Starting phenix.real_space_refine on Thu Jul 2 11:46:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xcn_38248/07_2026/8xcn_38248.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xcn_38248/07_2026/8xcn_38248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xcn_38248/07_2026/8xcn_38248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xcn_38248/07_2026/8xcn_38248.map" model { file = "/net/cci-nas-00/data/ceres_data/8xcn_38248/07_2026/8xcn_38248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xcn_38248/07_2026/8xcn_38248.cif" } resolution = 3.02 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= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 6 7.16 5 P 2 5.49 5 S 46 5.16 5 C 5420 2.51 5 N 1489 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 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: 8601 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4164 Classifications: {'peptide': 540} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 503} Chain: "B" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1080 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "C" Number of atoms: 3130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3130 Classifications: {'peptide': 413} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 387} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'F3S': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 167 Unusual residues: {'HEC': 3, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1} Unresolved non-hydrogen planarities: 25 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1767 SG CYS A 226 52.692 62.655 35.511 1.00 87.42 S ATOM 1738 SG CYS A 222 54.833 67.275 31.351 1.00 83.60 S ATOM 1698 SG CYS A 216 52.906 62.684 28.727 1.00 88.54 S Time building chain proxies: 1.58, per 1000 atoms: 0.18 Number of scatterers: 8601 At special positions: 0 Unit cell: (105.78, 107.5, 76.54, 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) Fe 6 26.01 S 46 16.00 P 2 15.00 O 1638 8.00 N 1489 7.00 C 5420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 204.2 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S A 602 " pdb="FE1 F3S A 602 " - pdb=" SG CYS A 226 " pdb="FE4 F3S A 602 " - pdb=" SG CYS A 216 " pdb="FE3 F3S A 602 " - pdb=" SG CYS A 222 " Number of angles added : 9 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 7 sheets defined 41.8% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 16 through 28 Processing helix chain 'A' and resid 43 through 53 Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.587A pdb=" N GLN A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.591A pdb=" N LYS A 97 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 removed outlier: 3.690A pdb=" N TRP A 111 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 Processing helix chain 'A' and resid 124 through 130 Processing helix chain 'A' and resid 138 through 154 removed outlier: 3.607A pdb=" N LEU A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 233 through 244 removed outlier: 4.165A pdb=" N ALA A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.565A pdb=" N SER A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 removed outlier: 4.041A pdb=" N MET A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 401 removed outlier: 3.625A pdb=" N ASP A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 463 removed outlier: 4.004A pdb=" N VAL A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.798A pdb=" N SER A 492 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.757A pdb=" N MET A 514 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 542 Processing helix chain 'B' and resid 49 through 63 Processing helix chain 'B' and resid 68 through 83 Processing helix chain 'B' and resid 85 through 100 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.532A pdb=" N TYR B 150 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 151 " --> pdb=" O LEU B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 147 through 151' Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.581A pdb=" N VAL B 171 " --> pdb=" O ASN B 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 51 Processing helix chain 'C' and resid 51 through 56 removed outlier: 4.212A pdb=" N CYS C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 105 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 127 through 142 removed outlier: 3.864A pdb=" N VAL C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 removed outlier: 3.880A pdb=" N TRP C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG C 172 " --> pdb=" O LYS C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 197 Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 245 through 255 Processing helix chain 'C' and resid 265 through 274 Processing helix chain 'C' and resid 279 through 291 Processing helix chain 'C' and resid 316 through 322 removed outlier: 3.504A pdb=" N SER C 322 " --> pdb=" O ASN C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 408 through 423 Processing helix chain 'C' and resid 431 through 440 Processing helix chain 'C' and resid 445 through 451 Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 249 removed outlier: 3.522A pdb=" N LYS A 247 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP A 9 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA A 282 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N THR A 266 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA A 267 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N TYR A 271 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL A 254 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 249 removed outlier: 3.522A pdb=" N LYS A 247 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ASP A 9 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.527A pdb=" N ILE A 87 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N HIS A 433 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 200 removed outlier: 5.215A pdb=" N SER A 347 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR A 368 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N SER A 330 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ILE A 467 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 70 through 73 Processing sheet with id=AA6, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AA7, first strand: chain 'C' and resid 384 through 388 324 hydrogen bonds defined for protein. 900 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: 0.93 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.57: 8733 1.57 - 2.15: 93 2.15 - 2.74: 6 2.74 - 3.32: 0 3.32 - 3.91: 3 Bond restraints: 8835 Sorted by residual: bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.906 -1.606 2.00e-02 2.50e+03 6.44e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 3.762 -1.529 2.00e-02 2.50e+03 5.84e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.736 -1.478 2.00e-02 2.50e+03 5.46e+03 bond pdb=" CB PRO A 144 " pdb=" CG PRO A 144 " ideal model delta sigma weight residual 1.492 0.987 0.505 5.00e-02 4.00e+02 1.02e+02 bond pdb=" CG PRO A 144 " pdb=" CD PRO A 144 " ideal model delta sigma weight residual 1.503 1.220 0.283 3.40e-02 8.65e+02 6.93e+01 ... (remaining 8830 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.75: 12061 14.75 - 29.50: 5 29.50 - 44.25: 10 44.25 - 59.00: 1 59.00 - 73.75: 1 Bond angle restraints: 12078 Sorted by residual: angle pdb=" CB PRO A 144 " pdb=" CG PRO A 144 " pdb=" CD PRO A 144 " ideal model delta sigma weight residual 106.10 179.85 -73.75 3.20e+00 9.77e-02 5.31e+02 angle pdb=" N PRO A 144 " pdb=" CD PRO A 144 " pdb=" CG PRO A 144 " ideal model delta sigma weight residual 103.20 76.60 26.60 1.50e+00 4.44e-01 3.14e+02 angle pdb=" CA PRO A 144 " pdb=" CB PRO A 144 " pdb=" CG PRO A 144 " ideal model delta sigma weight residual 104.50 71.64 32.86 1.90e+00 2.77e-01 2.99e+02 angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 68.36 46.39 3.00e+00 1.11e-01 2.39e+02 angle pdb=" S3 F3S A 602 " pdb="FE1 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 112.59 69.90 42.69 3.00e+00 1.11e-01 2.03e+02 ... (remaining 12073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.37: 4455 19.37 - 38.75: 580 38.75 - 58.12: 151 58.12 - 77.49: 29 77.49 - 96.87: 11 Dihedral angle restraints: 5226 sinusoidal: 2074 harmonic: 3152 Sorted by residual: dihedral pdb=" CA PHE A 80 " pdb=" C PHE A 80 " pdb=" N PRO A 81 " pdb=" CA PRO A 81 " ideal model delta harmonic sigma weight residual -180.00 -129.56 -50.44 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" N PRO A 144 " pdb=" CG PRO A 144 " pdb=" CD PRO A 144 " pdb=" CB PRO A 144 " ideal model delta sinusoidal sigma weight residual 30.00 126.87 -96.87 1 1.50e+01 4.44e-03 4.78e+01 dihedral pdb=" CA TYR A 79 " pdb=" C TYR A 79 " pdb=" N PHE A 80 " pdb=" CA PHE A 80 " ideal model delta harmonic sigma weight residual 180.00 148.02 31.98 0 5.00e+00 4.00e-02 4.09e+01 ... (remaining 5223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.449: 1276 3.449 - 6.898: 0 6.898 - 10.347: 0 10.347 - 13.796: 0 13.796 - 17.245: 1 Chirality restraints: 1277 Sorted by residual: chirality pdb=" S2 F3S A 602 " pdb="FE1 F3S A 602 " pdb="FE3 F3S A 602 " pdb="FE4 F3S A 602 " both_signs ideal model delta sigma weight residual False 10.77 -6.48 17.24 2.00e-01 2.50e+01 7.43e+03 chirality pdb=" CB ILE C 393 " pdb=" CA ILE C 393 " pdb=" CG1 ILE C 393 " pdb=" CG2 ILE C 393 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CG LEU A 35 " pdb=" CB LEU A 35 " pdb=" CD1 LEU A 35 " pdb=" CD2 LEU A 35 " both_signs ideal model delta sigma weight residual False -2.59 -2.90 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 1274 not shown) Planarity restraints: 1568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10 C 504 " 0.025 2.00e-02 2.50e+03 1.82e-01 9.99e+02 pdb=" C1M U10 C 504 " 0.034 2.00e-02 2.50e+03 pdb=" C2 U10 C 504 " -0.040 2.00e-02 2.50e+03 pdb=" C3 U10 C 504 " -0.039 2.00e-02 2.50e+03 pdb=" C4 U10 C 504 " -0.011 2.00e-02 2.50e+03 pdb=" C5 U10 C 504 " 0.062 2.00e-02 2.50e+03 pdb=" C6 U10 C 504 " 0.076 2.00e-02 2.50e+03 pdb=" C7 U10 C 504 " 0.119 2.00e-02 2.50e+03 pdb=" O2 U10 C 504 " -0.339 2.00e-02 2.50e+03 pdb=" O3 U10 C 504 " 0.447 2.00e-02 2.50e+03 pdb=" O4 U10 C 504 " -0.188 2.00e-02 2.50e+03 pdb=" O5 U10 C 504 " -0.144 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 U10 C 504 " 0.021 2.00e-02 2.50e+03 2.03e-01 5.17e+02 pdb=" C11 U10 C 504 " -0.170 2.00e-02 2.50e+03 pdb=" C7 U10 C 504 " -0.246 2.00e-02 2.50e+03 pdb=" C8 U10 C 504 " 0.337 2.00e-02 2.50e+03 pdb=" C9 U10 C 504 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 U10 C 504 " -0.154 2.00e-02 2.50e+03 1.26e-01 1.97e+02 pdb=" C28 U10 C 504 " 0.200 2.00e-02 2.50e+03 pdb=" C29 U10 C 504 " 0.037 2.00e-02 2.50e+03 pdb=" C30 U10 C 504 " 0.031 2.00e-02 2.50e+03 pdb=" C31 U10 C 504 " -0.113 2.00e-02 2.50e+03 ... (remaining 1565 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 2 1.97 - 2.70: 380 2.70 - 3.44: 13164 3.44 - 4.17: 22493 4.17 - 4.90: 39113 Nonbonded interactions: 75152 Sorted by model distance: nonbonded pdb=" OD2 ASP C 375 " pdb=" O1D HEC C 502 " model vdw 1.241 3.040 nonbonded pdb=" CG ASP C 375 " pdb=" O1D HEC C 502 " model vdw 1.377 3.270 nonbonded pdb=" NE2 GLN A 46 " pdb=" OD1 ASN A 50 " model vdw 1.988 3.120 nonbonded pdb=" O ARG A 358 " pdb=" OH TYR A 443 " model vdw 2.092 3.040 nonbonded pdb=" OG1 THR C 234 " pdb=" O PRO C 294 " model vdw 2.106 3.040 ... (remaining 75147 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.260 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 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 : 0.031 1.606 8849 Z= 1.565 Angle : 1.714 73.755 12087 Z= 0.727 Chirality : 0.485 17.245 1277 Planarity : 0.013 0.203 1568 Dihedral : 18.828 96.866 3214 Min Nonbonded Distance : 1.241 Molprobity Statistics. All-atom Clashscore : 22.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.15 % Allowed : 32.66 % Favored : 65.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: -0.97 (0.25), residues: 1083 helix: 0.00 (0.26), residues: 399 sheet: -1.14 (0.51), residues: 91 loop : -0.97 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 133 TYR 0.040 0.003 TYR A 182 PHE 0.018 0.002 PHE B 54 TRP 0.058 0.002 TRP A 173 HIS 0.021 0.001 HIS C 422 Details of bonding type rmsd/Z covalent geometry : bond 0.03018 / 1.46 ( 8835) covalent geometry : angle 1.67825 / 0.73 (12078) hydrogen bonds : bond 0.15315 / 10.67 ( 315) hydrogen bonds : angle 7.26087 / 5.18 ( 900) metal coordination : bond 0.00274 / 0.14 ( 3) metal coordination : angle 12.80312 / 7.67 ( 9) Misc. bond : bond 0.19108 / 9.43 ( 11) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 304 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 MET cc_start: 0.4887 (tpt) cc_final: 0.4682 (tpp) REVERT: A 330 SER cc_start: 0.8253 (m) cc_final: 0.7989 (t) REVERT: A 438 TYR cc_start: 0.4133 (t80) cc_final: 0.3841 (t80) REVERT: A 439 ASP cc_start: 0.7416 (m-30) cc_final: 0.7004 (t0) REVERT: A 453 GLN cc_start: 0.8496 (tp40) cc_final: 0.8005 (mm-40) REVERT: A 514 MET cc_start: 0.6719 (mmp) cc_final: 0.6294 (mpp) REVERT: B 51 ILE cc_start: 0.8267 (mt) cc_final: 0.7989 (tp) REVERT: B 53 ASP cc_start: 0.8567 (m-30) cc_final: 0.8262 (t0) REVERT: B 93 LEU cc_start: 0.8556 (mt) cc_final: 0.8343 (tp) REVERT: B 96 HIS cc_start: 0.8304 (m-70) cc_final: 0.8051 (m90) REVERT: B 100 ASN cc_start: 0.8856 (m-40) cc_final: 0.8420 (m-40) REVERT: B 134 GLU cc_start: 0.7744 (mp0) cc_final: 0.7431 (mt-10) REVERT: C 107 ILE cc_start: 0.8649 (mp) cc_final: 0.8354 (mm) REVERT: C 284 SER cc_start: 0.8052 (t) cc_final: 0.7712 (p) outliers start: 19 outliers final: 10 residues processed: 316 average time/residue: 0.0895 time to fit residues: 37.5485 Evaluate side-chains 182 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.0050 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 ASN A 312 ASN ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN A 539 ASN ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.137350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.119880 restraints weight = 17244.724| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.64 r_work: 0.3550 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.170 8849 Z= 0.185 Angle : 1.473 77.877 12087 Z= 0.511 Chirality : 0.051 0.781 1277 Planarity : 0.006 0.076 1568 Dihedral : 10.322 77.176 1301 Min Nonbonded Distance : 1.551 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 5.65 % Allowed : 24.52 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: -0.31 (0.25), residues: 1083 helix: 0.79 (0.27), residues: 396 sheet: -0.83 (0.54), residues: 81 loop : -0.77 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 192 TYR 0.018 0.002 TYR A 443 PHE 0.016 0.002 PHE C 250 TRP 0.018 0.002 TRP A 173 HIS 0.005 0.001 HIS C 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 ( 8835) covalent geometry : angle 1.30905 / 0.51 (12078) hydrogen bonds : bond 0.03878 / 2.62 ( 315) hydrogen bonds : angle 5.42688 / 3.86 ( 900) metal coordination : bond 0.00571 / 0.29 ( 3) metal coordination : angle 24.79884 / 14.50 ( 9) Misc. bond : bond 0.07078 / 4.02 ( 11) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8448 (ttp) cc_final: 0.7906 (ptm) REVERT: A 175 MET cc_start: 0.7704 (mtt) cc_final: 0.7435 (mtt) REVERT: A 211 ASP cc_start: 0.8464 (t0) cc_final: 0.7846 (t0) REVERT: A 312 ASN cc_start: 0.7620 (OUTLIER) cc_final: 0.6836 (m-40) REVERT: A 322 MET cc_start: 0.4260 (mmt) cc_final: 0.3881 (mmt) REVERT: A 346 MET cc_start: 0.9044 (mtt) cc_final: 0.8806 (mtp) REVERT: A 438 TYR cc_start: 0.5263 (t80) cc_final: 0.4633 (t80) REVERT: A 439 ASP cc_start: 0.7845 (m-30) cc_final: 0.6874 (t0) REVERT: A 514 MET cc_start: 0.5810 (OUTLIER) cc_final: 0.5409 (mpp) REVERT: B 53 ASP cc_start: 0.8651 (m-30) cc_final: 0.8162 (t0) REVERT: B 93 LEU cc_start: 0.8566 (mt) cc_final: 0.8245 (tp) REVERT: B 96 HIS cc_start: 0.8510 (m-70) cc_final: 0.8094 (m90) REVERT: B 100 ASN cc_start: 0.9012 (m-40) cc_final: 0.8573 (m-40) REVERT: B 102 TYR cc_start: 0.7346 (m-80) cc_final: 0.7102 (m-10) REVERT: B 103 GLN cc_start: 0.8845 (mm-40) cc_final: 0.8645 (tp40) REVERT: B 115 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7865 (p0) REVERT: B 140 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7818 (mtpt) REVERT: C 118 MET cc_start: 0.7936 (tpt) cc_final: 0.7656 (tpt) REVERT: C 210 PHE cc_start: 0.8729 (t80) cc_final: 0.8198 (t80) REVERT: C 267 MET cc_start: 0.8998 (tpt) cc_final: 0.8492 (tpt) REVERT: C 284 SER cc_start: 0.7984 (t) cc_final: 0.7690 (p) REVERT: C 374 ASN cc_start: 0.8469 (t0) cc_final: 0.8219 (t0) REVERT: C 410 GLU cc_start: 0.8941 (tp30) cc_final: 0.8720 (tp30) outliers start: 50 outliers final: 20 residues processed: 244 average time/residue: 0.0656 time to fit residues: 22.9680 Evaluate side-chains 182 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 316 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 33 optimal weight: 0.1980 chunk 42 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 15 optimal weight: 4.9990 chunk 94 optimal weight: 0.4980 chunk 50 optimal weight: 6.9990 chunk 88 optimal weight: 0.2980 chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 HIS A 46 GLN A 78 ASN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN A 345 GLN ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.114653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.094995 restraints weight = 16926.082| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 3.46 r_work: 0.3207 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.193 8849 Z= 0.228 Angle : 1.403 82.338 12087 Z= 0.475 Chirality : 0.069 1.780 1277 Planarity : 0.006 0.064 1568 Dihedral : 10.109 78.090 1297 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 6.10 % Allowed : 20.79 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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 (0.25), residues: 1083 helix: 1.22 (0.28), residues: 387 sheet: -0.12 (0.58), residues: 69 loop : -0.83 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 418 TYR 0.024 0.002 TYR B 142 PHE 0.025 0.002 PHE C 156 TRP 0.020 0.002 TRP A 173 HIS 0.008 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.23 ( 8835) covalent geometry : angle 1.16016 / 0.47 (12078) hydrogen bonds : bond 0.03589 / 2.41 ( 315) hydrogen bonds : angle 5.08376 / 3.59 ( 900) metal coordination : bond 0.02190 / 1.05 ( 3) metal coordination : angle 28.95902 / 22.35 ( 9) Misc. bond : bond 0.07930 / 4.70 ( 11) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 190 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8564 (p) REVERT: A 98 GLN cc_start: 0.6228 (mt0) cc_final: 0.6011 (mp10) REVERT: A 197 SER cc_start: 0.8300 (OUTLIER) cc_final: 0.7853 (p) REVERT: A 211 ASP cc_start: 0.8698 (t0) cc_final: 0.7963 (t0) REVERT: A 327 ILE cc_start: 0.8590 (mt) cc_final: 0.8233 (mp) REVERT: A 360 GLU cc_start: 0.8325 (pm20) cc_final: 0.8122 (pm20) REVERT: A 375 SER cc_start: 0.8562 (OUTLIER) cc_final: 0.8211 (m) REVERT: A 438 TYR cc_start: 0.5378 (t80) cc_final: 0.4716 (t80) REVERT: A 439 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7637 (t0) REVERT: A 485 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7679 (mpt) REVERT: A 517 SER cc_start: 0.7873 (p) cc_final: 0.7298 (p) REVERT: B 53 ASP cc_start: 0.8661 (m-30) cc_final: 0.8068 (t0) REVERT: B 56 GLN cc_start: 0.8840 (tt0) cc_final: 0.8329 (pt0) REVERT: B 93 LEU cc_start: 0.8732 (mt) cc_final: 0.8440 (mt) REVERT: B 96 HIS cc_start: 0.8595 (m-70) cc_final: 0.8377 (m90) REVERT: B 117 LEU cc_start: 0.8289 (mm) cc_final: 0.8033 (mt) REVERT: B 136 GLU cc_start: 0.8323 (pt0) cc_final: 0.7981 (pm20) REVERT: C 118 MET cc_start: 0.8197 (tpt) cc_final: 0.7758 (tpt) REVERT: C 161 ARG cc_start: 0.7906 (ptp-110) cc_final: 0.6663 (ptm160) REVERT: C 210 PHE cc_start: 0.8897 (t80) cc_final: 0.8480 (t80) REVERT: C 374 ASN cc_start: 0.8876 (t0) cc_final: 0.8565 (t0) REVERT: C 410 GLU cc_start: 0.9109 (tp30) cc_final: 0.8827 (tp30) outliers start: 54 outliers final: 24 residues processed: 229 average time/residue: 0.0657 time to fit residues: 21.6753 Evaluate side-chains 173 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 86 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN A 539 ASN B 118 HIS ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.110526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.091277 restraints weight = 17197.118| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.40 r_work: 0.3177 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.135 8849 Z= 0.170 Angle : 1.393 85.636 12087 Z= 0.445 Chirality : 0.059 1.320 1277 Planarity : 0.006 0.073 1568 Dihedral : 9.921 78.915 1297 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 5.08 % Allowed : 21.81 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.13 (0.26), residues: 1083 helix: 1.35 (0.28), residues: 387 sheet: -0.24 (0.60), residues: 76 loop : -0.68 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 133 TYR 0.021 0.002 TYR B 162 PHE 0.015 0.001 PHE A 80 TRP 0.026 0.001 TRP A 173 HIS 0.006 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 8835) covalent geometry : angle 1.10294 / 0.44 (12078) hydrogen bonds : bond 0.03282 / 2.17 ( 315) hydrogen bonds : angle 4.93845 / 3.51 ( 900) metal coordination : bond 0.00428 / 0.21 ( 3) metal coordination : angle 31.19182 / 22.04 ( 9) Misc. bond : bond 0.04623 / 2.53 ( 11) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASP cc_start: 0.8696 (t0) cc_final: 0.7929 (t0) REVERT: A 259 THR cc_start: 0.6073 (p) cc_final: 0.5632 (t) REVERT: A 327 ILE cc_start: 0.8865 (mt) cc_final: 0.8481 (mp) REVERT: A 360 GLU cc_start: 0.8262 (pm20) cc_final: 0.7962 (pm20) REVERT: A 375 SER cc_start: 0.8625 (OUTLIER) cc_final: 0.8276 (m) REVERT: B 56 GLN cc_start: 0.8896 (tt0) cc_final: 0.8197 (pt0) REVERT: B 117 LEU cc_start: 0.8263 (mm) cc_final: 0.7863 (mm) REVERT: B 129 TYR cc_start: 0.8504 (m-80) cc_final: 0.7949 (m-80) REVERT: B 136 GLU cc_start: 0.8337 (pt0) cc_final: 0.8012 (pm20) REVERT: C 97 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8542 (mp0) REVERT: C 118 MET cc_start: 0.8300 (tpt) cc_final: 0.7777 (tpt) REVERT: C 161 ARG cc_start: 0.7839 (ptp-110) cc_final: 0.6808 (ptm160) REVERT: C 210 PHE cc_start: 0.8890 (t80) cc_final: 0.8471 (t80) REVERT: C 354 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8479 (t) REVERT: C 374 ASN cc_start: 0.8926 (t0) cc_final: 0.8700 (t0) REVERT: C 395 MET cc_start: 0.8426 (ttp) cc_final: 0.7876 (ttp) REVERT: C 410 GLU cc_start: 0.9161 (tp30) cc_final: 0.8889 (tp30) outliers start: 45 outliers final: 25 residues processed: 202 average time/residue: 0.0638 time to fit residues: 18.9905 Evaluate side-chains 174 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 417 ASN Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 93 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 0.0970 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS A 503 HIS A 539 ASN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.109038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.089935 restraints weight = 17197.403| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.39 r_work: 0.3153 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.6392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 8849 Z= 0.156 Angle : 1.357 85.301 12087 Z= 0.436 Chirality : 0.058 1.337 1277 Planarity : 0.005 0.068 1568 Dihedral : 9.861 79.143 1296 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.41 % Allowed : 23.39 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % 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: 0.16 (0.26), residues: 1083 helix: 1.43 (0.28), residues: 386 sheet: -0.55 (0.58), residues: 76 loop : -0.66 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 418 TYR 0.020 0.001 TYR A 79 PHE 0.012 0.001 PHE A 270 TRP 0.029 0.001 TRP A 173 HIS 0.008 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 8835) covalent geometry : angle 1.08920 / 0.43 (12078) hydrogen bonds : bond 0.03085 / 2.04 ( 315) hydrogen bonds : angle 4.82445 / 3.43 ( 900) metal coordination : bond 0.00255 / 0.12 ( 3) metal coordination : angle 29.69233 / 20.57 ( 9) Misc. bond : bond 0.03192 / 1.77 ( 11) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 ASP cc_start: 0.8723 (t0) cc_final: 0.7965 (t0) REVERT: A 259 THR cc_start: 0.6241 (p) cc_final: 0.5753 (t) REVERT: A 327 ILE cc_start: 0.8869 (mt) cc_final: 0.8459 (mp) REVERT: A 356 ASP cc_start: 0.8093 (m-30) cc_final: 0.7715 (m-30) REVERT: A 360 GLU cc_start: 0.8262 (pm20) cc_final: 0.7994 (pm20) REVERT: A 438 TYR cc_start: 0.5446 (t80) cc_final: 0.4893 (t80) REVERT: B 56 GLN cc_start: 0.8785 (tt0) cc_final: 0.8229 (pt0) REVERT: B 102 TYR cc_start: 0.7355 (m-80) cc_final: 0.6770 (m-10) REVERT: B 129 TYR cc_start: 0.8425 (m-80) cc_final: 0.7862 (m-80) REVERT: B 136 GLU cc_start: 0.8282 (pt0) cc_final: 0.7964 (pm20) REVERT: C 97 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8568 (mp0) REVERT: C 118 MET cc_start: 0.8294 (tpt) cc_final: 0.7708 (tpt) REVERT: C 161 ARG cc_start: 0.7705 (ptp-110) cc_final: 0.7477 (ptp-110) REVERT: C 210 PHE cc_start: 0.8949 (t80) cc_final: 0.8534 (t80) REVERT: C 354 SER cc_start: 0.8682 (OUTLIER) cc_final: 0.8465 (t) REVERT: C 374 ASN cc_start: 0.8938 (t0) cc_final: 0.8721 (t0) REVERT: C 395 MET cc_start: 0.8356 (ttp) cc_final: 0.7902 (ttp) REVERT: C 410 GLU cc_start: 0.9151 (tp30) cc_final: 0.8880 (tp30) outliers start: 39 outliers final: 25 residues processed: 180 average time/residue: 0.0675 time to fit residues: 17.3400 Evaluate side-chains 169 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 36 optimal weight: 0.9980 chunk 62 optimal weight: 0.0470 chunk 94 optimal weight: 0.3980 chunk 56 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 13 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 HIS A 539 ASN ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.106849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.087961 restraints weight = 17132.320| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 3.30 r_work: 0.3132 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.6854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 8849 Z= 0.153 Angle : 1.238 83.382 12087 Z= 0.422 Chirality : 0.060 1.465 1277 Planarity : 0.005 0.062 1568 Dihedral : 9.791 79.158 1296 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.18 % Allowed : 23.50 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.26), residues: 1083 helix: 1.45 (0.28), residues: 387 sheet: -0.48 (0.57), residues: 76 loop : -0.59 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 490 TYR 0.017 0.001 TYR A 79 PHE 0.014 0.001 PHE B 86 TRP 0.028 0.001 TRP A 173 HIS 0.006 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 8835) covalent geometry : angle 1.06475 / 0.42 (12078) hydrogen bonds : bond 0.02896 / 1.93 ( 315) hydrogen bonds : angle 4.79671 / 3.43 ( 900) metal coordination : bond 0.00192 / 0.09 ( 3) metal coordination : angle 23.19318 / 15.80 ( 9) Misc. bond : bond 0.01841 / 1.02 ( 11) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7872 (p0) cc_final: 0.7334 (p0) REVERT: A 211 ASP cc_start: 0.8705 (t0) cc_final: 0.7988 (t0) REVERT: A 321 MET cc_start: 0.6987 (tpt) cc_final: 0.6580 (tpt) REVERT: A 322 MET cc_start: 0.5246 (mmt) cc_final: 0.4818 (mmt) REVERT: A 356 ASP cc_start: 0.8204 (m-30) cc_final: 0.7820 (m-30) REVERT: A 360 GLU cc_start: 0.8306 (pm20) cc_final: 0.8003 (pm20) REVERT: A 375 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8173 (m) REVERT: B 56 GLN cc_start: 0.8865 (tt0) cc_final: 0.8329 (pt0) REVERT: B 96 HIS cc_start: 0.7769 (t-170) cc_final: 0.7177 (t-170) REVERT: B 102 TYR cc_start: 0.7507 (m-80) cc_final: 0.6805 (m-80) REVERT: B 136 GLU cc_start: 0.8238 (pt0) cc_final: 0.7883 (pm20) REVERT: C 97 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8551 (mp0) REVERT: C 108 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6479 (mtt90) REVERT: C 118 MET cc_start: 0.8354 (tpt) cc_final: 0.7728 (tpt) REVERT: C 210 PHE cc_start: 0.8984 (t80) cc_final: 0.8582 (t80) REVERT: C 354 SER cc_start: 0.8777 (OUTLIER) cc_final: 0.8546 (t) REVERT: C 374 ASN cc_start: 0.8942 (t0) cc_final: 0.8740 (t0) REVERT: C 395 MET cc_start: 0.8305 (ttp) cc_final: 0.7724 (ttt) REVERT: C 410 GLU cc_start: 0.9146 (tp30) cc_final: 0.8876 (tp30) outliers start: 37 outliers final: 24 residues processed: 184 average time/residue: 0.0649 time to fit residues: 17.3033 Evaluate side-chains 172 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 78 optimal weight: 20.0000 chunk 70 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 61 optimal weight: 0.2980 chunk 104 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 59 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 HIS ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.103226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.084752 restraints weight = 17156.615| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.22 r_work: 0.3082 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.7245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 8849 Z= 0.151 Angle : 1.235 83.162 12087 Z= 0.417 Chirality : 0.061 1.481 1277 Planarity : 0.005 0.059 1568 Dihedral : 9.727 80.198 1294 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.63 % Allowed : 23.16 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % 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: 0.35 (0.26), residues: 1083 helix: 1.54 (0.28), residues: 387 sheet: -0.49 (0.58), residues: 76 loop : -0.51 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 490 TYR 0.017 0.001 TYR A 79 PHE 0.011 0.001 PHE C 158 TRP 0.026 0.001 TRP A 173 HIS 0.007 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 8835) covalent geometry : angle 1.05661 / 0.41 (12078) hydrogen bonds : bond 0.02893 / 1.90 ( 315) hydrogen bonds : angle 4.76152 / 3.39 ( 900) metal coordination : bond 0.00148 / 0.07 ( 3) metal coordination : angle 23.48904 / 16.22 ( 9) Misc. bond : bond 0.01686 / 0.87 ( 11) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.7982 (p0) cc_final: 0.7404 (p0) REVERT: A 151 CYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8576 (m) REVERT: A 211 ASP cc_start: 0.8692 (t0) cc_final: 0.7980 (t0) REVERT: A 223 MET cc_start: 0.7977 (mtt) cc_final: 0.7430 (mtp) REVERT: A 322 MET cc_start: 0.5754 (mmt) cc_final: 0.5547 (mmt) REVERT: A 356 ASP cc_start: 0.8274 (m-30) cc_final: 0.8007 (m-30) REVERT: A 375 SER cc_start: 0.8414 (OUTLIER) cc_final: 0.8087 (m) REVERT: A 479 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7825 (mt) REVERT: B 56 GLN cc_start: 0.8905 (tt0) cc_final: 0.8630 (tt0) REVERT: B 91 LYS cc_start: 0.9390 (mmtm) cc_final: 0.8988 (mmmt) REVERT: B 96 HIS cc_start: 0.7555 (t-170) cc_final: 0.7262 (t-170) REVERT: B 102 TYR cc_start: 0.7588 (m-80) cc_final: 0.7181 (m-10) REVERT: B 136 GLU cc_start: 0.8231 (pt0) cc_final: 0.7896 (pm20) REVERT: C 97 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8557 (mp0) REVERT: C 108 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6336 (mtt90) REVERT: C 118 MET cc_start: 0.8445 (tpt) cc_final: 0.7712 (tpt) REVERT: C 141 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8706 (mt-10) REVERT: C 210 PHE cc_start: 0.8987 (t80) cc_final: 0.8580 (t80) REVERT: C 354 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8554 (t) REVERT: C 395 MET cc_start: 0.8439 (ttp) cc_final: 0.7925 (ttt) REVERT: C 410 GLU cc_start: 0.9148 (tp30) cc_final: 0.8884 (tp30) outliers start: 41 outliers final: 29 residues processed: 194 average time/residue: 0.0688 time to fit residues: 19.1540 Evaluate side-chains 176 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 0.0770 chunk 85 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 ASN ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS A 503 HIS B 118 HIS ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.096201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.077130 restraints weight = 17171.817| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.14 r_work: 0.2937 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.8059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.122 8849 Z= 0.187 Angle : 1.272 82.777 12087 Z= 0.437 Chirality : 0.062 1.490 1277 Planarity : 0.005 0.058 1568 Dihedral : 9.773 82.282 1294 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.86 % Allowed : 23.95 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % 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: 0.40 (0.27), residues: 1083 helix: 1.51 (0.28), residues: 387 sheet: -0.30 (0.61), residues: 77 loop : -0.44 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 52 TYR 0.019 0.002 TYR A 271 PHE 0.021 0.002 PHE C 158 TRP 0.031 0.002 TRP A 173 HIS 0.008 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 ( 8835) covalent geometry : angle 1.08834 / 0.43 (12078) hydrogen bonds : bond 0.03123 / 2.13 ( 315) hydrogen bonds : angle 4.92767 / 3.50 ( 900) metal coordination : bond 0.00129 / 0.07 ( 3) metal coordination : angle 24.15397 / 17.85 ( 9) Misc. bond : bond 0.04409 / 2.49 ( 11) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ILE cc_start: 0.8064 (pt) cc_final: 0.7728 (mt) REVERT: A 37 ASP cc_start: 0.8318 (p0) cc_final: 0.7736 (p0) REVERT: A 80 PHE cc_start: 0.7718 (m-80) cc_final: 0.7417 (m-80) REVERT: A 96 TYR cc_start: 0.8362 (m-10) cc_final: 0.7231 (m-80) REVERT: A 151 CYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8612 (m) REVERT: A 211 ASP cc_start: 0.8715 (t0) cc_final: 0.8324 (t0) REVERT: A 293 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8328 (mm-30) REVERT: A 330 SER cc_start: 0.8457 (m) cc_final: 0.8165 (t) REVERT: A 356 ASP cc_start: 0.8436 (m-30) cc_final: 0.8114 (m-30) REVERT: A 360 GLU cc_start: 0.8552 (pm20) cc_final: 0.8314 (mp0) REVERT: A 375 SER cc_start: 0.8533 (OUTLIER) cc_final: 0.8169 (m) REVERT: A 442 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7587 (tp30) REVERT: A 476 ASN cc_start: 0.8296 (m-40) cc_final: 0.7918 (m-40) REVERT: A 479 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7953 (mt) REVERT: B 56 GLN cc_start: 0.8955 (tt0) cc_final: 0.8656 (tt0) REVERT: B 86 PHE cc_start: 0.7889 (t80) cc_final: 0.7206 (t80) REVERT: B 89 GLN cc_start: 0.8672 (mt0) cc_final: 0.7962 (mp10) REVERT: B 91 LYS cc_start: 0.9450 (mmtm) cc_final: 0.9137 (mmmt) REVERT: B 94 ARG cc_start: 0.9307 (mmm160) cc_final: 0.8925 (mmm-85) REVERT: B 96 HIS cc_start: 0.7819 (t-170) cc_final: 0.7441 (t-170) REVERT: B 102 TYR cc_start: 0.7717 (m-80) cc_final: 0.7214 (m-10) REVERT: C 97 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8591 (mp0) REVERT: C 108 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6557 (mtt90) REVERT: C 118 MET cc_start: 0.8616 (tpt) cc_final: 0.7965 (tpt) REVERT: C 354 SER cc_start: 0.8937 (OUTLIER) cc_final: 0.8674 (t) REVERT: C 410 GLU cc_start: 0.9166 (tp30) cc_final: 0.8907 (tp30) outliers start: 43 outliers final: 28 residues processed: 185 average time/residue: 0.0695 time to fit residues: 18.3305 Evaluate side-chains 174 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS A 171 ASN ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 HIS B 118 HIS ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.095938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.076676 restraints weight = 17194.848| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.17 r_work: 0.2932 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.8248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 8849 Z= 0.177 Angle : 1.276 83.062 12087 Z= 0.437 Chirality : 0.062 1.487 1277 Planarity : 0.005 0.070 1568 Dihedral : 9.771 81.608 1294 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.29 % Allowed : 24.18 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.27), residues: 1083 helix: 1.57 (0.28), residues: 387 sheet: -0.52 (0.61), residues: 77 loop : -0.42 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 490 TYR 0.052 0.002 TYR A 255 PHE 0.022 0.002 PHE C 158 TRP 0.030 0.001 TRP A 173 HIS 0.015 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 8835) covalent geometry : angle 1.08922 / 0.43 (12078) hydrogen bonds : bond 0.03060 / 2.07 ( 315) hydrogen bonds : angle 4.86148 / 3.45 ( 900) metal coordination : bond 0.00155 / 0.08 ( 3) metal coordination : angle 24.35686 / 18.13 ( 9) Misc. bond : bond 0.04304 / 2.72 ( 11) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8384 (p0) cc_final: 0.7823 (p0) REVERT: A 96 TYR cc_start: 0.8325 (m-10) cc_final: 0.7615 (m-80) REVERT: A 151 CYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8634 (m) REVERT: A 211 ASP cc_start: 0.8747 (t0) cc_final: 0.8026 (t0) REVERT: A 330 SER cc_start: 0.8457 (m) cc_final: 0.8140 (t) REVERT: A 356 ASP cc_start: 0.8469 (m-30) cc_final: 0.8114 (m-30) REVERT: A 360 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8284 (mp0) REVERT: A 375 SER cc_start: 0.8488 (OUTLIER) cc_final: 0.8189 (m) REVERT: A 425 TYR cc_start: 0.8757 (m-80) cc_final: 0.8519 (m-80) REVERT: A 438 TYR cc_start: 0.5701 (t80) cc_final: 0.5451 (t80) REVERT: A 442 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7624 (tp30) REVERT: A 479 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7912 (mt) REVERT: B 56 GLN cc_start: 0.8929 (tt0) cc_final: 0.8664 (tt0) REVERT: B 91 LYS cc_start: 0.9444 (mmtm) cc_final: 0.9025 (mmmt) REVERT: B 94 ARG cc_start: 0.9294 (mmm160) cc_final: 0.8994 (mmm-85) REVERT: B 96 HIS cc_start: 0.7852 (t-170) cc_final: 0.7320 (t-170) REVERT: B 102 TYR cc_start: 0.7589 (m-80) cc_final: 0.7080 (m-10) REVERT: B 112 MET cc_start: 0.8226 (tpp) cc_final: 0.7776 (tpp) REVERT: B 136 GLU cc_start: 0.8044 (pt0) cc_final: 0.7654 (pm20) REVERT: C 97 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8603 (mp0) REVERT: C 108 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.6508 (mtt90) REVERT: C 118 MET cc_start: 0.8625 (tpt) cc_final: 0.7943 (tpt) REVERT: C 210 PHE cc_start: 0.9138 (t80) cc_final: 0.8605 (t80) REVERT: C 354 SER cc_start: 0.8942 (OUTLIER) cc_final: 0.8682 (t) REVERT: C 395 MET cc_start: 0.8707 (ttp) cc_final: 0.8114 (ttt) REVERT: C 408 THR cc_start: 0.8152 (t) cc_final: 0.7939 (p) REVERT: C 410 GLU cc_start: 0.9176 (tp30) cc_final: 0.8912 (tp30) outliers start: 38 outliers final: 25 residues processed: 183 average time/residue: 0.0669 time to fit residues: 17.4693 Evaluate side-chains 177 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS A 290 ASN ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 HIS B 118 HIS ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.097052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.078157 restraints weight = 17346.267| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.13 r_work: 0.2955 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.8344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 8849 Z= 0.156 Angle : 1.236 83.414 12087 Z= 0.432 Chirality : 0.062 1.470 1277 Planarity : 0.005 0.064 1568 Dihedral : 9.765 81.420 1293 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.73 % Allowed : 24.97 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % 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: 0.45 (0.27), residues: 1083 helix: 1.57 (0.28), residues: 392 sheet: 0.10 (0.67), residues: 68 loop : -0.50 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 490 TYR 0.048 0.002 TYR A 255 PHE 0.024 0.002 PHE C 158 TRP 0.028 0.001 TRP A 173 HIS 0.014 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 8835) covalent geometry : angle 1.08140 / 0.43 (12078) hydrogen bonds : bond 0.02921 / 1.99 ( 315) hydrogen bonds : angle 4.82333 / 3.42 ( 900) metal coordination : bond 0.00228 / 0.11 ( 3) metal coordination : angle 21.95623 / 16.44 ( 9) Misc. bond : bond 0.02750 / 1.78 ( 11) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8341 (p0) cc_final: 0.7782 (p0) REVERT: A 151 CYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8688 (m) REVERT: A 211 ASP cc_start: 0.8740 (t0) cc_final: 0.8036 (t0) REVERT: A 330 SER cc_start: 0.8360 (m) cc_final: 0.8072 (t) REVERT: A 356 ASP cc_start: 0.8500 (m-30) cc_final: 0.8138 (m-30) REVERT: A 375 SER cc_start: 0.8459 (OUTLIER) cc_final: 0.8191 (m) REVERT: A 425 TYR cc_start: 0.8739 (m-80) cc_final: 0.8514 (m-80) REVERT: A 438 TYR cc_start: 0.5712 (t80) cc_final: 0.5335 (t80) REVERT: A 476 ASN cc_start: 0.7981 (m-40) cc_final: 0.7760 (m-40) REVERT: A 479 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7974 (mt) REVERT: B 56 GLN cc_start: 0.8936 (tt0) cc_final: 0.8700 (tt0) REVERT: B 86 PHE cc_start: 0.7944 (t80) cc_final: 0.7290 (t80) REVERT: B 89 GLN cc_start: 0.8703 (mt0) cc_final: 0.7939 (mp10) REVERT: B 91 LYS cc_start: 0.9434 (mmtm) cc_final: 0.9091 (mmmt) REVERT: B 96 HIS cc_start: 0.7850 (t-170) cc_final: 0.7317 (t-170) REVERT: B 102 TYR cc_start: 0.7595 (m-80) cc_final: 0.7177 (m-80) REVERT: B 112 MET cc_start: 0.8244 (tpp) cc_final: 0.7867 (tpp) REVERT: B 136 GLU cc_start: 0.8047 (pt0) cc_final: 0.7716 (pm20) REVERT: C 97 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8592 (mp0) REVERT: C 108 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6054 (mtm110) REVERT: C 118 MET cc_start: 0.8588 (tpt) cc_final: 0.7944 (tpt) REVERT: C 210 PHE cc_start: 0.9134 (t80) cc_final: 0.8640 (t80) REVERT: C 354 SER cc_start: 0.8933 (OUTLIER) cc_final: 0.8678 (t) REVERT: C 395 MET cc_start: 0.8569 (ttp) cc_final: 0.7917 (ttt) REVERT: C 408 THR cc_start: 0.8141 (t) cc_final: 0.7927 (p) REVERT: C 410 GLU cc_start: 0.9169 (tp30) cc_final: 0.8910 (tp30) outliers start: 33 outliers final: 20 residues processed: 187 average time/residue: 0.0687 time to fit residues: 18.4909 Evaluate side-chains 175 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 173 TRP Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 354 SER Chi-restraints excluded: chain C residue 384 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 77 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 55 optimal weight: 0.0770 chunk 3 optimal weight: 3.9990 chunk 92 optimal weight: 0.1980 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 HIS A 476 ASN ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 503 HIS B 118 HIS C 308 HIS ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.097641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.078664 restraints weight = 17414.044| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.17 r_work: 0.2967 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.8429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 8849 Z= 0.152 Angle : 1.202 83.395 12087 Z= 0.432 Chirality : 0.061 1.472 1277 Planarity : 0.005 0.064 1568 Dihedral : 9.786 81.453 1293 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.28 % Allowed : 25.08 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % 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: 0.54 (0.27), residues: 1083 helix: 1.66 (0.28), residues: 386 sheet: 0.44 (0.69), residues: 63 loop : -0.46 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 490 TYR 0.044 0.002 TYR A 255 PHE 0.024 0.002 PHE C 158 TRP 0.027 0.001 TRP A 173 HIS 0.006 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 8835) covalent geometry : angle 1.08244 / 0.43 (12078) hydrogen bonds : bond 0.02834 / 1.93 ( 315) hydrogen bonds : angle 4.78709 / 3.41 ( 900) metal coordination : bond 0.00188 / 0.09 ( 3) metal coordination : angle 19.21186 / 13.97 ( 9) Misc. bond : bond 0.01805 / 1.21 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1657.53 seconds wall clock time: 29 minutes 10.54 seconds (1750.54 seconds total)