1.35 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 626 TYR 0.022 0.002 TYR B 482 PHE 0.017 0.002 PHE B 424 TRP 0.015 0.001 TRP C 431 HIS 0.003 0.001 HIS B 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 7294) covalent geometry : angle 0.53500 / 0.28 ( 9921) hydrogen bonds : bond 0.04044 / 2.64 ( 360) hydrogen bonds : angle 4.52621 / 3.17 ( 1020) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 85 time to evaluate : 0.209 Fit side-chains REVERT: B 111 PHE cc_start: 0.7366 (OUTLIER) cc_final: 0.6910 (t80) REVERT: B 218 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6898 (t80) REVERT: B 361 SER cc_start: 0.8985 (t) cc_final: 0.8632 (p) REVERT: B 400 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6433 (tt0) REVERT: C 172 LYS cc_start: 0.5482 (OUTLIER) cc_final: 0.5100 (tppt) REVERT: C 204 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7584 (mm) REVERT: C 295 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6800 (tp) REVERT: C 539 HIS cc_start: 0.7893 (OUTLIER) cc_final: 0.7419 (t-90) outliers start: 59 outliers final: 40 residues processed: 129 average time/residue: 0.0729 time to fit residues: 13.0457 Evaluate side-chains 131 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 84 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 184 TRP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 320 PHE Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 539 HIS Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 85 optimal weight: 40.0000 chunk 55 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.254089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.198867 restraints weight = 21559.974| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 9.83 r_work: 0.3888 rms_B_bonded: 6.33 restraints_weight: 2.0000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3903 r_free = 0.3903 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3903 r_free = 0.3903 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7294 Z= 0.200 Angle : 0.566 5.694 9921 Z= 0.298 Chirality : 0.040 0.151 1140 Planarity : 0.003 0.035 1242 Dihedral : 6.036 58.924 997 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 42.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 7.72 % Allowed : 26.70 % Favored : 65.58 % 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: -0.67 (0.28), residues: 904 helix: 0.58 (0.24), residues: 489 sheet: -2.26 (0.64), residues: 64 loop : -1.49 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 626 TYR 0.024 0.002 TYR B 482 PHE 0.018 0.002 PHE B 424 TRP 0.018 0.001 TRP C 431 HIS 0.003 0.001 HIS B 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 ( 7294) covalent geometry : angle 0.56625 / 0.30 ( 9921) hydrogen bonds : bond 0.04297 / 2.81 ( 360) hydrogen bonds : angle 4.67535 / 3.29 ( 1020) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 84 time to evaluate : 0.194 Fit side-chains REVERT: B 111 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.6944 (t80) REVERT: B 218 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.6846 (t80) REVERT: B 361 SER cc_start: 0.8959 (t) cc_final: 0.8595 (p) REVERT: B 400 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.6408 (tt0) REVERT: C 172 LYS cc_start: 0.5232 (OUTLIER) cc_final: 0.3919 (tppt) REVERT: C 202 VAL cc_start: 0.7449 (OUTLIER) cc_final: 0.6706 (t) REVERT: C 295 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6792 (tp) REVERT: C 539 HIS cc_start: 0.7868 (OUTLIER) cc_final: 0.7362 (t-90) REVERT: C 604 ARG cc_start: 0.5963 (mmt180) cc_final: 0.5098 (mtt-85) outliers start: 59 outliers final: 45 residues processed: 129 average time/residue: 0.0672 time to fit residues: 12.0847 Evaluate side-chains 135 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 83 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 184 TRP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 320 PHE Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 539 HIS Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 87 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 0.3980 chunk 56 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.255477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.209400 restraints weight = 18107.596| |-----------------------------------------------------------------------------| r_work (start): 0.4344 rms_B_bonded: 6.19 r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4344 r_free = 0.4344 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4344 r_free = 0.4344 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.4344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7294 Z= 0.165 Angle : 0.522 5.645 9921 Z= 0.275 Chirality : 0.038 0.148 1140 Planarity : 0.003 0.037 1242 Dihedral : 5.940 59.117 997 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 42.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 7.33 % Allowed : 26.96 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.28), residues: 904 helix: 0.67 (0.24), residues: 492 sheet: -2.26 (0.64), residues: 64 loop : -1.45 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 626 TYR 0.022 0.002 TYR B 482 PHE 0.015 0.002 PHE B 424 TRP 0.016 0.001 TRP C 431 HIS 0.002 0.001 HIS B 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 ( 7294) covalent geometry : angle 0.52166 / 0.27 ( 9921) hydrogen bonds : bond 0.03962 / 2.59 ( 360) hydrogen bonds : angle 4.52791 / 3.18 ( 1020) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 89 time to evaluate : 0.178 Fit side-chains REVERT: B 111 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.6728 (t80) REVERT: B 218 PHE cc_start: 0.6912 (OUTLIER) cc_final: 0.6582 (t80) REVERT: B 361 SER cc_start: 0.8762 (t) cc_final: 0.8411 (p) REVERT: B 400 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6335 (tt0) REVERT: C 172 LYS cc_start: 0.6082 (OUTLIER) cc_final: 0.5393 (tppt) REVERT: C 202 VAL cc_start: 0.7402 (OUTLIER) cc_final: 0.6812 (t) REVERT: C 295 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.6906 (tp) REVERT: C 539 HIS cc_start: 0.7893 (OUTLIER) cc_final: 0.7414 (t-90) REVERT: C 591 PRO cc_start: 0.5399 (Cg_endo) cc_final: 0.5165 (Cg_exo) REVERT: C 604 ARG cc_start: 0.5939 (mmt180) cc_final: 0.5407 (mtt-85) outliers start: 56 outliers final: 46 residues processed: 133 average time/residue: 0.0793 time to fit residues: 14.5757 Evaluate side-chains 137 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 84 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 184 TRP Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 320 PHE Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 539 HIS Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 66 optimal weight: 20.0000 chunk 50 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.259461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.204135 restraints weight = 22072.906| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 10.20 r_work: 0.3941 rms_B_bonded: 6.43 restraints_weight: 2.0000 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3959 r_free = 0.3959 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3959 r_free = 0.3959 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7294 Z= 0.103 Angle : 0.455 5.754 9921 Z= 0.241 Chirality : 0.036 0.140 1140 Planarity : 0.003 0.032 1242 Dihedral : 5.723 59.660 997 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 41.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 6.41 % Allowed : 27.75 % Favored : 65.84 % 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: -0.19 (0.29), residues: 904 helix: 1.01 (0.24), residues: 494 sheet: -2.12 (0.65), residues: 64 loop : -1.36 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 626 TYR 0.018 0.001 TYR B 482 PHE 0.014 0.001 PHE B 117 TRP 0.013 0.001 TRP C 431 HIS 0.001 0.000 HIS C 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 7294) covalent geometry : angle 0.45475 / 0.24 ( 9921) hydrogen bonds : bond 0.03437 / 2.24 ( 360) hydrogen bonds : angle 4.25798 / 2.98 ( 1020) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 87 time to evaluate : 0.284 Fit side-chains REVERT: B 111 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.6927 (t80) REVERT: B 218 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.6769 (t80) REVERT: B 400 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.6368 (tt0) REVERT: C 172 LYS cc_start: 0.5343 (OUTLIER) cc_final: 0.4919 (tppt) REVERT: C 191 TRP cc_start: 0.7339 (m100) cc_final: 0.5582 (m-10) REVERT: C 198 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6566 (tp) REVERT: C 202 VAL cc_start: 0.7364 (OUTLIER) cc_final: 0.6595 (t) REVERT: C 204 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7451 (mm) REVERT: C 295 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6645 (tp) REVERT: C 304 ARG cc_start: 0.8472 (mmt90) cc_final: 0.8065 (mmt-90) REVERT: C 539 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.7293 (t-90) REVERT: C 591 PRO cc_start: 0.6546 (Cg_endo) cc_final: 0.6290 (Cg_exo) REVERT: C 604 ARG cc_start: 0.6020 (mmt180) cc_final: 0.5304 (mtt-85) outliers start: 49 outliers final: 38 residues processed: 126 average time/residue: 0.0825 time to fit residues: 14.3397 Evaluate side-chains 130 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 83 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 184 TRP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 320 PHE Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 539 HIS Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 62 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 86 optimal weight: 0.0010 chunk 38 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 58 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 49 ASN ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.261909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.215323 restraints weight = 19058.443| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 6.45 r_work (final): 0.4405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4405 r_free = 0.4405 target_work(ls_wunit_k1) = 0.215 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4405 r_free = 0.4405 target_work(ls_wunit_k1) = 0.215 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.4405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 7294 Z= 0.089 Angle : 0.426 5.970 9921 Z= 0.226 Chirality : 0.035 0.143 1140 Planarity : 0.003 0.029 1242 Dihedral : 5.509 59.570 997 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 42.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 5.89 % Allowed : 27.88 % Favored : 66.23 % 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: 0.23 (0.30), residues: 904 helix: 1.42 (0.25), residues: 489 sheet: -2.01 (0.67), residues: 64 loop : -1.24 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 626 TYR 0.017 0.001 TYR B 482 PHE 0.013 0.001 PHE B 117 TRP 0.010 0.001 TRP B 390 HIS 0.001 0.000 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 ( 7294) covalent geometry : angle 0.42622 / 0.23 ( 9921) hydrogen bonds : bond 0.03045 / 2.00 ( 360) hydrogen bonds : angle 4.04418 / 2.82 ( 1020) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 84 time to evaluate : 0.241 Fit side-chains REVERT: B 218 PHE cc_start: 0.6852 (OUTLIER) cc_final: 0.6567 (t80) REVERT: B 400 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.6441 (tt0) REVERT: C 172 LYS cc_start: 0.6029 (OUTLIER) cc_final: 0.5406 (tppt) REVERT: C 191 TRP cc_start: 0.6953 (m100) cc_final: 0.5455 (m-10) REVERT: C 202 VAL cc_start: 0.7290 (OUTLIER) cc_final: 0.6680 (t) REVERT: C 204 ILE cc_start: 0.7527 (OUTLIER) cc_final: 0.7217 (mm) REVERT: C 304 ARG cc_start: 0.7895 (mmt90) cc_final: 0.7598 (mmt-90) REVERT: C 539 HIS cc_start: 0.7807 (OUTLIER) cc_final: 0.7301 (t-90) REVERT: C 591 PRO cc_start: 0.5370 (Cg_endo) cc_final: 0.5162 (Cg_exo) outliers start: 45 outliers final: 38 residues processed: 117 average time/residue: 0.0706 time to fit residues: 11.5649 Evaluate side-chains 124 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 80 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 184 TRP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 320 PHE Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 539 HIS Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 77 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 23 optimal weight: 0.0570 chunk 42 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 55 optimal weight: 0.0970 chunk 75 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 45 optimal weight: 0.2980 overall best weight: 1.2900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.259182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.211658 restraints weight = 19613.020| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 6.78 r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4362 r_free = 0.4362 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4362 r_free = 0.4362 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.4362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 7294 Z= 0.127 Angle : 0.469 5.751 9921 Z= 0.247 Chirality : 0.037 0.145 1140 Planarity : 0.003 0.030 1242 Dihedral : 5.240 59.377 991 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 42.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 6.54 % Allowed : 27.36 % Favored : 66.10 % 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: 0.07 (0.29), residues: 904 helix: 1.27 (0.25), residues: 489 sheet: -2.12 (0.65), residues: 64 loop : -1.25 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 626 TYR 0.020 0.001 TYR B 482 PHE 0.014 0.001 PHE B 424 TRP 0.013 0.001 TRP C 431 HIS 0.002 0.000 HIS B 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 7294) covalent geometry : angle 0.46866 / 0.25 ( 9921) hydrogen bonds : bond 0.03453 / 2.26 ( 360) hydrogen bonds : angle 4.18091 / 2.93 ( 1020) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 82 time to evaluate : 0.238 Fit side-chains REVERT: B 218 PHE cc_start: 0.6905 (OUTLIER) cc_final: 0.6606 (t80) REVERT: B 400 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.6340 (tt0) REVERT: C 172 LYS cc_start: 0.6052 (OUTLIER) cc_final: 0.5436 (tppt) REVERT: C 191 TRP cc_start: 0.7014 (m100) cc_final: 0.5487 (m-10) REVERT: C 198 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6330 (tp) REVERT: C 202 VAL cc_start: 0.7302 (OUTLIER) cc_final: 0.6705 (t) REVERT: C 204 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7325 (mm) REVERT: C 485 MET cc_start: 0.4841 (mmt) cc_final: 0.3313 (ptp) REVERT: C 539 HIS cc_start: 0.7873 (OUTLIER) cc_final: 0.7209 (t-90) REVERT: C 591 PRO cc_start: 0.5417 (Cg_endo) cc_final: 0.5199 (Cg_exo) REVERT: C 604 ARG cc_start: 0.6003 (mmt180) cc_final: 0.5545 (mtt-85) outliers start: 50 outliers final: 42 residues processed: 122 average time/residue: 0.0763 time to fit residues: 12.9503 Evaluate side-chains 128 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 79 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 218 PHE Chi-restraints excluded: chain B residue 237 PHE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 368 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 400 GLN Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain C residue 172 LYS Chi-restraints excluded: chain C residue 184 TRP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 320 PHE Chi-restraints excluded: chain C residue 339 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 535 ARG Chi-restraints excluded: chain C residue 539 HIS Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 617 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.0670 chunk 44 optimal weight: 0.0060 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 2 optimal weight: 0.0980 chunk 49 optimal weight: 0.0020 chunk 9 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 70 optimal weight: 0.0020 overall best weight: 0.0350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.266648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.214450 restraints weight = 18750.301| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 9.34 r_work: 0.3992 rms_B_bonded: 7.29 restraints_weight: 2.0000 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4023 r_free = 0.4023 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4023 r_free = 0.4023 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.4023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 7294 Z= 0.071 Angle : 0.408 5.666 9921 Z= 0.217 Chirality : 0.035 0.123 1140 Planarity : 0.003 0.028 1242 Dihedral : 4.943 59.148 991 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 41.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.80 % Allowed : 30.10 % Favored : 66.10 % 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: 0.65 (0.30), residues: 904 helix: 1.87 (0.25), residues: 485 sheet: -1.98 (0.66), residues: 64 loop : -1.15 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 430 TYR 0.013 0.001 TYR B 482 PHE 0.014 0.001 PHE B 117 TRP 0.019 0.001 TRP C 431 HIS 0.008 0.001 HIS C 221 Details of bonding type rmsd/Z covalent geometry : bond 0.00160 / 0.07 ( 7294) covalent geometry : angle 0.40826 / 0.22 ( 9921) hydrogen bonds : bond 0.02647 / 1.75 ( 360) hydrogen bonds : angle 3.84444 / 2.67 ( 1020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1513.47 seconds wall clock time: 26 minutes 43.28 seconds (1603.28 seconds total)