Starting phenix.real_space_refine on Fri Jul 25 17:24:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d2v_27151/07_2025/8d2v_27151.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2v_27151/07_2025/8d2v_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d2v_27151/07_2025/8d2v_27151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2v_27151/07_2025/8d2v_27151.map" model { file = "/net/cci-nas-00/data/ceres_data/8d2v_27151/07_2025/8d2v_27151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2v_27151/07_2025/8d2v_27151.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 8, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 9} 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: {'GLN:plan1': 8, 'HIS:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 9} 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: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 6, 'ASP: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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 4, '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: 5.81, per 1000 atoms: 0.91 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: 1.58 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.64 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: 1.73 Time building geometry restraints manager: 1.78 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: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.700 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.750 ------------------------------------------------------------------------------- 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 : 6.24 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.021 0.002 TRP A 140 HIS 0.001 0.000 HIS A 156 PHE 0.022 0.002 PHE B 89 TYR 0.018 0.002 TYR A 43 ARG 0.003 0.000 ARG A 237 Details of bonding type rmsd hydrogen bonds : bond 0.11703 ( 380) hydrogen bonds : angle 6.18343 ( 1115) SS BOND : bond 0.00245 ( 4) SS BOND : angle 0.80526 ( 8) covalent geometry : bond 0.00992 ( 6564) covalent geometry : angle 1.27459 ( 8989) *********************** 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 : 0.615 Fit side-chains REVERT: A 242 ILE cc_start: 0.8081 (mt) cc_final: 0.7616 (mm) REVERT: B 70 SER cc_start: 0.8046 (t) cc_final: 0.7226 (m) REVERT: B 72 SER cc_start: 0.8202 (m) cc_final: 0.7856 (p) REVERT: B 154 MET cc_start: 0.8205 (mtt) cc_final: 0.7539 (mtm) REVERT: B 156 TRP cc_start: 0.8406 (m-90) cc_final: 0.7857 (m-90) REVERT: C 81 ILE cc_start: 0.7687 (mm) cc_final: 0.7456 (mt) REVERT: C 136 THR cc_start: 0.9103 (m) cc_final: 0.8872 (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: 0.1571 time to fit residues: 39.4053 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 : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.0020 chunk 65 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 30.0000 chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 67 optimal weight: 8.9990 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 78 optimal weight: 0.0270 overall best weight: 0.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 135 GLN A 238 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.161793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.143282 restraints weight = 16336.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.141532 restraints weight = 21731.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.142976 restraints weight = 18106.787| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3656 r_free = 0.3656 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6568 Z= 0.156 Angle : 0.819 11.662 8997 Z= 0.367 Chirality : 0.055 0.730 1070 Planarity : 0.006 0.057 1105 Dihedral : 16.878 138.854 1430 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.28), residues: 862 helix: 1.11 (0.26), residues: 372 sheet: -0.01 (0.41), residues: 176 loop : -2.41 (0.30), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 140 HIS 0.002 0.001 HIS A 230 PHE 0.031 0.002 PHE A 298 TYR 0.035 0.002 TYR A 358 ARG 0.004 0.000 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 380) hydrogen bonds : angle 4.67486 ( 1115) SS BOND : bond 0.00420 ( 4) SS BOND : angle 0.76517 ( 8) covalent geometry : bond 0.00333 ( 6564) covalent geometry : angle 0.81920 ( 8989) *********************** 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 140 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 242 ILE cc_start: 0.8441 (mt) cc_final: 0.7939 (mm) REVERT: A 369 ILE cc_start: 0.7958 (mm) cc_final: 0.7714 (mm) REVERT: A 462 GLU cc_start: 0.7464 (mp0) cc_final: 0.7174 (mt-10) REVERT: B 70 SER cc_start: 0.8618 (t) cc_final: 0.8059 (m) REVERT: B 88 LEU cc_start: 0.8176 (pp) cc_final: 0.7216 (mp) REVERT: C 81 ILE cc_start: 0.7973 (mm) cc_final: 0.7685 (mm) REVERT: C 93 CYS cc_start: 0.6005 (t) cc_final: 0.5713 (t) REVERT: C 112 ASN cc_start: 0.7485 (p0) cc_final: 0.7168 (p0) REVERT: C 136 THR cc_start: 0.8657 (m) cc_final: 0.8453 (p) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1505 time to fit residues: 29.7334 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 : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 30 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 53 optimal weight: 0.0370 chunk 50 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 32 optimal weight: 0.1980 chunk 72 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 47 optimal weight: 0.0570 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN B 134 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 = 0.3885 r_free = 0.3885 target = 0.161870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.149801 restraints weight = 29411.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.147075 restraints weight = 29536.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.145393 restraints weight = 14096.494| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 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 = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2648 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= 0.132 Angle : 0.665 7.087 8997 Z= 0.315 Chirality : 0.045 0.287 1070 Planarity : 0.006 0.067 1105 Dihedral : 12.755 130.390 1430 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.29), residues: 862 helix: 1.38 (0.26), residues: 376 sheet: 0.18 (0.40), residues: 196 loop : -2.17 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 135 HIS 0.000 0.000 HIS A 156 PHE 0.024 0.002 PHE A 298 TYR 0.017 0.002 TYR C 123 ARG 0.004 0.000 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 380) hydrogen bonds : angle 4.48865 ( 1115) SS BOND : bond 0.00364 ( 4) SS BOND : angle 0.51033 ( 8) covalent geometry : bond 0.00285 ( 6564) covalent geometry : angle 0.66516 ( 8989) *********************** 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 135 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 ILE cc_start: 0.8245 (mt) cc_final: 0.7805 (mm) REVERT: A 369 ILE cc_start: 0.8022 (mm) cc_final: 0.7804 (mm) REVERT: B 70 SER cc_start: 0.8553 (t) cc_final: 0.8012 (m) REVERT: B 88 LEU cc_start: 0.8197 (pp) cc_final: 0.7193 (mp) REVERT: C 81 ILE cc_start: 0.8036 (mm) cc_final: 0.7645 (mm) REVERT: C 136 THR cc_start: 0.8805 (m) cc_final: 0.8556 (p) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1559 time to fit residues: 29.0645 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 : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 66 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 0.0270 chunk 18 optimal weight: 0.0060 chunk 76 optimal weight: 0.7980 overall best weight: 0.4854 ------------------------------------------------------------------------------- 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 = 0.3879 r_free = 0.3879 target = 0.161421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.148363 restraints weight = 30290.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.147335 restraints weight = 31052.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.146144 restraints weight = 12134.016| |-----------------------------------------------------------------------------| 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: 11 | |-----------------------------------------------------------------------------| |-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: 0.7495 moved from start: 0.2905 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= 0.137 Angle : 0.644 6.657 8997 Z= 0.311 Chirality : 0.043 0.260 1070 Planarity : 0.005 0.056 1105 Dihedral : 11.972 124.286 1430 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.29), residues: 862 helix: 1.52 (0.27), residues: 377 sheet: 0.08 (0.42), residues: 178 loop : -2.11 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 95 HIS 0.000 0.000 HIS A 156 PHE 0.029 0.002 PHE A 486 TYR 0.014 0.001 TYR A 291 ARG 0.004 0.000 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 380) hydrogen bonds : angle 4.37305 ( 1115) SS BOND : bond 0.00359 ( 4) SS BOND : angle 0.55565 ( 8) covalent geometry : bond 0.00304 ( 6564) covalent geometry : angle 0.64437 ( 8989) *********************** 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 128 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 THR cc_start: 0.8665 (p) cc_final: 0.8384 (t) REVERT: A 242 ILE cc_start: 0.8320 (mt) cc_final: 0.8024 (mm) REVERT: A 369 ILE cc_start: 0.8038 (mm) cc_final: 0.7825 (mm) REVERT: A 421 GLU cc_start: 0.5831 (tt0) cc_final: 0.5519 (tm-30) REVERT: B 70 SER cc_start: 0.8536 (t) cc_final: 0.7974 (m) REVERT: B 88 LEU cc_start: 0.8136 (pp) cc_final: 0.6983 (mp) REVERT: B 154 MET cc_start: 0.7648 (mtm) cc_final: 0.7445 (mtm) REVERT: C 81 ILE cc_start: 0.7996 (mm) cc_final: 0.7668 (mm) REVERT: C 93 CYS cc_start: 0.5881 (t) cc_final: 0.5650 (t) REVERT: C 136 THR cc_start: 0.8788 (m) cc_final: 0.8524 (p) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1421 time to fit residues: 25.7204 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 : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 0.0570 chunk 32 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN B 159 GLN C 39 GLN C 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.158433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.144365 restraints weight = 36737.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.145739 restraints weight = 33164.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.144398 restraints weight = 10682.176| |-----------------------------------------------------------------------------| 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: 11 | |-----------------------------------------------------------------------------| |-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: 11 | |-----------------------------------------------------------------------------| r_final: 0.3650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6568 Z= 0.162 Angle : 0.676 8.407 8997 Z= 0.327 Chirality : 0.044 0.257 1070 Planarity : 0.005 0.056 1105 Dihedral : 11.589 119.852 1430 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.29), residues: 862 helix: 1.51 (0.27), residues: 376 sheet: -0.02 (0.41), residues: 180 loop : -2.03 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 95 HIS 0.000 0.000 HIS A 230 PHE 0.023 0.002 PHE A 298 TYR 0.031 0.002 TYR A 358 ARG 0.004 0.001 ARG C 13 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 380) hydrogen bonds : angle 4.43320 ( 1115) SS BOND : bond 0.00365 ( 4) SS BOND : angle 0.75124 ( 8) covalent geometry : bond 0.00367 ( 6564) covalent geometry : angle 0.67606 ( 8989) *********************** 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 125 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 THR cc_start: 0.8663 (p) cc_final: 0.8440 (t) REVERT: A 421 GLU cc_start: 0.5828 (tt0) cc_final: 0.5561 (tm-30) REVERT: B 70 SER cc_start: 0.8623 (t) cc_final: 0.8019 (m) REVERT: B 88 LEU cc_start: 0.8095 (pp) cc_final: 0.7245 (mp) REVERT: C 81 ILE cc_start: 0.8098 (mm) cc_final: 0.7722 (mm) REVERT: C 136 THR cc_start: 0.8772 (m) cc_final: 0.8470 (p) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1453 time to fit residues: 25.4932 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 : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 83 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 57 optimal weight: 0.0770 chunk 29 optimal weight: 0.0370 chunk 22 optimal weight: 50.0000 chunk 23 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 18 optimal weight: 0.0070 chunk 6 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 chunk 79 optimal weight: 6.9990 overall best weight: 0.2434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN B 159 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.161306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.148142 restraints weight = 34819.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.147778 restraints weight = 34627.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.146891 restraints weight = 13438.303| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 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 = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3269 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= 0.117 Angle : 0.620 6.650 8997 Z= 0.300 Chirality : 0.042 0.253 1070 Planarity : 0.005 0.056 1105 Dihedral : 11.081 116.575 1430 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.29), residues: 862 helix: 1.51 (0.27), residues: 378 sheet: 0.07 (0.41), residues: 180 loop : -2.02 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 344 HIS 0.001 0.000 HIS A 156 PHE 0.023 0.002 PHE A 431 TYR 0.022 0.001 TYR A 291 ARG 0.004 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.03631 ( 380) hydrogen bonds : angle 4.26534 ( 1115) SS BOND : bond 0.00403 ( 4) SS BOND : angle 0.55154 ( 8) covalent geometry : bond 0.00250 ( 6564) covalent geometry : angle 0.62044 ( 8989) *********************** 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 128 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7048 (tpt) cc_final: 0.6600 (tmm) REVERT: A 294 LEU cc_start: 0.8318 (tp) cc_final: 0.7976 (tt) REVERT: A 369 ILE cc_start: 0.8070 (mm) cc_final: 0.7821 (mm) REVERT: B 70 SER cc_start: 0.8496 (t) cc_final: 0.7922 (m) REVERT: B 88 LEU cc_start: 0.8019 (pp) cc_final: 0.7204 (mp) REVERT: B 120 LEU cc_start: 0.7159 (tt) cc_final: 0.6935 (tt) REVERT: C 81 ILE cc_start: 0.8020 (mm) cc_final: 0.7643 (mt) REVERT: C 136 THR cc_start: 0.8700 (m) cc_final: 0.8362 (p) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1461 time to fit residues: 26.1882 Evaluate side-chains 104 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 57 optimal weight: 0.0870 chunk 38 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.160045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.147175 restraints weight = 34325.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.146328 restraints weight = 31299.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.144568 restraints weight = 11982.723| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3341 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= 0.134 Angle : 0.640 6.776 8997 Z= 0.309 Chirality : 0.043 0.248 1070 Planarity : 0.005 0.055 1105 Dihedral : 10.884 115.823 1430 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.29), residues: 862 helix: 1.56 (0.27), residues: 379 sheet: 0.11 (0.41), residues: 176 loop : -1.97 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 46 HIS 0.001 0.000 HIS A 156 PHE 0.030 0.002 PHE A 431 TYR 0.033 0.002 TYR A 358 ARG 0.005 0.001 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 380) hydrogen bonds : angle 4.28470 ( 1115) SS BOND : bond 0.00295 ( 4) SS BOND : angle 0.73085 ( 8) covalent geometry : bond 0.00300 ( 6564) covalent geometry : angle 0.63972 ( 8989) *********************** 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 127 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 ILE cc_start: 0.8135 (mm) cc_final: 0.7894 (mm) REVERT: A 486 PHE cc_start: 0.7693 (m-80) cc_final: 0.7467 (m-80) REVERT: B 70 SER cc_start: 0.8532 (t) cc_final: 0.7993 (m) REVERT: B 88 LEU cc_start: 0.8162 (pp) cc_final: 0.7301 (mp) REVERT: C 81 ILE cc_start: 0.8047 (mm) cc_final: 0.7604 (mt) REVERT: C 136 THR cc_start: 0.8736 (m) cc_final: 0.8375 (p) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1426 time to fit residues: 25.6195 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 : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 58 optimal weight: 0.0270 chunk 85 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.158054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.145684 restraints weight = 31429.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.144417 restraints weight = 29130.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.142681 restraints weight = 11786.746| |-----------------------------------------------------------------------------| 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: 22 | |-----------------------------------------------------------------------------| |-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: 22 | |-----------------------------------------------------------------------------| r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6568 Z= 0.153 Angle : 0.654 7.042 8997 Z= 0.319 Chirality : 0.043 0.245 1070 Planarity : 0.005 0.055 1105 Dihedral : 10.832 116.401 1430 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.29), residues: 862 helix: 1.49 (0.27), residues: 378 sheet: -0.03 (0.40), residues: 178 loop : -2.00 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 46 HIS 0.001 0.000 HIS A 156 PHE 0.030 0.002 PHE A 431 TYR 0.029 0.002 TYR A 291 ARG 0.005 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 380) hydrogen bonds : angle 4.35110 ( 1115) SS BOND : bond 0.00368 ( 4) SS BOND : angle 0.71255 ( 8) covalent geometry : bond 0.00350 ( 6564) covalent geometry : angle 0.65362 ( 8989) *********************** 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 127 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.6348 (tp) cc_final: 0.5986 (tt) REVERT: A 333 ILE cc_start: 0.8740 (mm) cc_final: 0.8423 (mm) REVERT: A 385 SER cc_start: 0.7558 (t) cc_final: 0.7004 (p) REVERT: B 70 SER cc_start: 0.8502 (t) cc_final: 0.7912 (m) REVERT: B 88 LEU cc_start: 0.8174 (pp) cc_final: 0.7374 (mp) REVERT: C 81 ILE cc_start: 0.8071 (mm) cc_final: 0.7659 (mt) REVERT: C 136 THR cc_start: 0.8750 (m) cc_final: 0.8375 (p) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1484 time to fit residues: 26.5245 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 : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 2 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 41 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.157861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.146064 restraints weight = 26659.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.144772 restraints weight = 27044.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.142153 restraints weight = 11544.507| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 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 = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6568 Z= 0.157 Angle : 0.665 7.072 8997 Z= 0.324 Chirality : 0.044 0.244 1070 Planarity : 0.005 0.055 1105 Dihedral : 10.761 115.796 1430 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.29), residues: 862 helix: 1.51 (0.27), residues: 380 sheet: -0.23 (0.39), residues: 180 loop : -2.02 (0.33), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 46 HIS 0.000 0.000 HIS A 156 PHE 0.030 0.002 PHE A 431 TYR 0.022 0.002 TYR A 291 ARG 0.006 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 380) hydrogen bonds : angle 4.39677 ( 1115) SS BOND : bond 0.00432 ( 4) SS BOND : angle 0.99201 ( 8) covalent geometry : bond 0.00358 ( 6564) covalent geometry : angle 0.66441 ( 8989) *********************** 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 125 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.6392 (tp) cc_final: 0.6010 (tt) REVERT: A 315 PHE cc_start: 0.7902 (t80) cc_final: 0.7489 (t80) REVERT: A 369 ILE cc_start: 0.8283 (mm) cc_final: 0.8006 (mm) REVERT: A 385 SER cc_start: 0.7524 (t) cc_final: 0.7160 (p) REVERT: B 70 SER cc_start: 0.8529 (t) cc_final: 0.7899 (m) REVERT: B 120 LEU cc_start: 0.7143 (tt) cc_final: 0.6683 (tt) REVERT: C 81 ILE cc_start: 0.8093 (mm) cc_final: 0.7706 (mt) REVERT: C 136 THR cc_start: 0.8747 (m) cc_final: 0.8369 (p) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1413 time to fit residues: 25.0567 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 : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 61 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 7 optimal weight: 0.0050 chunk 4 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 0.0370 chunk 62 optimal weight: 0.2980 overall best weight: 0.3472 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.161087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.148354 restraints weight = 33997.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.146801 restraints weight = 30519.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.145454 restraints weight = 11960.240| |-----------------------------------------------------------------------------| 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: 11 | |-----------------------------------------------------------------------------| |-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: 11 | |-----------------------------------------------------------------------------| r_final: 0.3650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3637 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= 0.129 Angle : 0.640 9.090 8997 Z= 0.311 Chirality : 0.042 0.244 1070 Planarity : 0.005 0.056 1105 Dihedral : 10.471 114.242 1430 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.29), residues: 862 helix: 1.54 (0.26), residues: 381 sheet: -0.16 (0.39), residues: 180 loop : -2.01 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 112 HIS 0.001 0.000 HIS A 156 PHE 0.027 0.002 PHE A 431 TYR 0.013 0.001 TYR A 291 ARG 0.006 0.001 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 380) hydrogen bonds : angle 4.25374 ( 1115) SS BOND : bond 0.00348 ( 4) SS BOND : angle 0.74112 ( 8) covalent geometry : bond 0.00282 ( 6564) covalent geometry : angle 0.63971 ( 8989) ********************** 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 116 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.6370 (tp) cc_final: 0.6005 (tt) REVERT: A 315 PHE cc_start: 0.7819 (t80) cc_final: 0.7446 (t80) REVERT: A 333 ILE cc_start: 0.8752 (mm) cc_final: 0.8340 (mm) REVERT: A 369 ILE cc_start: 0.8285 (mm) cc_final: 0.8015 (mm) REVERT: B 70 SER cc_start: 0.8494 (t) cc_final: 0.7913 (m) REVERT: B 120 LEU cc_start: 0.7116 (tt) cc_final: 0.6888 (tt) REVERT: C 81 ILE cc_start: 0.8071 (mm) cc_final: 0.7671 (mt) REVERT: C 136 THR cc_start: 0.8744 (m) cc_final: 0.8378 (p) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1555 time to fit residues: 25.4226 Evaluate side-chains 98 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 0.0040 chunk 42 optimal weight: 0.0970 chunk 11 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 21 optimal weight: 0.0020 chunk 7 optimal weight: 0.0170 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 0.0570 chunk 73 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.0354 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.165930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.152977 restraints weight = 31565.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.152950 restraints weight = 30221.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.152510 restraints weight = 10837.218| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3752 r_free = 0.3752 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3752 r_free = 0.3752 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6568 Z= 0.111 Angle : 0.606 7.953 8997 Z= 0.295 Chirality : 0.041 0.241 1070 Planarity : 0.005 0.056 1105 Dihedral : 9.937 113.706 1430 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.29), residues: 862 helix: 1.69 (0.27), residues: 380 sheet: 0.05 (0.40), residues: 176 loop : -1.98 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 112 HIS 0.001 0.000 HIS A 156 PHE 0.023 0.001 PHE A 431 TYR 0.011 0.001 TYR A 489 ARG 0.006 0.001 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 380) hydrogen bonds : angle 4.07781 ( 1115) SS BOND : bond 0.00275 ( 4) SS BOND : angle 0.60250 ( 8) covalent geometry : bond 0.00229 ( 6564) covalent geometry : angle 0.60636 ( 8989) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2393.97 seconds wall clock time: 42 minutes 5.31 seconds (2525.31 seconds total)