Starting phenix.real_space_refine on Sat Aug 23 02:43:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jej_36190/08_2025/8jej_36190.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jej_36190/08_2025/8jej_36190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jej_36190/08_2025/8jej_36190.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jej_36190/08_2025/8jej_36190.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jej_36190/08_2025/8jej_36190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jej_36190/08_2025/8jej_36190.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.047 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 5421 2.51 5 N 1490 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8604 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 4167 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: 20 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 20 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1767 SG CYS A 226 52.668 65.790 36.133 1.00 17.16 S ATOM 1738 SG CYS A 222 53.574 70.572 32.001 1.00 21.97 S ATOM 1698 SG CYS A 216 52.124 65.227 29.426 1.00 25.68 S Time building chain proxies: 2.03, per 1000 atoms: 0.24 Number of scatterers: 8604 At special positions: 0 Unit cell: (103.53, 109.62, 76.56, 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 1639 8.00 N 1490 7.00 C 5421 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 274.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 42 helices and 8 sheets defined 41.1% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 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 55 through 61 Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.609A pdb=" N LYS A 97 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 3.744A 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 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.614A pdb=" N SER A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 388 through 401 Processing helix chain 'A' and resid 440 through 462 removed outlier: 4.243A pdb=" N VAL A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 450 " --> pdb=" O LYS A 446 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 Processing helix chain 'A' and resid 522 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 101 Processing helix chain 'B' and resid 104 through 111 Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'C' and resid 41 through 50 Processing helix chain 'C' and resid 52 through 57 removed outlier: 3.883A pdb=" N HIS C 56 " --> pdb=" O CYS C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 106 removed outlier: 3.532A pdb=" N GLY C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 127 through 142 removed outlier: 4.015A pdb=" N VAL C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 185 through 197 Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 215 through 219 removed outlier: 3.870A pdb=" N TYR C 219 " --> pdb=" O GLN C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 256 Processing helix chain 'C' and resid 265 through 274 Processing helix chain 'C' and resid 275 through 278 removed outlier: 3.508A pdb=" N LEU C 278 " --> pdb=" O LEU C 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 275 through 278' Processing helix chain 'C' and resid 279 through 291 Processing helix chain 'C' and resid 317 through 324 removed outlier: 3.915A 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 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: 6.825A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP A 9 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL A 286 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 11 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA A 282 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N THR A 266 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 265 " --> pdb=" O THR A 259 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR A 259 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA A 267 " --> pdb=" O MET A 257 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N MET A 257 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER A 269 " --> pdb=" O TYR A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.825A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP A 9 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL A 286 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 11 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N PHE A 507 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE A 285 " --> pdb=" O PHE A 507 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.404A pdb=" N ILE A 87 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N HIS A 433 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 157 Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 200 removed outlier: 5.479A pdb=" N SER A 347 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR A 368 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 366 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY A 328 " --> pdb=" O MET A 469 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N MET A 469 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER A 330 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE A 467 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 70 through 73 Processing sheet with id=AA7, first strand: chain 'C' and resid 223 through 224 Processing sheet with id=AA8, first strand: chain 'C' and resid 384 through 388 317 hydrogen bonds defined for protein. 867 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.76: 8745 1.76 - 2.30: 90 2.30 - 2.85: 0 2.85 - 3.39: 0 3.39 - 3.93: 3 Bond restraints: 8838 Sorted by residual: bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.928 -1.628 2.00e-02 2.50e+03 6.63e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.816 -1.558 2.00e-02 2.50e+03 6.06e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 3.786 -1.553 2.00e-02 2.50e+03 6.03e+03 bond pdb=" C2D HEC C 502 " pdb=" C3D HEC C 502 " ideal model delta sigma weight residual 1.544 1.331 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C2D HEC C 503 " pdb=" C3D HEC C 503 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.12e+02 ... (remaining 8833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.50: 12061 9.50 - 19.00: 10 19.00 - 28.50: 1 28.50 - 38.00: 8 38.00 - 47.50: 2 Bond angle restraints: 12082 Sorted by residual: angle pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " pdb=" S3 F3S A 602 " ideal model delta sigma weight residual 114.75 67.25 47.50 3.00e+00 1.11e-01 2.51e+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 67.92 44.67 3.00e+00 1.11e-01 2.22e+02 angle pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S4 F3S A 602 " ideal model delta sigma weight residual 103.26 68.73 34.53 3.00e+00 1.11e-01 1.32e+02 angle pdb=" S1 F3S A 602 " pdb="FE3 F3S A 602 " pdb=" S2 F3S A 602 " ideal model delta sigma weight residual 103.25 69.61 33.64 3.00e+00 1.11e-01 1.26e+02 angle pdb="FE1 F3S A 602 " pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 72.09 39.35 32.74 3.00e+00 1.11e-01 1.19e+02 ... (remaining 12077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 4991 35.83 - 71.65: 215 71.65 - 107.47: 18 107.47 - 143.30: 1 143.30 - 179.12: 1 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 -105.59 -74.41 0 5.00e+00 4.00e-02 2.21e+02 dihedral pdb=" C27 U10 C 504 " pdb=" C28 U10 C 504 " pdb=" C29 U10 C 504 " pdb=" C31 U10 C 504 " ideal model delta sinusoidal sigma weight residual 181.72 2.59 179.12 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2C HEC C 501 " pdb=" C3C HEC C 501 " pdb=" CAC HEC C 501 " pdb=" CBC HEC C 501 " ideal model delta sinusoidal sigma weight residual 60.00 -11.17 71.17 2 1.00e+01 1.00e-02 4.30e+01 ... (remaining 5223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.460: 1276 3.460 - 6.920: 0 6.920 - 10.380: 0 10.380 - 13.840: 0 13.840 - 17.300: 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 -6.53 17.30 2.00e-01 2.50e+01 7.48e+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 2.27 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CA PRO B 160 " pdb=" N PRO B 160 " pdb=" C PRO B 160 " pdb=" CB PRO B 160 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1274 not shown) Planarity restraints: 1569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10 C 504 " 0.013 2.00e-02 2.50e+03 1.00e-01 1.75e+02 pdb=" C1M U10 C 504 " -0.117 2.00e-02 2.50e+03 pdb=" C2 U10 C 504 " 0.092 2.00e-02 2.50e+03 pdb=" C3 U10 C 504 " 0.053 2.00e-02 2.50e+03 pdb=" C4 U10 C 504 " -0.184 2.00e-02 2.50e+03 pdb=" C5 U10 C 504 " 0.046 2.00e-02 2.50e+03 pdb=" C6 U10 C 504 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 80 " 0.125 5.00e-02 4.00e+02 1.92e-01 5.92e+01 pdb=" N PRO A 81 " -0.333 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " 0.115 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " 0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CBD HEC C 501 " -0.032 2.00e-02 2.50e+03 6.75e-02 4.56e+01 pdb=" CGD HEC C 501 " 0.117 2.00e-02 2.50e+03 pdb=" O1D HEC C 501 " -0.042 2.00e-02 2.50e+03 pdb=" O2D HEC C 501 " -0.043 2.00e-02 2.50e+03 ... (remaining 1566 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 307 2.71 - 3.26: 8611 3.26 - 3.81: 15309 3.81 - 4.35: 20471 4.35 - 4.90: 32177 Nonbonded interactions: 76875 Sorted by model distance: nonbonded pdb=" N GLU C 129 " pdb=" OE1 GLU C 129 " model vdw 2.165 3.120 nonbonded pdb=" OH TYR A 139 " pdb=" O PRO A 168 " model vdw 2.243 3.040 nonbonded pdb=" S4 F3S A 602 " pdb="FE4 F3S A 602 " model vdw 2.259 2.688 nonbonded pdb=" S3 F3S A 602 " pdb="FE3 F3S A 602 " model vdw 2.261 2.688 nonbonded pdb=" S1 F3S A 602 " pdb="FE1 F3S A 602 " model vdw 2.262 2.688 ... (remaining 76870 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.790 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 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 : 0.030 1.628 8853 Z= 1.508 Angle : 1.356 47.497 12091 Z= 0.502 Chirality : 0.486 17.300 1277 Planarity : 0.008 0.192 1569 Dihedral : 18.651 179.124 3214 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.60 % Allowed : 16.70 % Favored : 80.70 % 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 aren not related in a simple way. whole: 0.11 (0.25), residues: 1083 helix: 1.15 (0.27), residues: 379 sheet: 0.08 (0.54), residues: 92 loop : -0.60 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 94 TYR 0.023 0.001 TYR A 443 PHE 0.019 0.001 PHE A 270 TRP 0.010 0.001 TRP A 338 HIS 0.005 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.03034 ( 8838) covalent geometry : angle 1.33580 (12082) hydrogen bonds : bond 0.13801 ( 314) hydrogen bonds : angle 6.84134 ( 867) metal coordination : bond 0.00068 ( 3) metal coordination : angle 8.70977 ( 9) Misc. bond : bond 0.06444 ( 12) *********************** 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 127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: B 164 HIS cc_start: 0.7121 (OUTLIER) cc_final: 0.6242 (m-70) REVERT: C 187 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.6888 (m-30) outliers start: 23 outliers final: 21 residues processed: 123 average time/residue: 0.5439 time to fit residues: 71.1601 Evaluate side-chains 127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 422 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 449 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.0970 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.0060 chunk 33 optimal weight: 0.0270 chunk 65 optimal weight: 0.0060 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.2068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS ** C 124 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 = 0.3491 r_free = 0.3491 target = 0.132944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.108829 restraints weight = 9272.368| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.36 r_work: 0.3165 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 8853 Z= 0.212 Angle : 1.479 60.577 12091 Z= 0.461 Chirality : 0.052 0.983 1277 Planarity : 0.006 0.122 1569 Dihedral : 11.567 142.902 1322 Min Nonbonded Distance : 1.414 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.48 % Allowed : 16.03 % Favored : 81.49 % 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 aren not related in a simple way. whole: 0.57 (0.26), residues: 1083 helix: 1.53 (0.27), residues: 391 sheet: 1.23 (0.65), residues: 71 loop : -0.46 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 205 TYR 0.018 0.001 TYR A 443 PHE 0.011 0.001 PHE A 270 TRP 0.008 0.001 TRP A 51 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 8838) covalent geometry : angle 1.22357 (12082) hydrogen bonds : bond 0.03274 ( 314) hydrogen bonds : angle 5.24276 ( 867) metal coordination : bond 0.03265 ( 3) metal coordination : angle 30.47037 ( 9) Misc. bond : bond 0.01449 ( 12) *********************** 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 136 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.270 Fit side-chains REVERT: A 189 GLU cc_start: 0.7307 (pt0) cc_final: 0.6995 (pt0) REVERT: A 389 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7489 (mttt) REVERT: B 164 HIS cc_start: 0.6864 (OUTLIER) cc_final: 0.5065 (m-70) REVERT: C 110 ASP cc_start: 0.7827 (OUTLIER) cc_final: 0.7481 (p0) REVERT: C 187 ASP cc_start: 0.7542 (m-30) cc_final: 0.7282 (t70) outliers start: 22 outliers final: 9 residues processed: 123 average time/residue: 0.5502 time to fit residues: 71.8337 Evaluate side-chains 117 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 389 LYS Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 88 optimal weight: 0.0370 chunk 0 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 70 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 overall best weight: 1.5062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 476 ASN A 501 HIS B 138 ASN ** C 124 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 = 0.3417 r_free = 0.3417 target = 0.126621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.101515 restraints weight = 9067.992| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.37 r_work: 0.3071 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 8853 Z= 0.197 Angle : 1.451 81.645 12091 Z= 0.440 Chirality : 0.062 1.403 1277 Planarity : 0.006 0.106 1569 Dihedral : 11.347 103.322 1294 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.66 % Rotamer: Outliers : 2.26 % Allowed : 17.38 % Favored : 80.36 % 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 aren not related in a simple way. whole: 0.47 (0.26), residues: 1083 helix: 1.39 (0.27), residues: 388 sheet: 0.63 (0.60), residues: 81 loop : -0.41 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 94 TYR 0.014 0.002 TYR A 443 PHE 0.022 0.002 PHE A 80 TRP 0.013 0.002 TRP A 338 HIS 0.007 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 8838) covalent geometry : angle 1.10952 (12082) hydrogen bonds : bond 0.04413 ( 314) hydrogen bonds : angle 5.42746 ( 867) metal coordination : bond 0.00700 ( 3) metal coordination : angle 34.28404 ( 9) Misc. bond : bond 0.04143 ( 12) *********************** 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 129 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.376 Fit side-chains REVERT: A 84 ASN cc_start: 0.8115 (t0) cc_final: 0.7748 (t0) REVERT: B 154 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7856 (mtt180) REVERT: B 164 HIS cc_start: 0.7428 (OUTLIER) cc_final: 0.6193 (m-70) REVERT: C 187 ASP cc_start: 0.7549 (m-30) cc_final: 0.7207 (t70) REVERT: C 302 THR cc_start: 0.7309 (OUTLIER) cc_final: 0.7017 (t) outliers start: 20 outliers final: 11 residues processed: 122 average time/residue: 0.5898 time to fit residues: 75.9965 Evaluate side-chains 123 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 450 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 501 HIS B 138 ASN ** C 124 ASN ** 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 = 0.3427 r_free = 0.3427 target = 0.127478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.102610 restraints weight = 9169.543| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.37 r_work: 0.3082 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 8853 Z= 0.172 Angle : 1.445 81.367 12091 Z= 0.428 Chirality : 0.063 1.484 1277 Planarity : 0.006 0.093 1569 Dihedral : 10.920 89.554 1294 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.66 % Rotamer: Outliers : 2.93 % Allowed : 17.49 % Favored : 79.57 % 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 aren not related in a simple way. whole: 0.46 (0.26), residues: 1083 helix: 1.35 (0.27), residues: 393 sheet: 1.01 (0.62), residues: 73 loop : -0.45 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 94 TYR 0.014 0.002 TYR A 443 PHE 0.017 0.002 PHE A 80 TRP 0.010 0.001 TRP A 338 HIS 0.005 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 8838) covalent geometry : angle 1.09432 (12082) hydrogen bonds : bond 0.03989 ( 314) hydrogen bonds : angle 5.27567 ( 867) metal coordination : bond 0.00399 ( 3) metal coordination : angle 34.61384 ( 9) Misc. bond : bond 0.05792 ( 12) *********************** 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 138 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.235 Fit side-chains REVERT: A 84 ASN cc_start: 0.8132 (t0) cc_final: 0.7736 (t0) REVERT: A 152 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8139 (tp30) REVERT: A 276 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7108 (tp40) REVERT: A 468 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7975 (mt-10) REVERT: B 154 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7854 (mtt180) REVERT: B 164 HIS cc_start: 0.7493 (OUTLIER) cc_final: 0.6174 (m-70) REVERT: C 110 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7533 (p0) REVERT: C 143 LYS cc_start: 0.7117 (ttpp) cc_final: 0.6906 (tttp) REVERT: C 182 HIS cc_start: 0.7794 (m-70) cc_final: 0.7473 (m-70) REVERT: C 187 ASP cc_start: 0.7552 (m-30) cc_final: 0.7227 (t70) REVERT: C 302 THR cc_start: 0.7346 (OUTLIER) cc_final: 0.7068 (t) REVERT: C 395 MET cc_start: 0.8903 (ttt) cc_final: 0.8611 (ttt) outliers start: 26 outliers final: 11 residues processed: 123 average time/residue: 0.5988 time to fit residues: 78.0236 Evaluate side-chains 129 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 258 THR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 449 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 66 optimal weight: 0.1980 chunk 22 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 65 optimal weight: 0.0170 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 ASN ** C 124 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 = 0.3469 r_free = 0.3469 target = 0.130979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.107060 restraints weight = 9195.522| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.31 r_work: 0.3118 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.146 8853 Z= 0.139 Angle : 1.407 81.981 12091 Z= 0.408 Chirality : 0.061 1.470 1277 Planarity : 0.005 0.079 1569 Dihedral : 10.275 87.917 1294 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.88 % Favored : 96.03 % Rotamer: Outliers : 2.60 % Allowed : 18.06 % Favored : 79.35 % 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 aren not related in a simple way. whole: 0.62 (0.26), residues: 1083 helix: 1.51 (0.27), residues: 396 sheet: 1.07 (0.63), residues: 73 loop : -0.39 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 94 TYR 0.014 0.001 TYR A 443 PHE 0.013 0.001 PHE A 270 TRP 0.009 0.001 TRP A 51 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8838) covalent geometry : angle 1.06559 (12082) hydrogen bonds : bond 0.03362 ( 314) hydrogen bonds : angle 4.99939 ( 867) metal coordination : bond 0.00360 ( 3) metal coordination : angle 33.67310 ( 9) Misc. bond : bond 0.04366 ( 12) *********************** 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 143 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.282 Fit side-chains REVERT: A 84 ASN cc_start: 0.8099 (t0) cc_final: 0.7696 (t0) REVERT: A 152 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8116 (tp30) REVERT: A 189 GLU cc_start: 0.7274 (pt0) cc_final: 0.6994 (tm-30) REVERT: A 247 LYS cc_start: 0.8603 (tttp) cc_final: 0.8318 (tttm) REVERT: A 276 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7075 (tp40) REVERT: A 468 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7950 (mt-10) REVERT: B 154 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7804 (mtt180) REVERT: B 164 HIS cc_start: 0.7322 (OUTLIER) cc_final: 0.5510 (m-70) REVERT: C 110 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7584 (p0) REVERT: C 187 ASP cc_start: 0.7581 (m-30) cc_final: 0.7342 (t0) REVERT: C 443 LYS cc_start: 0.7926 (pttt) cc_final: 0.7461 (pttp) outliers start: 23 outliers final: 10 residues processed: 130 average time/residue: 0.5733 time to fit residues: 79.2974 Evaluate side-chains 132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 315 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 68 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 19 optimal weight: 0.0870 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN B 138 ASN ** C 124 ASN ** 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 = 0.3451 r_free = 0.3451 target = 0.129422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.105303 restraints weight = 9173.369| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.31 r_work: 0.3101 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.168 8853 Z= 0.156 Angle : 1.422 82.011 12091 Z= 0.419 Chirality : 0.062 1.483 1277 Planarity : 0.005 0.077 1569 Dihedral : 10.372 87.753 1292 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.38 % Rotamer: Outliers : 2.26 % Allowed : 17.95 % Favored : 79.80 % 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 aren not related in a simple way. whole: 0.62 (0.26), residues: 1083 helix: 1.50 (0.27), residues: 396 sheet: 1.03 (0.63), residues: 73 loop : -0.37 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 94 TYR 0.013 0.001 TYR A 443 PHE 0.016 0.001 PHE A 80 TRP 0.008 0.001 TRP A 338 HIS 0.005 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8838) covalent geometry : angle 1.08090 (12082) hydrogen bonds : bond 0.03639 ( 314) hydrogen bonds : angle 5.07137 ( 867) metal coordination : bond 0.00399 ( 3) metal coordination : angle 33.88336 ( 9) Misc. bond : bond 0.05193 ( 12) *********************** 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 135 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.274 Fit side-chains REVERT: A 84 ASN cc_start: 0.8143 (t0) cc_final: 0.7737 (t0) REVERT: A 152 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8133 (tp30) REVERT: A 189 GLU cc_start: 0.7264 (pt0) cc_final: 0.6967 (tm-30) REVERT: A 247 LYS cc_start: 0.8657 (tttp) cc_final: 0.8379 (tttm) REVERT: A 276 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7089 (tp40) REVERT: A 384 MET cc_start: 0.8870 (mtp) cc_final: 0.8477 (mtp) REVERT: B 154 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7835 (mtt180) REVERT: B 164 HIS cc_start: 0.7474 (OUTLIER) cc_final: 0.5861 (m-70) REVERT: C 110 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7616 (p0) REVERT: C 187 ASP cc_start: 0.7583 (m-30) cc_final: 0.7313 (t0) outliers start: 20 outliers final: 10 residues processed: 124 average time/residue: 0.6211 time to fit residues: 81.6012 Evaluate side-chains 130 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 449 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 103 optimal weight: 0.2980 chunk 10 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 ASN ** C 124 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 = 0.3470 r_free = 0.3470 target = 0.130914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.106916 restraints weight = 9259.936| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.33 r_work: 0.3127 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 8853 Z= 0.143 Angle : 1.408 82.097 12091 Z= 0.411 Chirality : 0.061 1.473 1277 Planarity : 0.005 0.073 1569 Dihedral : 10.216 87.414 1292 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.16 % Favored : 95.75 % Rotamer: Outliers : 2.60 % Allowed : 17.49 % Favored : 79.91 % 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 aren not related in a simple way. whole: 0.68 (0.26), residues: 1083 helix: 1.57 (0.27), residues: 396 sheet: 1.02 (0.63), residues: 73 loop : -0.34 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 94 TYR 0.025 0.001 TYR A 79 PHE 0.014 0.001 PHE A 270 TRP 0.008 0.001 TRP A 51 HIS 0.004 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8838) covalent geometry : angle 1.06916 (12082) hydrogen bonds : bond 0.03418 ( 314) hydrogen bonds : angle 4.97989 ( 867) metal coordination : bond 0.00368 ( 3) metal coordination : angle 33.58971 ( 9) Misc. bond : bond 0.05041 ( 12) *********************** 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 133 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 152 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8116 (tp30) REVERT: A 189 GLU cc_start: 0.7238 (pt0) cc_final: 0.6959 (tm-30) REVERT: A 247 LYS cc_start: 0.8590 (tttp) cc_final: 0.8342 (tttm) REVERT: A 276 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7147 (tp40) REVERT: A 384 MET cc_start: 0.8869 (mtp) cc_final: 0.8433 (mtp) REVERT: A 468 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7878 (mt-10) REVERT: B 154 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7746 (mtt180) REVERT: B 164 HIS cc_start: 0.7397 (OUTLIER) cc_final: 0.5732 (m-70) REVERT: C 110 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7606 (p0) REVERT: C 187 ASP cc_start: 0.7580 (m-30) cc_final: 0.7314 (t0) outliers start: 23 outliers final: 11 residues processed: 121 average time/residue: 0.6027 time to fit residues: 77.2942 Evaluate side-chains 122 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 449 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 99 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 0.0870 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN B 138 ASN ** C 124 ASN ** 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 = 0.3467 r_free = 0.3467 target = 0.130721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.106793 restraints weight = 9134.370| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.30 r_work: 0.3135 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.184 8853 Z= 0.147 Angle : 1.413 82.064 12091 Z= 0.414 Chirality : 0.061 1.475 1277 Planarity : 0.005 0.072 1569 Dihedral : 10.251 87.375 1292 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 2.48 % Allowed : 18.06 % Favored : 79.46 % 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 aren not related in a simple way. whole: 0.71 (0.26), residues: 1083 helix: 1.62 (0.27), residues: 390 sheet: 1.03 (0.63), residues: 73 loop : -0.32 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 94 TYR 0.027 0.001 TYR A 79 PHE 0.014 0.001 PHE A 270 TRP 0.008 0.001 TRP A 51 HIS 0.004 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8838) covalent geometry : angle 1.07509 (12082) hydrogen bonds : bond 0.03474 ( 314) hydrogen bonds : angle 4.97940 ( 867) metal coordination : bond 0.00380 ( 3) metal coordination : angle 33.61934 ( 9) Misc. bond : bond 0.05349 ( 12) *********************** 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 127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8161 (t0) cc_final: 0.7770 (t0) REVERT: A 152 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8113 (tp30) REVERT: A 189 GLU cc_start: 0.7232 (pt0) cc_final: 0.6957 (tm-30) REVERT: A 247 LYS cc_start: 0.8590 (tttp) cc_final: 0.8344 (tttm) REVERT: A 276 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7103 (tp40) REVERT: A 468 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7892 (mt-10) REVERT: B 154 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7816 (mtt180) REVERT: B 164 HIS cc_start: 0.7470 (OUTLIER) cc_final: 0.5898 (m-70) REVERT: C 110 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7611 (p0) REVERT: C 129 GLU cc_start: 0.7861 (mp0) cc_final: 0.7559 (mp0) REVERT: C 143 LYS cc_start: 0.7160 (ttpp) cc_final: 0.6871 (tttp) REVERT: C 187 ASP cc_start: 0.7541 (m-30) cc_final: 0.7265 (t0) outliers start: 22 outliers final: 11 residues processed: 116 average time/residue: 0.5917 time to fit residues: 72.4614 Evaluate side-chains 122 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 449 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 20 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 93 optimal weight: 0.0870 chunk 37 optimal weight: 0.9980 chunk 68 optimal weight: 0.0070 chunk 104 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 ASN ** C 124 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 = 0.3491 r_free = 0.3491 target = 0.132627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.108996 restraints weight = 9131.667| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.30 r_work: 0.3160 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.192 8853 Z= 0.137 Angle : 1.403 82.245 12091 Z= 0.407 Chirality : 0.060 1.468 1277 Planarity : 0.005 0.069 1569 Dihedral : 10.094 88.712 1292 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.79 % Favored : 96.12 % Rotamer: Outliers : 2.37 % Allowed : 18.51 % Favored : 79.12 % 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 aren not related in a simple way. whole: 0.78 (0.26), residues: 1083 helix: 1.68 (0.27), residues: 390 sheet: 1.03 (0.63), residues: 73 loop : -0.28 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 94 TYR 0.026 0.001 TYR A 79 PHE 0.014 0.001 PHE C 210 TRP 0.009 0.001 TRP A 51 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8838) covalent geometry : angle 1.06936 (12082) hydrogen bonds : bond 0.03236 ( 314) hydrogen bonds : angle 4.89055 ( 867) metal coordination : bond 0.00361 ( 3) metal coordination : angle 33.28664 ( 9) Misc. bond : bond 0.05732 ( 12) *********************** 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 135 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8099 (t0) cc_final: 0.7691 (t0) REVERT: A 152 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8118 (tp30) REVERT: A 189 GLU cc_start: 0.7224 (pt0) cc_final: 0.6987 (tm-30) REVERT: A 247 LYS cc_start: 0.8557 (tttp) cc_final: 0.8315 (tttm) REVERT: A 276 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7091 (tp40) REVERT: A 468 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7893 (mt-10) REVERT: B 154 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7710 (mtt180) REVERT: B 164 HIS cc_start: 0.7347 (OUTLIER) cc_final: 0.5489 (m-70) REVERT: C 110 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7667 (p0) REVERT: C 129 GLU cc_start: 0.7842 (mp0) cc_final: 0.7538 (mp0) REVERT: C 143 LYS cc_start: 0.7153 (ttpp) cc_final: 0.6853 (tttp) REVERT: C 187 ASP cc_start: 0.7560 (m-30) cc_final: 0.7306 (t0) outliers start: 21 outliers final: 10 residues processed: 123 average time/residue: 0.5337 time to fit residues: 69.7549 Evaluate side-chains 126 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN B 138 ASN ** C 124 ASN ** 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 = 0.3455 r_free = 0.3455 target = 0.129677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.105501 restraints weight = 9132.841| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.32 r_work: 0.3104 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.193 8853 Z= 0.162 Angle : 1.429 81.726 12091 Z= 0.421 Chirality : 0.062 1.482 1277 Planarity : 0.005 0.073 1569 Dihedral : 10.384 89.761 1292 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.16 % Favored : 95.75 % Rotamer: Outliers : 1.92 % Allowed : 19.19 % Favored : 78.89 % 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 aren not related in a simple way. whole: 0.70 (0.26), residues: 1083 helix: 1.58 (0.27), residues: 390 sheet: 1.09 (0.63), residues: 73 loop : -0.32 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 94 TYR 0.027 0.001 TYR A 79 PHE 0.016 0.001 PHE A 80 TRP 0.010 0.001 TRP A 338 HIS 0.005 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8838) covalent geometry : angle 1.08946 (12082) hydrogen bonds : bond 0.03658 ( 314) hydrogen bonds : angle 5.02337 ( 867) metal coordination : bond 0.00403 ( 3) metal coordination : angle 33.91972 ( 9) Misc. bond : bond 0.05652 ( 12) ********************** 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 125 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8175 (t0) cc_final: 0.7767 (t0) REVERT: A 152 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8129 (tp30) REVERT: A 189 GLU cc_start: 0.7247 (pt0) cc_final: 0.6939 (tm-30) REVERT: A 276 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7094 (tp40) REVERT: A 468 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: B 154 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7838 (mtt180) REVERT: B 164 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.6039 (m-70) REVERT: C 75 MET cc_start: 0.8413 (mpm) cc_final: 0.8058 (mmt) REVERT: C 110 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7668 (p0) REVERT: C 129 GLU cc_start: 0.7850 (mp0) cc_final: 0.7534 (mp0) REVERT: C 143 LYS cc_start: 0.7145 (ttpp) cc_final: 0.6902 (tttp) REVERT: C 187 ASP cc_start: 0.7451 (m-30) cc_final: 0.7176 (t0) outliers start: 17 outliers final: 9 residues processed: 117 average time/residue: 0.5294 time to fit residues: 65.5473 Evaluate side-chains 120 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 276 GLN Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 468 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 104 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 6 optimal weight: 0.0370 chunk 98 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 overall best weight: 1.2862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS B 138 ASN ** C 124 ASN ** 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 = 0.3433 r_free = 0.3433 target = 0.127769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.103380 restraints weight = 9202.181| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.32 r_work: 0.3094 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.232 8853 Z= 0.182 Angle : 1.449 81.483 12091 Z= 0.434 Chirality : 0.064 1.490 1277 Planarity : 0.006 0.076 1569 Dihedral : 10.633 87.551 1292 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.20 % Rotamer: Outliers : 1.92 % Allowed : 19.53 % Favored : 78.56 % 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 aren not related in a simple way. whole: 0.55 (0.26), residues: 1083 helix: 1.46 (0.27), residues: 391 sheet: 0.63 (0.60), residues: 81 loop : -0.37 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 94 TYR 0.029 0.002 TYR A 79 PHE 0.022 0.002 PHE A 80 TRP 0.013 0.002 TRP A 338 HIS 0.006 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00420 ( 8838) covalent geometry : angle 1.10613 (12082) hydrogen bonds : bond 0.04005 ( 314) hydrogen bonds : angle 5.17214 ( 867) metal coordination : bond 0.00464 ( 3) metal coordination : angle 34.33286 ( 9) Misc. bond : bond 0.07058 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2896.18 seconds wall clock time: 50 minutes 0.04 seconds (3000.04 seconds total)