Starting phenix.real_space_refine on Thu Jul 2 08:29:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d2v_27151/07_2026/8d2v_27151.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2v_27151/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8d2v_27151/07_2026/8d2v_27151.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d2v_27151/07_2026/8d2v_27151.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d2v_27151/07_2026/8d2v_27151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2v_27151/07_2026/8d2v_27151.map" model { file = "/net/cci-nas-00/data/ceres_data/8d2v_27151/07_2026/8d2v_27151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2v_27151/07_2026/8d2v_27151.cif" } 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-6108/lib/python3.11/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: 2.21, per 1000 atoms: 0.35 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: 0.53 Conformation dependent library (CDL) restraints added in 458.3 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: 0.15 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: 0.82 Time building geometry restraints manager: 0.72 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: 3505 25.37 - 50.74: 132 50.74 - 76.12: 17 76.12 - 101.49: 2 101.49 - 126.86: 2 Dihedral angle restraints: 3658 sinusoidal: 1198 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=" C23 ZGS A 601 " pdb=" O24 ZGS A 601 " pdb=" P25 ZGS A 601 " pdb=" O26 ZGS A 601 " ideal model delta sinusoidal sigma weight residual 177.58 63.08 114.50 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" CA GLY B 75 " pdb=" C GLY B 75 " pdb=" N PRO B 76 " pdb=" CA PRO B 76 " ideal model delta harmonic sigma weight residual -180.00 -162.27 -17.73 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 3655 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: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 8.020 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 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 : 13.647 126.860 2078 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/Z covalent geometry : bond 0.00992 / 0.50 ( 6564) covalent geometry : angle 1.27459 / 0.54 ( 8989) SS BOND : bond 0.00245 / 0.12 ( 4) SS BOND : angle 0.80526 / 0.44 ( 8) hydrogen bonds : bond 0.11703 / 8.04 ( 380) hydrogen bonds : angle 6.18343 / 4.52 ( 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 : 0.149 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: 0.0608 time to fit residues: 15.2523 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 : 0.151 ------------------------------------------------------------------------------- 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... 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 = 0.3848 r_free = 0.3848 target = 0.158403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.144923 restraints weight = 31624.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.145621 restraints weight = 32041.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.144096 restraints weight = 11344.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.145123 restraints weight = 7798.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.145393 restraints weight = 5343.598| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- 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 = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3661 r_free = 0.3661 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.3661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6568 Z= 0.175 Angle : 0.672 6.702 8997 Z= 0.338 Chirality : 0.045 0.244 1070 Planarity : 0.006 0.066 1105 Dihedral : 11.598 137.127 1030 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.19 % Allowed : 2.25 % Favored : 97.57 % 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: -0.52 (0.28), residues: 862 helix: 1.10 (0.26), residues: 373 sheet: -0.10 (0.41), residues: 177 loop : -2.33 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 92 TYR 0.029 0.002 TYR A 358 PHE 0.038 0.002 PHE A 298 TRP 0.017 0.002 TRP C 95 HIS 0.001 0.001 HIS A 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 ( 6564) covalent geometry : angle 0.67138 / 0.34 ( 8989) SS BOND : bond 0.00389 / 0.20 ( 4) SS BOND : angle 0.92358 / 0.50 ( 8) hydrogen bonds : bond 0.04112 / 2.85 ( 380) hydrogen bonds : angle 4.85440 / 3.49 ( 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 136 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: A 462 GLU cc_start: 0.7563 (mp0) cc_final: 0.7327 (mt-10) REVERT: B 70 SER cc_start: 0.8664 (t) cc_final: 0.8077 (m) REVERT: B 88 LEU cc_start: 0.8161 (pp) cc_final: 0.7051 (mp) REVERT: C 72 GLN cc_start: 0.6815 (pm20) cc_final: 0.6378 (mt0) REVERT: C 81 ILE cc_start: 0.8003 (mm) cc_final: 0.7721 (mt) REVERT: C 93 CYS cc_start: 0.6059 (t) cc_final: 0.5804 (t) REVERT: C 112 ASN cc_start: 0.7582 (p0) cc_final: 0.7286 (p0) REVERT: C 136 THR cc_start: 0.8702 (m) cc_final: 0.8475 (p) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.0590 time to fit residues: 11.4065 Evaluate side-chains 108 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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: 0.9980 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 31 optimal weight: 0.0030 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3868 r_free = 0.3868 target = 0.159791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.148052 restraints weight = 25180.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.145000 restraints weight = 29140.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.143142 restraints weight = 13208.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.143885 restraints weight = 10956.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.144313 restraints weight = 6940.638| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3641 |-occupancy refinement: start-------------------------------------------------| | 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 | |-----------------------------------------------------------------------------| |-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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2453 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= 0.138 Angle : 0.616 6.747 8997 Z= 0.309 Chirality : 0.043 0.191 1070 Planarity : 0.005 0.065 1105 Dihedral : 11.034 125.889 1030 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % 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: -0.26 (0.29), residues: 862 helix: 1.34 (0.26), residues: 378 sheet: 0.06 (0.41), residues: 176 loop : -2.29 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 92 TYR 0.016 0.002 TYR A 291 PHE 0.028 0.002 PHE A 298 TRP 0.024 0.002 TRP B 135 HIS 0.001 0.000 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 ( 6564) covalent geometry : angle 0.61556 / 0.31 ( 8989) SS BOND : bond 0.00442 / 0.22 ( 4) SS BOND : angle 0.57477 / 0.31 ( 8) hydrogen bonds : bond 0.03905 / 2.70 ( 380) hydrogen bonds : angle 4.63357 / 3.34 ( 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 138 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.6489 (tp) cc_final: 0.6122 (tt) REVERT: A 369 ILE cc_start: 0.8068 (mm) cc_final: 0.7818 (mm) REVERT: A 385 SER cc_start: 0.7488 (t) cc_final: 0.7080 (p) REVERT: A 459 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8534 (mm-40) REVERT: B 70 SER cc_start: 0.8597 (t) cc_final: 0.8029 (m) REVERT: B 88 LEU cc_start: 0.8139 (pp) cc_final: 0.7125 (mp) REVERT: C 72 GLN cc_start: 0.6970 (pm20) cc_final: 0.6066 (mt0) REVERT: C 81 ILE cc_start: 0.8065 (mm) cc_final: 0.7685 (mm) REVERT: C 136 THR cc_start: 0.8782 (m) cc_final: 0.8551 (p) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.0553 time to fit residues: 10.9807 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 8 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 16 optimal weight: 0.2980 chunk 0 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 17 optimal weight: 0.0170 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3868 r_free = 0.3868 target = 0.159850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.148074 restraints weight = 25355.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.144838 restraints weight = 27954.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.142248 restraints weight = 15724.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.143251 restraints weight = 13473.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.143572 restraints weight = 7934.334| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3635 |-occupancy refinement: start-------------------------------------------------| | 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 | |-----------------------------------------------------------------------------| |-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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6568 Z= 0.131 Angle : 0.614 6.714 8997 Z= 0.306 Chirality : 0.043 0.179 1070 Planarity : 0.005 0.059 1105 Dihedral : 10.815 121.390 1030 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.19 % Allowed : 0.94 % Favored : 98.88 % 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: 0.06 (0.29), residues: 862 helix: 1.54 (0.27), residues: 377 sheet: 0.21 (0.39), residues: 198 loop : -2.18 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 191 TYR 0.018 0.002 TYR A 291 PHE 0.030 0.002 PHE A 486 TRP 0.016 0.001 TRP C 106 HIS 0.000 0.000 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 6564) covalent geometry : angle 0.61390 / 0.31 ( 8989) SS BOND : bond 0.00356 / 0.18 ( 4) SS BOND : angle 0.54566 / 0.28 ( 8) hydrogen bonds : bond 0.03740 / 2.57 ( 380) hydrogen bonds : angle 4.45352 / 3.18 ( 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 137 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 ILE cc_start: 0.8721 (mm) cc_final: 0.8462 (mm) REVERT: A 369 ILE cc_start: 0.8046 (mm) cc_final: 0.7820 (mm) REVERT: A 385 SER cc_start: 0.7640 (t) cc_final: 0.7141 (p) REVERT: A 459 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8590 (mm-40) REVERT: B 70 SER cc_start: 0.8585 (t) cc_final: 0.8038 (m) REVERT: B 88 LEU cc_start: 0.8118 (pp) cc_final: 0.6947 (mp) REVERT: C 72 GLN cc_start: 0.6893 (pm20) cc_final: 0.6273 (mt0) REVERT: C 81 ILE cc_start: 0.8028 (mm) cc_final: 0.7691 (mm) REVERT: C 136 THR cc_start: 0.8768 (m) cc_final: 0.8552 (p) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.0521 time to fit residues: 10.0330 Evaluate side-chains 111 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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: 0.9980 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 60 optimal weight: 4.9990 chunk 29 optimal weight: 0.3980 chunk 46 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.158675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.140930 restraints weight = 21186.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.143695 restraints weight = 30320.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.144736 restraints weight = 14351.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.145914 restraints weight = 9500.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.145858 restraints weight = 7052.258| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3673 r_free = 0.3673 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3673 r_free = 0.3673 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (7 function evaluations) r_final: 0.3673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2940 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= 0.150 Angle : 0.635 7.864 8997 Z= 0.316 Chirality : 0.043 0.173 1070 Planarity : 0.005 0.058 1105 Dihedral : 10.743 119.166 1030 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.19 % Allowed : 1.87 % Favored : 97.94 % 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: -0.08 (0.29), residues: 862 helix: 1.53 (0.27), residues: 377 sheet: 0.11 (0.41), residues: 178 loop : -2.24 (0.31), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 191 TYR 0.019 0.002 TYR A 291 PHE 0.024 0.002 PHE A 427 TRP 0.019 0.002 TRP C 95 HIS 0.001 0.000 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 6564) covalent geometry : angle 0.63473 / 0.32 ( 8989) SS BOND : bond 0.00372 / 0.19 ( 4) SS BOND : angle 0.69253 / 0.36 ( 8) hydrogen bonds : bond 0.03864 / 2.67 ( 380) hydrogen bonds : angle 4.40249 / 3.16 ( 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 134 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.6278 (tp) cc_final: 0.5919 (tt) REVERT: A 294 LEU cc_start: 0.8388 (tp) cc_final: 0.7941 (tt) REVERT: A 333 ILE cc_start: 0.8749 (mm) cc_final: 0.8447 (mm) REVERT: A 369 ILE cc_start: 0.8041 (mm) cc_final: 0.7801 (mm) REVERT: A 385 SER cc_start: 0.7590 (t) cc_final: 0.7095 (p) REVERT: A 459 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8631 (mm-40) REVERT: B 70 SER cc_start: 0.8634 (t) cc_final: 0.8058 (m) REVERT: B 88 LEU cc_start: 0.8066 (pp) cc_final: 0.7218 (mp) REVERT: C 72 GLN cc_start: 0.6823 (pm20) cc_final: 0.6121 (mt0) REVERT: C 81 ILE cc_start: 0.8117 (mm) cc_final: 0.7732 (mm) REVERT: C 136 THR cc_start: 0.8768 (m) cc_final: 0.8541 (p) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.0465 time to fit residues: 9.0338 Evaluate side-chains 108 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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: 0.0770 chunk 0 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.158389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.146519 restraints weight = 28764.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.143717 restraints weight = 29643.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.141077 restraints weight = 13417.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.142216 restraints weight = 9207.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.142594 restraints weight = 6256.198| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 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 = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6568 Z= 0.144 Angle : 0.628 6.848 8997 Z= 0.313 Chirality : 0.043 0.177 1070 Planarity : 0.005 0.057 1105 Dihedral : 10.520 116.952 1030 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.19 % Allowed : 1.12 % Favored : 98.69 % 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: -0.08 (0.29), residues: 862 helix: 1.54 (0.27), residues: 377 sheet: -0.11 (0.40), residues: 180 loop : -2.11 (0.32), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 191 TYR 0.010 0.001 TYR A 489 PHE 0.038 0.002 PHE A 431 TRP 0.015 0.001 TRP C 95 HIS 0.001 0.000 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 6564) covalent geometry : angle 0.62751 / 0.31 ( 8989) SS BOND : bond 0.00384 / 0.20 ( 4) SS BOND : angle 0.70374 / 0.38 ( 8) hydrogen bonds : bond 0.03853 / 2.63 ( 380) hydrogen bonds : angle 4.37851 / 3.14 ( 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 131 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.6497 (tp) cc_final: 0.6088 (tt) REVERT: A 333 ILE cc_start: 0.8791 (mm) cc_final: 0.8421 (mm) REVERT: A 369 ILE cc_start: 0.8118 (mm) cc_final: 0.7898 (mm) REVERT: A 421 GLU cc_start: 0.6159 (tt0) cc_final: 0.5870 (tm-30) REVERT: A 459 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8633 (mm-40) REVERT: B 70 SER cc_start: 0.8610 (t) cc_final: 0.8039 (m) REVERT: B 88 LEU cc_start: 0.8157 (pp) cc_final: 0.7343 (mp) REVERT: C 72 GLN cc_start: 0.6992 (pm20) cc_final: 0.6577 (mt0) REVERT: C 81 ILE cc_start: 0.8027 (mm) cc_final: 0.7664 (mt) REVERT: C 136 THR cc_start: 0.8837 (m) cc_final: 0.8547 (p) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.0539 time to fit residues: 10.0462 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 : 0.200 ------------------------------------------------------------------------------- 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: 0.4980 chunk 50 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 chunk 68 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 76 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.158755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.146880 restraints weight = 24857.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.146117 restraints weight = 27662.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.144666 restraints weight = 11961.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.145505 restraints weight = 9230.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.146049 restraints weight = 5920.913| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3168 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 : 0.622 6.868 8997 Z= 0.307 Chirality : 0.043 0.176 1070 Planarity : 0.005 0.056 1105 Dihedral : 10.361 115.228 1030 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.19 % Allowed : 1.69 % Favored : 98.13 % 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: -0.03 (0.29), residues: 862 helix: 1.59 (0.27), residues: 376 sheet: -0.06 (0.39), residues: 178 loop : -2.09 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 191 TYR 0.038 0.002 TYR A 358 PHE 0.033 0.002 PHE A 431 TRP 0.012 0.001 TRP C 106 HIS 0.000 0.000 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 6564) covalent geometry : angle 0.62189 / 0.31 ( 8989) SS BOND : bond 0.00304 / 0.16 ( 4) SS BOND : angle 0.70596 / 0.37 ( 8) hydrogen bonds : bond 0.03763 / 2.58 ( 380) hydrogen bonds : angle 4.31862 / 3.09 ( 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 130 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.6313 (tp) cc_final: 0.5952 (tt) REVERT: A 110 MET cc_start: 0.7070 (tpt) cc_final: 0.6861 (mmm) REVERT: A 294 LEU cc_start: 0.8342 (tp) cc_final: 0.7949 (tt) REVERT: A 333 ILE cc_start: 0.8828 (mm) cc_final: 0.8422 (mm) REVERT: A 369 ILE cc_start: 0.8102 (mm) cc_final: 0.7890 (mm) REVERT: A 459 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8589 (mm-40) REVERT: B 70 SER cc_start: 0.8483 (t) cc_final: 0.7955 (m) REVERT: B 88 LEU cc_start: 0.8064 (pp) cc_final: 0.7259 (mp) REVERT: C 72 GLN cc_start: 0.6860 (pm20) cc_final: 0.6502 (mt0) REVERT: C 81 ILE cc_start: 0.8064 (mm) cc_final: 0.7651 (mt) REVERT: C 136 THR cc_start: 0.8727 (m) cc_final: 0.8413 (p) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.0557 time to fit residues: 10.2874 Evaluate side-chains 108 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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: 2.9990 chunk 9 optimal weight: 0.0970 chunk 5 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 47 optimal weight: 0.0000 chunk 52 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 overall best weight: 0.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.159886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.148151 restraints weight = 28420.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.145944 restraints weight = 27353.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.144281 restraints weight = 13117.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.144681 restraints weight = 11590.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.145772 restraints weight = 6731.586| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (10 function evaluations) r_final: 0.3650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3284 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= 0.124 Angle : 0.614 6.978 8997 Z= 0.304 Chirality : 0.042 0.175 1070 Planarity : 0.005 0.055 1105 Dihedral : 10.151 114.236 1030 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % 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: -0.01 (0.29), residues: 862 helix: 1.58 (0.27), residues: 379 sheet: -0.13 (0.39), residues: 180 loop : -2.03 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 191 TYR 0.022 0.002 TYR A 291 PHE 0.029 0.002 PHE A 431 TRP 0.012 0.001 TRP C 106 HIS 0.000 0.000 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 6564) covalent geometry : angle 0.61363 / 0.30 ( 8989) SS BOND : bond 0.00365 / 0.19 ( 4) SS BOND : angle 0.85834 / 0.46 ( 8) hydrogen bonds : bond 0.03751 / 2.58 ( 380) hydrogen bonds : angle 4.29312 / 3.06 ( 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 128 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.6405 (tp) cc_final: 0.6043 (tt) REVERT: A 333 ILE cc_start: 0.8816 (mm) cc_final: 0.8429 (mm) REVERT: A 369 ILE cc_start: 0.8150 (mm) cc_final: 0.7931 (mm) REVERT: A 459 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8504 (mm-40) REVERT: B 70 SER cc_start: 0.8444 (t) cc_final: 0.7878 (m) REVERT: B 139 ILE cc_start: 0.7906 (tt) cc_final: 0.6982 (tt) REVERT: C 72 GLN cc_start: 0.6885 (pm20) cc_final: 0.6453 (mt0) REVERT: C 81 ILE cc_start: 0.8064 (mm) cc_final: 0.7631 (mt) REVERT: C 136 THR cc_start: 0.8811 (m) cc_final: 0.8480 (p) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.0539 time to fit residues: 10.0600 Evaluate side-chains 106 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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: 3.9990 chunk 58 optimal weight: 0.0970 chunk 17 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 64 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.159482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.146974 restraints weight = 24854.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.143313 restraints weight = 28414.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.142852 restraints weight = 13047.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.142902 restraints weight = 11245.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.143987 restraints weight = 6587.138| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (17 function evaluations) r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6568 Z= 0.148 Angle : 0.648 8.942 8997 Z= 0.320 Chirality : 0.043 0.181 1070 Planarity : 0.005 0.054 1105 Dihedral : 10.133 114.713 1030 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.19 % Allowed : 0.94 % Favored : 98.88 % 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: -0.06 (0.29), residues: 862 helix: 1.58 (0.27), residues: 379 sheet: -0.29 (0.39), residues: 180 loop : -2.02 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 191 TYR 0.035 0.002 TYR A 358 PHE 0.029 0.002 PHE A 431 TRP 0.052 0.002 TRP A 112 HIS 0.001 0.000 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 6564) covalent geometry : angle 0.64730 / 0.32 ( 8989) SS BOND : bond 0.00374 / 0.19 ( 4) SS BOND : angle 0.95260 / 0.52 ( 8) hydrogen bonds : bond 0.03853 / 2.67 ( 380) hydrogen bonds : angle 4.31388 / 3.10 ( 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 119 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.6403 (tp) cc_final: 0.6030 (tt) REVERT: A 110 MET cc_start: 0.6645 (tpt) cc_final: 0.6381 (mmm) REVERT: A 333 ILE cc_start: 0.8763 (mm) cc_final: 0.8410 (mm) REVERT: A 459 GLN cc_start: 0.8978 (mm-40) cc_final: 0.8568 (mm-40) REVERT: B 70 SER cc_start: 0.8474 (t) cc_final: 0.7892 (m) REVERT: B 120 LEU cc_start: 0.7112 (tt) cc_final: 0.6426 (tp) REVERT: B 139 ILE cc_start: 0.7961 (tt) cc_final: 0.6906 (tt) REVERT: C 72 GLN cc_start: 0.6962 (pm20) cc_final: 0.6211 (mt0) REVERT: C 81 ILE cc_start: 0.8055 (mm) cc_final: 0.7637 (mt) REVERT: C 136 THR cc_start: 0.8771 (m) cc_final: 0.8433 (p) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.0583 time to fit residues: 9.8188 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 : 0.258 ------------------------------------------------------------------------------- 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: 0.8980 chunk 70 optimal weight: 0.3980 chunk 3 optimal weight: 0.0270 chunk 75 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 55 optimal weight: 0.0370 chunk 14 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.161505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.148117 restraints weight = 24610.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.145806 restraints weight = 31382.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.144266 restraints weight = 13855.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.144765 restraints weight = 11672.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.145135 restraints weight = 7084.542| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3641 |-occupancy refinement: start-------------------------------------------------| | 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: 22 | |-----------------------------------------------------------------------------| |-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: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3498 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= 0.125 Angle : 0.622 8.908 8997 Z= 0.305 Chirality : 0.042 0.179 1070 Planarity : 0.005 0.055 1105 Dihedral : 9.848 113.047 1030 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.19 % Allowed : 0.37 % Favored : 99.44 % 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: 1.59 (0.27), residues: 381 sheet: -0.24 (0.39), residues: 180 loop : -2.04 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 191 TYR 0.020 0.002 TYR A 291 PHE 0.027 0.002 PHE A 431 TRP 0.031 0.002 TRP A 112 HIS 0.000 0.000 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 6564) covalent geometry : angle 0.62232 / 0.30 ( 8989) SS BOND : bond 0.00342 / 0.17 ( 4) SS BOND : angle 0.76961 / 0.43 ( 8) hydrogen bonds : bond 0.03679 / 2.53 ( 380) hydrogen bonds : angle 4.14449 / 2.94 ( 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 127 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.6450 (tp) cc_final: 0.6074 (tt) REVERT: A 110 MET cc_start: 0.6711 (tpt) cc_final: 0.6465 (mmm) REVERT: A 315 PHE cc_start: 0.7747 (t80) cc_final: 0.7324 (t80) REVERT: A 333 ILE cc_start: 0.8815 (mm) cc_final: 0.8445 (mm) REVERT: A 369 ILE cc_start: 0.8233 (mm) cc_final: 0.7945 (mm) REVERT: A 459 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8590 (mm-40) REVERT: B 70 SER cc_start: 0.8454 (t) cc_final: 0.7913 (m) REVERT: B 120 LEU cc_start: 0.6977 (tt) cc_final: 0.6724 (tp) REVERT: C 72 GLN cc_start: 0.7012 (pm20) cc_final: 0.6514 (mt0) REVERT: C 81 ILE cc_start: 0.8075 (mm) cc_final: 0.7694 (mt) REVERT: C 136 THR cc_start: 0.8787 (m) cc_final: 0.8433 (p) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.0693 time to fit residues: 12.3171 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 : 0.217 ------------------------------------------------------------------------------- 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: 2.9990 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 0.0040 chunk 76 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.159117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.143576 restraints weight = 20735.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.143908 restraints weight = 27596.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.140704 restraints weight = 13379.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.141027 restraints weight = 15767.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.142719 restraints weight = 10372.239| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3514 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= 0.142 Angle : 0.630 7.106 8997 Z= 0.312 Chirality : 0.043 0.187 1070 Planarity : 0.005 0.056 1105 Dihedral : 9.861 113.541 1030 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.19 % Allowed : 0.37 % Favored : 99.44 % 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: 378 sheet: -0.34 (0.39), residues: 180 loop : -1.98 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 191 TYR 0.029 0.002 TYR A 358 PHE 0.047 0.002 PHE A 431 TRP 0.017 0.002 TRP C 46 HIS 0.001 0.000 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 6564) covalent geometry : angle 0.62979 / 0.31 ( 8989) SS BOND : bond 0.00321 / 0.16 ( 4) SS BOND : angle 0.69867 / 0.39 ( 8) hydrogen bonds : bond 0.03787 / 2.58 ( 380) hydrogen bonds : angle 4.22076 / 3.02 ( 1115) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1092.78 seconds wall clock time: 19 minutes 34.33 seconds (1174.33 seconds total)