Starting phenix.real_space_refine on Fri Nov 15 17:15:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jek_36191/11_2024/8jek_36191.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jek_36191/11_2024/8jek_36191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jek_36191/11_2024/8jek_36191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jek_36191/11_2024/8jek_36191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jek_36191/11_2024/8jek_36191.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jek_36191/11_2024/8jek_36191.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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 5440 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 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8623 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: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 186 Unusual residues: {'HEC': 3, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1} Unresolved non-hydrogen planarities: 5 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1767 SG CYS A 226 51.827 64.206 39.994 1.00 27.34 S ATOM 1738 SG CYS A 222 50.728 68.892 44.226 1.00 28.24 S ATOM 1698 SG CYS A 216 52.433 63.595 46.715 1.00 34.01 S Time building chain proxies: 5.75, per 1000 atoms: 0.67 Number of scatterers: 8623 At special positions: 0 Unit cell: (104.4, 108.75, 77.43, 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 5440 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: 2.67 Conformation dependent library (CDL) restraints added in 1.1 seconds 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 41.4% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 16 through 29 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: 3.923A pdb=" N LYS A 97 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.924A pdb=" N THR A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 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 233 through 244 removed outlier: 4.173A 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: 3.588A 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 387 through 401 removed outlier: 3.651A pdb=" N LEU A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 462 removed outlier: 4.194A pdb=" N VAL A 444 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.523A pdb=" N THR A 513 " --> pdb=" O THR A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 541 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 112 Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.548A pdb=" N SER B 172 " --> pdb=" O TYR B 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 51 Processing helix chain 'C' and resid 51 through 56 removed outlier: 4.313A pdb=" N CYS C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS C 56 " --> pdb=" O CYS C 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 51 through 56' Processing helix chain 'C' and resid 95 through 106 removed outlier: 3.518A pdb=" N GLY C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.915A pdb=" N ARG C 125 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 141 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: 3.685A 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 Processing helix chain 'C' and resid 279 through 291 Processing helix chain 'C' and resid 317 through 324 removed outlier: 3.752A 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: 6.657A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP A 9 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N VAL A 286 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A 11 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A 282 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N THR A 266 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLU A 258 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE A 268 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ALA A 256 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE A 270 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL A 254 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.657A pdb=" N LEU A 34 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A 10 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU A 36 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP A 9 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N VAL A 286 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A 11 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N PHE A 507 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 6.466A 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: 6.429A pdb=" N ILE A 87 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 4.759A 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: 5.457A pdb=" N SER A 347 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR A 368 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY A 328 " --> pdb=" O MET A 469 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N MET A 469 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N SER A 330 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 4.241A 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 225 Processing sheet with id=AA8, first strand: chain 'C' and resid 384 through 388 319 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: 2.45 Time building geometry restraints manager: 3.01 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: 8764 1.76 - 2.31: 90 2.31 - 2.85: 0 2.85 - 3.39: 0 3.39 - 3.94: 3 Bond restraints: 8857 Sorted by residual: bond pdb=" S2 F3S A 602 " pdb="FE3 F3S A 602 " ideal model delta sigma weight residual 2.300 3.935 -1.635 2.00e-02 2.50e+03 6.69e+03 bond pdb=" S4 F3S A 602 " pdb="FE1 F3S A 602 " ideal model delta sigma weight residual 2.233 3.818 -1.585 2.00e-02 2.50e+03 6.28e+03 bond pdb=" S1 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 2.258 3.789 -1.531 2.00e-02 2.50e+03 5.86e+03 bond pdb=" C2D HEC C 502 " pdb=" C3D HEC C 502 " ideal model delta sigma weight residual 1.544 1.329 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C2D HEC C 503 " pdb=" C3D HEC C 503 " ideal model delta sigma weight residual 1.544 1.333 0.211 2.00e-02 2.50e+03 1.11e+02 ... (remaining 8852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.46: 12088 9.46 - 18.93: 6 18.93 - 28.39: 0 28.39 - 37.85: 8 37.85 - 47.31: 2 Bond angle restraints: 12104 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 67.44 47.31 3.00e+00 1.11e-01 2.49e+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 67.16 45.43 3.00e+00 1.11e-01 2.29e+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 68.87 34.38 3.00e+00 1.11e-01 1.31e+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 69.18 34.08 3.00e+00 1.11e-01 1.29e+02 angle pdb="FE3 F3S A 602 " pdb=" S2 F3S A 602 " pdb="FE4 F3S A 602 " ideal model delta sigma weight residual 71.75 39.22 32.53 3.00e+00 1.11e-01 1.18e+02 ... (remaining 12099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.62: 5052 34.62 - 69.24: 170 69.24 - 103.86: 18 103.86 - 138.48: 0 138.48 - 173.09: 1 Dihedral angle restraints: 5241 sinusoidal: 2089 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 -119.72 -60.28 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" C37 U10 C 504 " pdb=" C38 U10 C 504 " pdb=" C39 U10 C 504 " pdb=" C41 U10 C 504 " ideal model delta sinusoidal sigma weight residual -5.63 167.47 -173.09 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C2C HEC C 502 " pdb=" C3C HEC C 502 " pdb=" CAC HEC C 502 " pdb=" CBC HEC C 502 " ideal model delta sinusoidal sigma weight residual -120.00 -38.15 -81.85 2 1.00e+01 1.00e-02 4.70e+01 ... (remaining 5238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.462: 1276 3.462 - 6.924: 0 6.924 - 10.386: 0 10.386 - 13.848: 0 13.848 - 17.310: 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 -6.54 17.31 2.00e-01 2.50e+01 7.49e+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 2.32 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" C3' FAD A 601 " pdb=" C2' FAD A 601 " pdb=" C4' FAD A 601 " pdb=" O3' FAD A 601 " both_signs ideal model delta sigma weight residual False -2.55 -2.34 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1274 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10 C 504 " -0.001 2.00e-02 2.50e+03 9.06e-02 1.44e+02 pdb=" C1M U10 C 504 " 0.063 2.00e-02 2.50e+03 pdb=" C2 U10 C 504 " 0.028 2.00e-02 2.50e+03 pdb=" C3 U10 C 504 " -0.133 2.00e-02 2.50e+03 pdb=" C4 U10 C 504 " 0.144 2.00e-02 2.50e+03 pdb=" C5 U10 C 504 " 0.015 2.00e-02 2.50e+03 pdb=" C6 U10 C 504 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CBD HEC C 501 " -0.033 2.00e-02 2.50e+03 6.99e-02 4.88e+01 pdb=" CGD HEC C 501 " 0.121 2.00e-02 2.50e+03 pdb=" O1D HEC C 501 " -0.043 2.00e-02 2.50e+03 pdb=" O2D HEC C 501 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 80 " -0.101 5.00e-02 4.00e+02 1.56e-01 3.91e+01 pdb=" N PRO A 81 " 0.271 5.00e-02 4.00e+02 pdb=" CA PRO A 81 " -0.089 5.00e-02 4.00e+02 pdb=" CD PRO A 81 " -0.081 5.00e-02 4.00e+02 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 450 2.72 - 3.27: 8576 3.27 - 3.81: 15262 3.81 - 4.36: 19757 4.36 - 4.90: 32516 Nonbonded interactions: 76561 Sorted by model distance: nonbonded pdb=" O ALA C 397 " pdb=" OG SER C 402 " model vdw 2.178 3.040 nonbonded pdb=" OH TYR A 118 " pdb=" O SER A 517 " model vdw 2.189 3.040 nonbonded pdb=" O ARG A 358 " pdb=" OH TYR A 443 " model vdw 2.195 3.040 nonbonded pdb=" OG SER C 354 " pdb=" OD1 ASP C 356 " model vdw 2.219 3.040 nonbonded pdb=" S4 F3S A 602 " pdb="FE4 F3S A 602 " model vdw 2.257 2.688 ... (remaining 76556 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: 0.010 Normalize map: mean=0, sd=1: 0.870 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.290 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 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 1.635 8857 Z= 1.597 Angle : 1.339 47.314 12104 Z= 0.518 Chirality : 0.487 17.310 1277 Planarity : 0.008 0.156 1572 Dihedral : 17.134 173.095 3229 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.69 % Allowed : 13.21 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1083 helix: 1.47 (0.28), residues: 363 sheet: 0.37 (0.64), residues: 72 loop : -0.70 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 111 HIS 0.006 0.001 HIS A 110 PHE 0.017 0.001 PHE A 270 TYR 0.014 0.001 TYR A 79 ARG 0.002 0.000 ARG C 125 *********************** 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 122 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 1.000 Fit side-chains REVERT: A 505 ASN cc_start: 0.7804 (t0) cc_final: 0.7253 (t0) REVERT: C 315 TYR cc_start: 0.6711 (OUTLIER) cc_final: 0.5098 (p90) outliers start: 15 outliers final: 13 residues processed: 117 average time/residue: 1.1256 time to fit residues: 142.8887 Evaluate side-chains 118 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 368 TYR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 445 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 8857 Z= 0.324 Angle : 1.323 68.807 12104 Z= 0.491 Chirality : 0.099 3.152 1277 Planarity : 0.006 0.111 1572 Dihedral : 12.304 153.489 1318 Min Nonbonded Distance : 1.477 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.20 % Rotamer: Outliers : 2.71 % Allowed : 11.74 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1083 helix: 1.51 (0.27), residues: 387 sheet: 0.38 (0.64), residues: 73 loop : -0.67 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 111 HIS 0.004 0.001 HIS A 76 PHE 0.015 0.001 PHE A 270 TYR 0.016 0.001 TYR A 79 ARG 0.004 0.000 ARG A 205 *********************** 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 135 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 171 ASN cc_start: 0.8748 (m110) cc_final: 0.8460 (m110) REVERT: A 478 HIS cc_start: 0.7518 (OUTLIER) cc_final: 0.7085 (p-80) REVERT: C 135 TYR cc_start: 0.8327 (t80) cc_final: 0.8079 (t80) REVERT: C 143 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.6981 (pttp) outliers start: 24 outliers final: 10 residues processed: 121 average time/residue: 0.9129 time to fit residues: 119.6451 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 : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN C 326 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 8857 Z= 0.302 Angle : 1.092 85.055 12104 Z= 0.426 Chirality : 0.062 1.379 1277 Planarity : 0.006 0.101 1572 Dihedral : 12.057 150.072 1309 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.80 % Favored : 95.11 % Rotamer: Outliers : 2.93 % Allowed : 12.75 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.26), residues: 1083 helix: 1.50 (0.27), residues: 387 sheet: 0.31 (0.64), residues: 73 loop : -0.69 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 173 HIS 0.005 0.001 HIS C 200 PHE 0.017 0.002 PHE A 270 TYR 0.018 0.001 TYR A 79 ARG 0.004 0.000 ARG A 205 *********************** 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 135 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 478 HIS cc_start: 0.7645 (OUTLIER) cc_final: 0.7207 (p-80) REVERT: A 539 ASN cc_start: 0.8338 (t0) cc_final: 0.7975 (t0) REVERT: C 135 TYR cc_start: 0.8350 (t80) cc_final: 0.8123 (t80) REVERT: C 143 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.6951 (pttp) outliers start: 26 outliers final: 14 residues processed: 121 average time/residue: 1.0983 time to fit residues: 143.4819 Evaluate side-chains 123 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 65 optimal weight: 0.0770 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 505 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 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 0.108 8857 Z= 0.254 Angle : 1.056 83.149 12104 Z= 0.410 Chirality : 0.061 1.426 1277 Planarity : 0.006 0.099 1572 Dihedral : 11.792 144.983 1308 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.62 % Favored : 95.29 % Rotamer: Outliers : 2.71 % Allowed : 13.54 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1083 helix: 1.59 (0.27), residues: 387 sheet: 0.39 (0.63), residues: 72 loop : -0.66 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 173 HIS 0.004 0.001 HIS C 200 PHE 0.016 0.001 PHE A 270 TYR 0.018 0.001 TYR A 79 ARG 0.002 0.000 ARG C 323 *********************** 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 131 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 171 ASN cc_start: 0.8782 (m110) cc_final: 0.8494 (m110) REVERT: A 478 HIS cc_start: 0.7595 (OUTLIER) cc_final: 0.7131 (p-80) REVERT: A 539 ASN cc_start: 0.8338 (t0) cc_final: 0.7975 (t0) REVERT: C 118 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.5759 (tpt) REVERT: C 143 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.6956 (pttp) REVERT: C 267 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8392 (tpt) outliers start: 24 outliers final: 14 residues processed: 118 average time/residue: 1.0554 time to fit residues: 134.5263 Evaluate side-chains 122 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.0040 chunk 59 optimal weight: 0.0470 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.6096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 8857 Z= 0.339 Angle : 1.083 81.869 12104 Z= 0.428 Chirality : 0.064 1.470 1277 Planarity : 0.006 0.106 1572 Dihedral : 11.917 143.359 1308 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.36 % Favored : 94.55 % Rotamer: Outliers : 2.93 % Allowed : 13.66 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1083 helix: 1.47 (0.27), residues: 385 sheet: 0.28 (0.63), residues: 73 loop : -0.69 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 128 HIS 0.006 0.001 HIS C 200 PHE 0.019 0.002 PHE A 80 TYR 0.019 0.002 TYR A 79 ARG 0.002 0.000 ARG C 323 *********************** 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 130 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 478 HIS cc_start: 0.7696 (OUTLIER) cc_final: 0.7247 (p-80) REVERT: A 539 ASN cc_start: 0.8394 (t0) cc_final: 0.8026 (t0) REVERT: B 112 MET cc_start: 0.8250 (ttp) cc_final: 0.8048 (ttp) REVERT: B 183 PHE cc_start: 0.6782 (OUTLIER) cc_final: 0.5903 (p90) REVERT: C 118 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.5766 (tpt) REVERT: C 135 TYR cc_start: 0.8278 (t80) cc_final: 0.8066 (t80) REVERT: C 143 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.6972 (pttp) outliers start: 26 outliers final: 17 residues processed: 117 average time/residue: 1.1220 time to fit residues: 141.5742 Evaluate side-chains 124 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 8857 Z= 0.333 Angle : 1.079 81.534 12104 Z= 0.426 Chirality : 0.064 1.485 1277 Planarity : 0.006 0.107 1572 Dihedral : 11.880 140.564 1308 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.26 % Favored : 94.64 % Rotamer: Outliers : 3.16 % Allowed : 13.54 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.25), residues: 1083 helix: 1.37 (0.27), residues: 392 sheet: 0.31 (0.63), residues: 73 loop : -0.68 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 128 HIS 0.006 0.001 HIS C 200 PHE 0.018 0.002 PHE A 270 TYR 0.019 0.002 TYR A 79 ARG 0.002 0.000 ARG C 323 *********************** 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: 28 poor density : 107 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 HIS cc_start: 0.7704 (OUTLIER) cc_final: 0.7262 (p-80) REVERT: A 539 ASN cc_start: 0.8413 (t0) cc_final: 0.8040 (t0) REVERT: B 112 MET cc_start: 0.8248 (ttp) cc_final: 0.8032 (ttp) REVERT: B 126 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6917 (mtp180) REVERT: B 183 PHE cc_start: 0.6747 (OUTLIER) cc_final: 0.5743 (p90) REVERT: C 118 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.5777 (tpt) REVERT: C 135 TYR cc_start: 0.8290 (t80) cc_final: 0.8057 (t80) REVERT: C 143 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.6979 (pttp) outliers start: 28 outliers final: 18 residues processed: 122 average time/residue: 1.1110 time to fit residues: 145.8570 Evaluate side-chains 126 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 87 optimal weight: 0.0570 chunk 58 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 8857 Z= 0.227 Angle : 1.038 81.894 12104 Z= 0.402 Chirality : 0.062 1.485 1277 Planarity : 0.005 0.104 1572 Dihedral : 11.438 130.284 1308 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.71 % Allowed : 14.11 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.26), residues: 1083 helix: 1.59 (0.27), residues: 393 sheet: 0.42 (0.63), residues: 72 loop : -0.54 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 51 HIS 0.004 0.001 HIS A 110 PHE 0.015 0.001 PHE A 270 TYR 0.015 0.001 TYR A 79 ARG 0.002 0.000 ARG C 323 *********************** 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 128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ASN cc_start: 0.8788 (m110) cc_final: 0.8546 (m110) REVERT: A 478 HIS cc_start: 0.7496 (OUTLIER) cc_final: 0.7081 (p-80) REVERT: A 539 ASN cc_start: 0.8378 (t0) cc_final: 0.8028 (t0) REVERT: B 112 MET cc_start: 0.8211 (ttp) cc_final: 0.7971 (ttp) REVERT: B 126 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6709 (mtp180) REVERT: C 118 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.5783 (tpt) REVERT: C 143 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.6925 (pttp) REVERT: C 315 TYR cc_start: 0.6673 (OUTLIER) cc_final: 0.5447 (p90) outliers start: 24 outliers final: 14 residues processed: 117 average time/residue: 1.1289 time to fit residues: 142.0482 Evaluate side-chains 120 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.3980 chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 8857 Z= 0.228 Angle : 1.046 82.022 12104 Z= 0.405 Chirality : 0.062 1.482 1277 Planarity : 0.006 0.107 1572 Dihedral : 11.250 121.114 1308 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.93 % Allowed : 13.77 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 1083 helix: 1.65 (0.27), residues: 393 sheet: 0.53 (0.65), residues: 71 loop : -0.50 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 111 HIS 0.004 0.001 HIS C 200 PHE 0.016 0.001 PHE A 270 TYR 0.016 0.001 TYR A 79 ARG 0.002 0.000 ARG C 323 *********************** 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 128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7593 (m-30) REVERT: A 171 ASN cc_start: 0.8820 (m110) cc_final: 0.8585 (m110) REVERT: A 478 HIS cc_start: 0.7494 (OUTLIER) cc_final: 0.7032 (p-80) REVERT: A 539 ASN cc_start: 0.8346 (t0) cc_final: 0.7996 (t0) REVERT: B 112 MET cc_start: 0.8239 (ttp) cc_final: 0.8003 (ttp) REVERT: B 126 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6717 (mtp85) REVERT: C 118 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.5781 (tpt) REVERT: C 143 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.6924 (pttp) REVERT: C 267 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8457 (tpt) outliers start: 26 outliers final: 16 residues processed: 115 average time/residue: 1.0788 time to fit residues: 133.8718 Evaluate side-chains 123 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 8857 Z= 0.236 Angle : 1.049 82.076 12104 Z= 0.406 Chirality : 0.062 1.482 1277 Planarity : 0.005 0.104 1572 Dihedral : 11.185 116.031 1308 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.60 % Allowed : 14.33 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.26), residues: 1083 helix: 1.66 (0.27), residues: 393 sheet: 0.53 (0.65), residues: 71 loop : -0.50 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 111 HIS 0.004 0.001 HIS A 76 PHE 0.017 0.001 PHE A 270 TYR 0.017 0.001 TYR A 79 ARG 0.002 0.000 ARG C 323 *********************** 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 123 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7605 (m-30) REVERT: A 171 ASN cc_start: 0.8802 (m110) cc_final: 0.8551 (m110) REVERT: A 460 LYS cc_start: 0.7523 (tttm) cc_final: 0.7261 (tmtm) REVERT: A 478 HIS cc_start: 0.7500 (OUTLIER) cc_final: 0.7035 (p-80) REVERT: A 539 ASN cc_start: 0.8370 (t0) cc_final: 0.8015 (t0) REVERT: B 112 MET cc_start: 0.8240 (ttp) cc_final: 0.7998 (ttp) REVERT: B 126 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6735 (mtp85) REVERT: C 118 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.5786 (tpt) REVERT: C 143 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.6926 (pttp) REVERT: C 267 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8500 (tpt) outliers start: 23 outliers final: 16 residues processed: 112 average time/residue: 1.0658 time to fit residues: 129.2151 Evaluate side-chains 120 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 315 TYR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 429 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 0.0570 chunk 71 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 8857 Z= 0.224 Angle : 1.047 82.199 12104 Z= 0.404 Chirality : 0.061 1.475 1277 Planarity : 0.005 0.102 1572 Dihedral : 11.032 109.387 1308 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.60 % Allowed : 14.56 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.26), residues: 1083 helix: 1.71 (0.27), residues: 393 sheet: 0.52 (0.65), residues: 71 loop : -0.49 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 111 HIS 0.003 0.001 HIS A 76 PHE 0.016 0.001 PHE A 270 TYR 0.015 0.001 TYR A 79 ARG 0.002 0.000 ARG C 323 ********************** 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: 23 poor density : 102 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7566 (m-30) REVERT: A 171 ASN cc_start: 0.8823 (m110) cc_final: 0.8581 (m110) REVERT: A 460 LYS cc_start: 0.7489 (tttm) cc_final: 0.7232 (tmtm) REVERT: A 478 HIS cc_start: 0.7432 (OUTLIER) cc_final: 0.6981 (p-80) REVERT: A 539 ASN cc_start: 0.8368 (t0) cc_final: 0.8019 (t0) REVERT: B 112 MET cc_start: 0.8219 (ttp) cc_final: 0.7973 (ttp) REVERT: B 126 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6702 (mtp85) REVERT: B 180 MET cc_start: 0.8327 (mmm) cc_final: 0.8112 (tpt) REVERT: C 118 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.5783 (tpt) REVERT: C 143 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.6897 (pttp) REVERT: C 267 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8507 (tpt) outliers start: 23 outliers final: 14 residues processed: 114 average time/residue: 1.0517 time to fit residues: 130.3683 Evaluate side-chains 120 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 478 HIS Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 HIS Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 LYS Chi-restraints excluded: chain C residue 152 THR Chi-restraints excluded: chain C residue 267 MET 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 91 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 85 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 0.0170 overall best weight: 1.2622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.134555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.108624 restraints weight = 8715.977| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.19 r_work: 0.3056 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 8857 Z= 0.293 Angle : 1.079 81.722 12104 Z= 0.422 Chirality : 0.063 1.487 1277 Planarity : 0.006 0.104 1572 Dihedral : 11.197 110.430 1306 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.08 % Favored : 94.83 % Rotamer: Outliers : 2.26 % Allowed : 15.12 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.10 % Twisted Proline : 1.49 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1083 helix: 1.58 (0.27), residues: 392 sheet: 0.54 (0.64), residues: 72 loop : -0.58 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 128 HIS 0.005 0.001 HIS C 200 PHE 0.020 0.001 PHE A 80 TYR 0.020 0.001 TYR A 79 ARG 0.002 0.000 ARG A 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3020.06 seconds wall clock time: 57 minutes 39.32 seconds (3459.32 seconds total)