Starting phenix.real_space_refine on Tue Mar 3 18:12:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d2v_27151/03_2026/8d2v_27151.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2v_27151/03_2026/8d2v_27151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d2v_27151/03_2026/8d2v_27151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2v_27151/03_2026/8d2v_27151.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d2v_27151/03_2026/8d2v_27151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2v_27151/03_2026/8d2v_27151.map" } resolution = 4.1 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= 0.003 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1603 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 30 5.16 5 Na 1 4.78 5 C 4186 2.51 5 N 995 2.21 5 O 1175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6388 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3326 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 460, 3304 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 299 Unresolved non-hydrogen angles: 362 Unresolved non-hydrogen dihedrals: 245 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ARG:plan': 9, 'GLU:plan': 7, 'GLN:plan1': 8, 'ASP:plan': 5, 'ASN:plan1': 5, 'PHE:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 157 Conformer: "B" Number of residues, atoms: 460, 3304 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 299 Unresolved non-hydrogen angles: 362 Unresolved non-hydrogen dihedrals: 245 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ARG:plan': 9, 'GLU:plan': 7, 'GLN:plan1': 8, 'ASP:plan': 5, 'ASN:plan1': 5, 'PHE:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 157 bond proxies already assigned to first conformer: 3368 Chain: "B" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1375 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 14, 'TRANS': 186} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 6, 'GLN:plan1': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1371 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 12, 'TRANS': 190} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 4, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "A" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 316 Unusual residues: {' NA': 1, 'LMT': 8, 'ZGS': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 84 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 84 " occ=0.50 residue: pdb=" N APHE A 396 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 396 " occ=0.50 Time building chain proxies: 2.12, per 1000 atoms: 0.33 Number of scatterers: 6388 At special positions: 0 Unit cell: (71.74, 72.584, 141.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 1 15.00 Na 1 11.00 O 1175 8.00 N 995 7.00 C 4186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 86 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 93 " distance=2.03 Simple disulfide: pdb=" SG CYS C 139 " - pdb=" SG CYS C 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 362.6 milliseconds 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1568 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 9 sheets defined 45.5% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 48 through 68 removed outlier: 3.783A pdb=" N GLY A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLN A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 100 Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 109 through 128 Proline residue: A 118 - end of helix removed outlier: 3.590A pdb=" N LEU A 122 " --> pdb=" O PRO A 118 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TRP A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 162 Proline residue: A 158 - end of helix Processing helix chain 'A' and resid 162 through 167 removed outlier: 4.595A pdb=" N SER A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 200 Processing helix chain 'A' and resid 232 through 262 Processing helix chain 'A' and resid 277 through 288 Processing helix chain 'A' and resid 288 through 320 removed outlier: 3.579A pdb=" N LEU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU A 309 " --> pdb=" O PHE A 305 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY A 310 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 320 " --> pdb=" O CYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 351 Proline residue: A 342 - end of helix Processing helix chain 'A' and resid 352 through 362 removed outlier: 3.635A pdb=" N THR A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A 362 " --> pdb=" O TYR A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 removed outlier: 4.523A pdb=" N PHE A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 414 Proline residue: A 399 - end of helix Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 419 through 451 removed outlier: 3.522A pdb=" N PHE A 424 " --> pdb=" O HIS A 420 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 471 Processing helix chain 'A' and resid 473 through 488 Processing helix chain 'A' and resid 493 through 507 removed outlier: 3.865A pdb=" N GLN A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASN A 499 " --> pdb=" O LYS A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 123 Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.005A pdb=" N LYS B 11 " --> pdb=" O ASN B 102 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 32 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR B 48 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP B 34 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.954A pdb=" N ALA B 127 " --> pdb=" O ILE B 174 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE B 174 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL B 129 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU B 172 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N PHE B 131 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALA B 170 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N MET B 168 " --> pdb=" O PRO B 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 149 removed outlier: 4.566A pdb=" N TRP B 143 " --> pdb=" O GLN B 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'C' and resid 56 through 58 removed outlier: 5.514A pdb=" N TRP C 46 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N PHE C 38 " --> pdb=" O TRP C 46 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 121 through 123 removed outlier: 3.628A pdb=" N VAL C 176 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N TRP C 170 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 121 through 123 removed outlier: 3.628A pdb=" N VAL C 176 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N TRP C 170 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 185 through 187 392 hydrogen bonds defined for protein. 1115 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.98 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 964 1.31 - 1.44: 1856 1.44 - 1.56: 3666 1.56 - 1.69: 36 1.69 - 1.81: 42 Bond restraints: 6564 Sorted by residual: bond pdb=" C1B LMT A 609 " pdb=" O5B LMT A 609 " ideal model delta sigma weight residual 1.393 1.517 -0.124 2.00e-02 2.50e+03 3.84e+01 bond pdb=" C1B LMT A 606 " pdb=" O5B LMT A 606 " ideal model delta sigma weight residual 1.393 1.517 -0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C1B LMT A 605 " pdb=" O5B LMT A 605 " ideal model delta sigma weight residual 1.393 1.515 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C1B LMT A 604 " pdb=" O5B LMT A 604 " ideal model delta sigma weight residual 1.393 1.514 -0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" C1B LMT A 602 " pdb=" O5B LMT A 602 " ideal model delta sigma weight residual 1.393 1.512 -0.119 2.00e-02 2.50e+03 3.57e+01 ... (remaining 6559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.29: 8869 5.29 - 10.58: 109 10.58 - 15.87: 5 15.87 - 21.17: 2 21.17 - 26.46: 4 Bond angle restraints: 8989 Sorted by residual: angle pdb=" N GLY B 97 " pdb=" CA GLY B 97 " pdb=" C GLY B 97 " ideal model delta sigma weight residual 113.18 86.72 26.46 2.37e+00 1.78e-01 1.25e+02 angle pdb=" C03 ZGS A 601 " pdb=" C04 ZGS A 601 " pdb=" C05 ZGS A 601 " ideal model delta sigma weight residual 127.34 152.42 -25.08 3.00e+00 1.11e-01 6.99e+01 angle pdb=" C09 ZGS A 601 " pdb=" C10 ZGS A 601 " pdb=" C11 ZGS A 601 " ideal model delta sigma weight residual 127.16 152.19 -25.03 3.00e+00 1.11e-01 6.96e+01 angle pdb=" C06 ZGS A 601 " pdb=" C07 ZGS A 601 " pdb=" C08 ZGS A 601 " ideal model delta sigma weight residual 127.52 152.28 -24.76 3.00e+00 1.11e-01 6.81e+01 angle pdb=" C04 ZGS A 601 " pdb=" C05 ZGS A 601 " pdb=" C06 ZGS A 601 " ideal model delta sigma weight residual 110.70 130.45 -19.75 3.00e+00 1.11e-01 4.33e+01 ... (remaining 8984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.37: 3655 25.37 - 50.74: 199 50.74 - 76.12: 72 76.12 - 101.49: 58 101.49 - 126.86: 74 Dihedral angle restraints: 4058 sinusoidal: 1598 harmonic: 2460 Sorted by residual: dihedral pdb=" C23 ZGS A 601 " pdb=" O24 ZGS A 601 " pdb=" P25 ZGS A 601 " pdb=" O28 ZGS A 601 " ideal model delta sinusoidal sigma weight residual 66.18 -166.96 -126.86 1 3.00e+01 1.11e-03 1.71e+01 dihedral pdb=" O2B LMT A 606 " pdb=" C2B LMT A 606 " pdb=" C3B LMT A 606 " pdb=" O3B LMT A 606 " ideal model delta sinusoidal sigma weight residual 63.73 -174.52 -121.75 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C1B LMT A 606 " pdb=" C2B LMT A 606 " pdb=" C3B LMT A 606 " pdb=" O3B LMT A 606 " ideal model delta sinusoidal sigma weight residual -175.52 -54.27 -121.25 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 4055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 858 0.058 - 0.116: 176 0.116 - 0.175: 29 0.175 - 0.233: 6 0.233 - 0.291: 1 Chirality restraints: 1070 Sorted by residual: chirality pdb=" C1B LMT A 607 " pdb=" C2B LMT A 607 " pdb=" O1B LMT A 607 " pdb=" O5B LMT A 607 " both_signs ideal model delta sigma weight residual False -2.20 -2.49 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C4' LMT A 606 " pdb=" C3' LMT A 606 " pdb=" C5' LMT A 606 " pdb=" O1B LMT A 606 " both_signs ideal model delta sigma weight residual False -2.55 -2.33 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C1B LMT A 602 " pdb=" C2B LMT A 602 " pdb=" O1B LMT A 602 " pdb=" O5B LMT A 602 " both_signs ideal model delta sigma weight residual False -2.20 -2.40 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 1067 not shown) Planarity restraints: 1105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 103 " -0.048 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO C 104 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO C 104 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 104 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 46 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO C 47 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 47 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 47 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 75 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO B 76 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 76 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 76 " -0.031 5.00e-02 4.00e+02 ... (remaining 1102 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1524 2.79 - 3.32: 5616 3.32 - 3.84: 10714 3.84 - 4.37: 11332 4.37 - 4.90: 20286 Nonbonded interactions: 49472 Sorted by model distance: nonbonded pdb=" OE1 GLN A 62 " pdb=" OG1 THR A 444 " model vdw 2.262 3.040 nonbonded pdb=" N GLY B 97 " pdb=" O GLY B 97 " model vdw 2.279 2.496 nonbonded pdb=" OD2 ASP A 72 " pdb=" O6B LMT A 606 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR A 129 " pdb=" O4' LMT A 605 " model vdw 2.308 3.040 nonbonded pdb=" O VAL A 332 " pdb=" OG SER A 336 " model vdw 2.310 3.040 ... (remaining 49467 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.700 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 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 : 0.010 0.124 6568 Z= 0.499 Angle : 1.274 26.456 8997 Z= 0.535 Chirality : 0.051 0.291 1070 Planarity : 0.007 0.073 1105 Dihedral : 28.636 126.860 2478 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.75 % Allowed : 7.12 % Favored : 92.13 % 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: -1.27 (0.27), residues: 862 helix: 0.05 (0.24), residues: 370 sheet: 0.01 (0.39), residues: 188 loop : -2.51 (0.31), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.018 0.002 TYR A 43 PHE 0.022 0.002 PHE B 89 TRP 0.021 0.002 TRP A 140 HIS 0.001 0.000 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00992 ( 6564) covalent geometry : angle 1.27459 ( 8989) SS BOND : bond 0.00245 ( 4) SS BOND : angle 0.80526 ( 8) hydrogen bonds : bond 0.11703 ( 380) hydrogen bonds : angle 6.18343 ( 1115) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 183 time to evaluate : 0.191 Fit side-chains REVERT: A 242 ILE cc_start: 0.8081 (mt) cc_final: 0.7617 (mm) REVERT: B 70 SER cc_start: 0.8046 (t) cc_final: 0.7208 (m) REVERT: B 72 SER cc_start: 0.8202 (m) cc_final: 0.7848 (p) REVERT: B 154 MET cc_start: 0.8205 (mtt) cc_final: 0.7540 (mtm) REVERT: B 156 TRP cc_start: 0.8406 (m-90) cc_final: 0.7858 (m-90) REVERT: C 81 ILE cc_start: 0.7687 (mm) cc_final: 0.7457 (mt) REVERT: C 136 THR cc_start: 0.9103 (m) cc_final: 0.8873 (p) REVERT: C 190 PHE cc_start: 0.7268 (t80) cc_final: 0.7053 (t80) outliers start: 3 outliers final: 0 residues processed: 185 average time/residue: 0.0648 time to fit residues: 16.4958 Evaluate side-chains 109 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 30.0000 chunk 74 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN B 153 ASN C 99 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.157986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.144988 restraints weight = 31036.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.144468 restraints weight = 32300.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.143120 restraints weight = 12750.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.143793 restraints weight = 9131.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.143965 restraints weight = 6008.743| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6568 Z= 0.192 Angle : 0.847 11.282 8997 Z= 0.382 Chirality : 0.055 0.605 1070 Planarity : 0.006 0.067 1105 Dihedral : 19.257 133.719 1430 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.19 % Allowed : 2.81 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.28), residues: 862 helix: 1.03 (0.26), residues: 376 sheet: -0.10 (0.41), residues: 177 loop : -2.36 (0.30), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 92 TYR 0.030 0.002 TYR A 358 PHE 0.039 0.002 PHE A 298 TRP 0.018 0.002 TRP C 95 HIS 0.002 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 6564) covalent geometry : angle 0.84700 ( 8989) SS BOND : bond 0.01209 ( 4) SS BOND : angle 0.95231 ( 8) hydrogen bonds : bond 0.04146 ( 380) hydrogen bonds : angle 4.82221 ( 1115) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.6256 (tp) cc_final: 0.6051 (tp) REVERT: A 462 GLU cc_start: 0.7572 (mp0) cc_final: 0.7302 (mt-10) REVERT: B 70 SER cc_start: 0.8651 (t) cc_final: 0.8043 (m) REVERT: B 88 LEU cc_start: 0.8172 (pp) cc_final: 0.7072 (mp) REVERT: C 72 GLN cc_start: 0.6849 (pm20) cc_final: 0.6392 (mt0) REVERT: C 81 ILE cc_start: 0.8006 (mm) cc_final: 0.7723 (mt) REVERT: C 93 CYS cc_start: 0.6073 (t) cc_final: 0.5805 (t) REVERT: C 112 ASN cc_start: 0.7540 (p0) cc_final: 0.7220 (p0) REVERT: C 136 THR cc_start: 0.8739 (m) cc_final: 0.8500 (p) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.0617 time to fit residues: 12.1045 Evaluate side-chains 110 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 41 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 31 optimal weight: 0.2980 chunk 52 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 328 ASN B 153 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.159995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.145897 restraints weight = 25056.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.143098 restraints weight = 31899.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.140432 restraints weight = 15342.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.141288 restraints weight = 13923.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.141921 restraints weight = 8115.465| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3593 r_free = 0.3593 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6568 Z= 0.144 Angle : 0.693 7.382 8997 Z= 0.328 Chirality : 0.045 0.284 1070 Planarity : 0.005 0.061 1105 Dihedral : 13.364 125.325 1430 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.19 % Allowed : 1.31 % Favored : 98.50 % 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: -0.28 (0.28), residues: 862 helix: 1.29 (0.26), residues: 376 sheet: 0.08 (0.41), residues: 176 loop : -2.25 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 92 TYR 0.019 0.002 TYR C 123 PHE 0.028 0.002 PHE A 298 TRP 0.022 0.002 TRP B 135 HIS 0.000 0.000 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6564) covalent geometry : angle 0.69324 ( 8989) SS BOND : bond 0.00526 ( 4) SS BOND : angle 0.62034 ( 8) hydrogen bonds : bond 0.03956 ( 380) hydrogen bonds : angle 4.64300 ( 1115) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 ILE cc_start: 0.8075 (mm) cc_final: 0.7823 (mm) REVERT: A 459 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8574 (mm-40) REVERT: B 70 SER cc_start: 0.8569 (t) cc_final: 0.8023 (m) REVERT: B 88 LEU cc_start: 0.8234 (pp) cc_final: 0.7183 (mp) REVERT: C 72 GLN cc_start: 0.6936 (pm20) cc_final: 0.6644 (mt0) REVERT: C 81 ILE cc_start: 0.8086 (mm) cc_final: 0.7708 (mm) REVERT: C 136 THR cc_start: 0.8805 (m) cc_final: 0.8592 (p) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.0646 time to fit residues: 11.7101 Evaluate side-chains 105 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN B 134 ASN C 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.154492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.142168 restraints weight = 24603.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.141184 restraints weight = 27581.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.138895 restraints weight = 13649.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.140030 restraints weight = 11190.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.139962 restraints weight = 7344.855| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6568 Z= 0.235 Angle : 0.750 7.434 8997 Z= 0.368 Chirality : 0.047 0.262 1070 Planarity : 0.006 0.072 1105 Dihedral : 12.528 120.306 1430 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.19 % Allowed : 2.06 % Favored : 97.75 % 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: -0.28 (0.29), residues: 862 helix: 1.32 (0.27), residues: 375 sheet: -0.08 (0.42), residues: 180 loop : -2.22 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 237 TYR 0.023 0.002 TYR A 291 PHE 0.026 0.003 PHE A 298 TRP 0.032 0.002 TRP C 95 HIS 0.001 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 6564) covalent geometry : angle 0.74960 ( 8989) SS BOND : bond 0.00472 ( 4) SS BOND : angle 0.87295 ( 8) hydrogen bonds : bond 0.04226 ( 380) hydrogen bonds : angle 4.76982 ( 1115) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 THR cc_start: 0.8705 (p) cc_final: 0.8422 (t) REVERT: A 369 ILE cc_start: 0.8145 (mm) cc_final: 0.7922 (mm) REVERT: B 70 SER cc_start: 0.8697 (t) cc_final: 0.8108 (m) REVERT: B 88 LEU cc_start: 0.8342 (pp) cc_final: 0.7114 (mp) REVERT: C 72 GLN cc_start: 0.6980 (pm20) cc_final: 0.6124 (mt0) REVERT: C 81 ILE cc_start: 0.8124 (mm) cc_final: 0.7765 (mt) REVERT: C 93 CYS cc_start: 0.6013 (t) cc_final: 0.5796 (t) REVERT: C 136 THR cc_start: 0.8852 (m) cc_final: 0.8640 (p) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0611 time to fit residues: 10.8871 Evaluate side-chains 100 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 50 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 29 optimal weight: 0.1980 chunk 46 optimal weight: 0.0770 chunk 35 optimal weight: 0.6980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.158971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.141924 restraints weight = 20461.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.142977 restraints weight = 28966.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.142000 restraints weight = 13903.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.142582 restraints weight = 10991.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.142842 restraints weight = 7426.943| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6568 Z= 0.133 Angle : 0.659 6.875 8997 Z= 0.320 Chirality : 0.044 0.262 1070 Planarity : 0.005 0.060 1105 Dihedral : 11.963 117.438 1430 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.19 % Allowed : 1.50 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.29), residues: 862 helix: 1.53 (0.27), residues: 376 sheet: 0.08 (0.39), residues: 194 loop : -2.20 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 191 TYR 0.037 0.002 TYR A 358 PHE 0.032 0.002 PHE A 431 TRP 0.013 0.001 TRP A 344 HIS 0.000 0.000 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6564) covalent geometry : angle 0.65903 ( 8989) SS BOND : bond 0.00415 ( 4) SS BOND : angle 0.71499 ( 8) hydrogen bonds : bond 0.03841 ( 380) hydrogen bonds : angle 4.49936 ( 1115) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.6377 (tp) cc_final: 0.5964 (tt) REVERT: A 333 ILE cc_start: 0.8682 (mm) cc_final: 0.8441 (mm) REVERT: A 369 ILE cc_start: 0.8125 (mm) cc_final: 0.7921 (mm) REVERT: A 385 SER cc_start: 0.7677 (t) cc_final: 0.7207 (p) REVERT: A 421 GLU cc_start: 0.5992 (tt0) cc_final: 0.5685 (tm-30) REVERT: A 459 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8578 (mm-40) REVERT: B 70 SER cc_start: 0.8615 (t) cc_final: 0.8012 (m) REVERT: B 88 LEU cc_start: 0.7925 (pp) cc_final: 0.7012 (mp) REVERT: C 72 GLN cc_start: 0.7069 (pm20) cc_final: 0.6267 (mt0) REVERT: C 81 ILE cc_start: 0.8101 (mm) cc_final: 0.7695 (mt) REVERT: C 136 THR cc_start: 0.8908 (m) cc_final: 0.8658 (p) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.0628 time to fit residues: 11.6770 Evaluate side-chains 107 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 23 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 78 optimal weight: 0.0980 chunk 73 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.158984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.146938 restraints weight = 28353.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.144634 restraints weight = 28730.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.142115 restraints weight = 13411.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.143420 restraints weight = 9820.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.143524 restraints weight = 6488.970| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6568 Z= 0.133 Angle : 0.649 6.783 8997 Z= 0.315 Chirality : 0.043 0.255 1070 Planarity : 0.005 0.055 1105 Dihedral : 11.642 115.535 1430 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.19 % Allowed : 1.31 % Favored : 98.50 % 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: -0.03 (0.29), residues: 862 helix: 1.60 (0.27), residues: 375 sheet: -0.00 (0.40), residues: 178 loop : -2.13 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 191 TYR 0.022 0.002 TYR A 291 PHE 0.030 0.002 PHE A 431 TRP 0.018 0.001 TRP C 106 HIS 0.000 0.000 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6564) covalent geometry : angle 0.64931 ( 8989) SS BOND : bond 0.00380 ( 4) SS BOND : angle 0.67564 ( 8) hydrogen bonds : bond 0.03774 ( 380) hydrogen bonds : angle 4.44652 ( 1115) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.6448 (tp) cc_final: 0.6001 (tt) REVERT: A 110 MET cc_start: 0.7181 (tpt) cc_final: 0.6927 (mmm) REVERT: A 333 ILE cc_start: 0.8759 (mm) cc_final: 0.8490 (mm) REVERT: A 369 ILE cc_start: 0.8106 (mm) cc_final: 0.7885 (mm) REVERT: A 385 SER cc_start: 0.7656 (t) cc_final: 0.7195 (p) REVERT: A 459 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8486 (mm-40) REVERT: B 70 SER cc_start: 0.8460 (t) cc_final: 0.7926 (m) REVERT: B 88 LEU cc_start: 0.8003 (pp) cc_final: 0.7124 (mp) REVERT: B 139 ILE cc_start: 0.8072 (tt) cc_final: 0.7260 (tt) REVERT: C 72 GLN cc_start: 0.6971 (pm20) cc_final: 0.6585 (mt0) REVERT: C 81 ILE cc_start: 0.8050 (mm) cc_final: 0.7667 (mt) REVERT: C 136 THR cc_start: 0.8843 (m) cc_final: 0.8584 (p) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.0609 time to fit residues: 11.1464 Evaluate side-chains 105 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 41 optimal weight: 0.1980 chunk 68 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 56 optimal weight: 0.2980 chunk 76 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.158628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.146512 restraints weight = 24524.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.142594 restraints weight = 28167.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.140286 restraints weight = 15277.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.141239 restraints weight = 14713.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.142177 restraints weight = 8080.434| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6568 Z= 0.132 Angle : 0.652 8.146 8997 Z= 0.314 Chirality : 0.043 0.251 1070 Planarity : 0.005 0.054 1105 Dihedral : 11.323 114.695 1430 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.19 % Allowed : 1.50 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.29), residues: 862 helix: 1.65 (0.27), residues: 377 sheet: -0.01 (0.40), residues: 178 loop : -2.12 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 191 TYR 0.017 0.001 TYR C 123 PHE 0.024 0.002 PHE A 431 TRP 0.016 0.001 TRP C 106 HIS 0.000 0.000 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6564) covalent geometry : angle 0.65160 ( 8989) SS BOND : bond 0.00347 ( 4) SS BOND : angle 0.69637 ( 8) hydrogen bonds : bond 0.03722 ( 380) hydrogen bonds : angle 4.34767 ( 1115) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.6435 (tp) cc_final: 0.6011 (tt) REVERT: A 333 ILE cc_start: 0.8726 (mm) cc_final: 0.8460 (mm) REVERT: A 369 ILE cc_start: 0.8169 (mm) cc_final: 0.7946 (mm) REVERT: A 385 SER cc_start: 0.7755 (t) cc_final: 0.7254 (p) REVERT: A 459 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8515 (mm-40) REVERT: B 70 SER cc_start: 0.8483 (t) cc_final: 0.8107 (m) REVERT: B 88 LEU cc_start: 0.8006 (pp) cc_final: 0.7197 (mp) REVERT: B 139 ILE cc_start: 0.8050 (tt) cc_final: 0.7145 (tt) REVERT: C 72 GLN cc_start: 0.7066 (pm20) cc_final: 0.6612 (mt0) REVERT: C 81 ILE cc_start: 0.8102 (mm) cc_final: 0.7674 (mt) REVERT: C 136 THR cc_start: 0.8809 (m) cc_final: 0.8517 (p) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.0682 time to fit residues: 12.4104 Evaluate side-chains 110 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 47 optimal weight: 0.0020 chunk 52 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.159021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.146594 restraints weight = 27808.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.145775 restraints weight = 29888.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.143764 restraints weight = 11852.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.145253 restraints weight = 9327.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.145101 restraints weight = 6172.999| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3664 r_free = 0.3664 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3664 r_free = 0.3664 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6568 Z= 0.148 Angle : 0.665 6.998 8997 Z= 0.327 Chirality : 0.044 0.248 1070 Planarity : 0.005 0.055 1105 Dihedral : 11.162 115.489 1430 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.19 % Allowed : 0.75 % Favored : 99.06 % 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: -0.04 (0.29), residues: 862 helix: 1.58 (0.27), residues: 379 sheet: -0.15 (0.40), residues: 180 loop : -2.07 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 191 TYR 0.027 0.002 TYR A 291 PHE 0.038 0.002 PHE A 431 TRP 0.057 0.002 TRP A 112 HIS 0.001 0.000 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6564) covalent geometry : angle 0.66523 ( 8989) SS BOND : bond 0.00330 ( 4) SS BOND : angle 0.66934 ( 8) hydrogen bonds : bond 0.03927 ( 380) hydrogen bonds : angle 4.40325 ( 1115) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.6281 (tp) cc_final: 0.5898 (tt) REVERT: A 110 MET cc_start: 0.6785 (tpt) cc_final: 0.6506 (mmm) REVERT: A 333 ILE cc_start: 0.8807 (mm) cc_final: 0.8331 (mm) REVERT: A 369 ILE cc_start: 0.8156 (mm) cc_final: 0.7935 (mm) REVERT: A 459 GLN cc_start: 0.8980 (mm-40) cc_final: 0.8536 (mm-40) REVERT: B 70 SER cc_start: 0.8625 (t) cc_final: 0.8079 (m) REVERT: B 88 LEU cc_start: 0.8012 (pp) cc_final: 0.7245 (mp) REVERT: B 120 LEU cc_start: 0.7180 (tt) cc_final: 0.6497 (tp) REVERT: B 139 ILE cc_start: 0.8020 (tt) cc_final: 0.7170 (tt) REVERT: C 72 GLN cc_start: 0.7022 (pm20) cc_final: 0.6201 (mt0) REVERT: C 81 ILE cc_start: 0.8087 (mm) cc_final: 0.7654 (mt) REVERT: C 136 THR cc_start: 0.8728 (m) cc_final: 0.8413 (p) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.0650 time to fit residues: 11.4107 Evaluate side-chains 101 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 81 optimal weight: 0.2980 chunk 58 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.157543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.145343 restraints weight = 25015.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.142262 restraints weight = 27431.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.139546 restraints weight = 12219.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.140118 restraints weight = 14173.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.141428 restraints weight = 7409.579| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6568 Z= 0.161 Angle : 0.680 7.162 8997 Z= 0.333 Chirality : 0.044 0.246 1070 Planarity : 0.005 0.057 1105 Dihedral : 11.030 116.490 1430 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.19 % Allowed : 0.56 % Favored : 99.25 % 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: -0.09 (0.29), residues: 862 helix: 1.52 (0.27), residues: 379 sheet: -0.20 (0.40), residues: 180 loop : -2.05 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 191 TYR 0.041 0.002 TYR A 358 PHE 0.037 0.002 PHE A 431 TRP 0.032 0.002 TRP A 112 HIS 0.001 0.001 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 6564) covalent geometry : angle 0.68021 ( 8989) SS BOND : bond 0.00332 ( 4) SS BOND : angle 0.74119 ( 8) hydrogen bonds : bond 0.03944 ( 380) hydrogen bonds : angle 4.42318 ( 1115) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.6409 (tp) cc_final: 0.6024 (tt) REVERT: A 333 ILE cc_start: 0.8777 (mm) cc_final: 0.8435 (mm) REVERT: A 459 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8418 (mm-40) REVERT: B 7 PRO cc_start: 0.7428 (Cg_endo) cc_final: 0.7045 (Cg_exo) REVERT: B 70 SER cc_start: 0.8655 (t) cc_final: 0.8085 (m) REVERT: C 72 GLN cc_start: 0.7022 (pm20) cc_final: 0.6260 (mt0) REVERT: C 81 ILE cc_start: 0.8100 (mm) cc_final: 0.7660 (mt) REVERT: C 136 THR cc_start: 0.8770 (m) cc_final: 0.8411 (p) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0618 time to fit residues: 10.5616 Evaluate side-chains 103 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 17 optimal weight: 0.0170 chunk 70 optimal weight: 0.9990 chunk 3 optimal weight: 0.0970 chunk 75 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.159834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.147700 restraints weight = 24503.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.144279 restraints weight = 27300.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.142364 restraints weight = 14582.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.143160 restraints weight = 12454.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.143775 restraints weight = 7606.605| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6568 Z= 0.127 Angle : 0.642 7.094 8997 Z= 0.310 Chirality : 0.042 0.246 1070 Planarity : 0.005 0.056 1105 Dihedral : 10.659 115.561 1430 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.19 % Allowed : 0.75 % Favored : 99.06 % 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: 0.00 (0.29), residues: 862 helix: 1.60 (0.27), residues: 380 sheet: -0.20 (0.40), residues: 180 loop : -2.00 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 191 TYR 0.012 0.001 TYR A 291 PHE 0.034 0.002 PHE A 431 TRP 0.017 0.001 TRP C 106 HIS 0.001 0.000 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6564) covalent geometry : angle 0.64201 ( 8989) SS BOND : bond 0.00294 ( 4) SS BOND : angle 0.53142 ( 8) hydrogen bonds : bond 0.03679 ( 380) hydrogen bonds : angle 4.23048 ( 1115) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.6398 (tp) cc_final: 0.6017 (tt) REVERT: A 369 ILE cc_start: 0.8285 (mm) cc_final: 0.7996 (mm) REVERT: A 459 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8478 (mp10) REVERT: B 7 PRO cc_start: 0.7388 (Cg_endo) cc_final: 0.7010 (Cg_exo) REVERT: B 70 SER cc_start: 0.8634 (t) cc_final: 0.8066 (m) REVERT: C 72 GLN cc_start: 0.7045 (pm20) cc_final: 0.6271 (mt0) REVERT: C 81 ILE cc_start: 0.8048 (mm) cc_final: 0.7666 (mt) REVERT: C 136 THR cc_start: 0.8728 (m) cc_final: 0.8384 (p) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.0590 time to fit residues: 10.0148 Evaluate side-chains 100 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 76 optimal weight: 0.4980 chunk 82 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.158250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.141605 restraints weight = 20549.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.144108 restraints weight = 30329.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.144054 restraints weight = 14087.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.144059 restraints weight = 11196.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.144340 restraints weight = 8989.396| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6568 Z= 0.152 Angle : 0.664 7.138 8997 Z= 0.323 Chirality : 0.044 0.243 1070 Planarity : 0.005 0.055 1105 Dihedral : 10.587 115.804 1430 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.19 % Allowed : 0.19 % Favored : 99.63 % 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: 0.04 (0.29), residues: 862 helix: 1.63 (0.27), residues: 379 sheet: -0.22 (0.40), residues: 180 loop : -1.94 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 191 TYR 0.026 0.002 TYR A 358 PHE 0.034 0.002 PHE A 431 TRP 0.018 0.002 TRP C 46 HIS 0.001 0.000 HIS A 156 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 6564) covalent geometry : angle 0.66397 ( 8989) SS BOND : bond 0.00295 ( 4) SS BOND : angle 0.59906 ( 8) hydrogen bonds : bond 0.03793 ( 380) hydrogen bonds : angle 4.32355 ( 1115) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1094.96 seconds wall clock time: 19 minutes 33.47 seconds (1173.47 seconds total)