Starting phenix.real_space_refine on Tue Aug 4 22:07:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vhd_65063/08_2026/9vhd_65063.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vhd_65063/08_2026/9vhd_65063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vhd_65063/08_2026/9vhd_65063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vhd_65063/08_2026/9vhd_65063.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vhd_65063/08_2026/9vhd_65063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vhd_65063/08_2026/9vhd_65063.map" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 4504 2.51 5 N 1144 2.21 5 O 1200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6878 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3439 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 18, 'TRANS': 453} Chain: "A" Number of atoms: 3439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3439 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 18, 'TRANS': 453} Time building chain proxies: 1.66, per 1000 atoms: 0.24 Number of scatterers: 6878 At special positions: 0 Unit cell: (82.77, 72.09, 116.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1200 8.00 N 1144 7.00 C 4504 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=0, symmetry=0 Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 386.3 milliseconds 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1656 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 0 sheets defined 89.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'B' and resid 48 through 75 removed outlier: 3.665A pdb=" N LEU B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N GLN B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 84 removed outlier: 3.864A pdb=" N ILE B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 104 removed outlier: 4.337A pdb=" N TYR B 97 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL B 98 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU B 104 " --> pdb=" O THR B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.589A pdb=" N GLY B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 109 " --> pdb=" O MET B 105 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY B 112 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASP B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 137 removed outlier: 3.785A pdb=" N ILE B 137 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 159 removed outlier: 3.517A pdb=" N LEU B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 170 removed outlier: 3.768A pdb=" N ALA B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE B 170 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 202 removed outlier: 3.612A pdb=" N ASN B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR B 187 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA B 188 " --> pdb=" O GLY B 184 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 212 through 228 removed outlier: 4.750A pdb=" N ILE B 216 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 264 Proline residue: B 261 - end of helix Processing helix chain 'B' and resid 267 through 288 Processing helix chain 'B' and resid 289 through 291 No H-bonds generated for 'chain 'B' and resid 289 through 291' Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.808A pdb=" N LEU B 300 " --> pdb=" O PRO B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 334 removed outlier: 3.602A pdb=" N VAL B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 346 through 364 removed outlier: 3.695A pdb=" N VAL B 350 " --> pdb=" O PHE B 346 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN B 362 " --> pdb=" O GLY B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 390 removed outlier: 3.706A pdb=" N LEU B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 423 removed outlier: 4.065A pdb=" N ASN B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL B 402 " --> pdb=" O PHE B 398 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU B 403 " --> pdb=" O PRO B 399 " (cutoff:3.500A) Proline residue: B 404 - end of helix removed outlier: 4.151A pdb=" N VAL B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) Proline residue: B 418 - end of helix Processing helix chain 'B' and resid 427 through 466 removed outlier: 4.010A pdb=" N ARG B 431 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLY B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Proline residue: B 434 - end of helix removed outlier: 4.439A pdb=" N GLY B 447 " --> pdb=" O GLN B 443 " (cutoff:3.500A) Proline residue: B 448 - end of helix Processing helix chain 'B' and resid 471 through 475 removed outlier: 3.520A pdb=" N ALA B 474 " --> pdb=" O PRO B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 506 Processing helix chain 'B' and resid 511 through 516 removed outlier: 3.571A pdb=" N VAL B 515 " --> pdb=" O THR B 511 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA B 516 " --> pdb=" O SER B 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 511 through 516' Processing helix chain 'A' and resid 49 through 75 removed outlier: 4.685A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLN A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 84 removed outlier: 3.810A pdb=" N ILE A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 104 removed outlier: 3.528A pdb=" N ILE A 94 " --> pdb=" O ARG A 90 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU A 104 " --> pdb=" O THR A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.708A pdb=" N ARG A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ASP A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 137 removed outlier: 3.810A pdb=" N ILE A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 159 Processing helix chain 'A' and resid 160 through 170 removed outlier: 3.920A pdb=" N ALA A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 202 removed outlier: 4.065A pdb=" N THR A 187 " --> pdb=" O PHE A 183 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 212 through 227 removed outlier: 4.504A pdb=" N ILE A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 218 " --> pdb=" O VAL A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 264 Proline residue: A 261 - end of helix Processing helix chain 'A' and resid 267 through 288 removed outlier: 3.532A pdb=" N LEU A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 297 through 302 removed outlier: 3.822A pdb=" N LEU A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A 302 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 334 Processing helix chain 'A' and resid 338 through 346 Processing helix chain 'A' and resid 346 through 364 removed outlier: 3.965A pdb=" N VAL A 350 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN A 362 " --> pdb=" O GLY A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 390 removed outlier: 3.627A pdb=" N LEU A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 423 removed outlier: 4.464A pdb=" N ASN A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 401 " --> pdb=" O TYR A 397 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL A 402 " --> pdb=" O PHE A 398 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU A 403 " --> pdb=" O PRO A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix removed outlier: 3.998A pdb=" N VAL A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 431 through 465 removed outlier: 4.701A pdb=" N GLY A 447 " --> pdb=" O GLN A 443 " (cutoff:3.500A) Proline residue: A 448 - end of helix Processing helix chain 'A' and resid 471 through 475 Processing helix chain 'A' and resid 476 through 506 Processing helix chain 'A' and resid 512 through 517 removed outlier: 3.701A pdb=" N HIS A 517 " --> pdb=" O GLN A 513 " (cutoff:3.500A) 569 hydrogen bonds defined for protein. 1689 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.86 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2181 1.34 - 1.46: 1378 1.46 - 1.58: 3399 1.58 - 1.70: 0 1.70 - 1.81: 56 Bond restraints: 7014 Sorted by residual: bond pdb=" C PHE B 398 " pdb=" N PRO B 399 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.28e-02 6.10e+03 1.20e+00 bond pdb=" N ILE B 395 " pdb=" CA ILE B 395 " ideal model delta sigma weight residual 1.468 1.457 0.011 1.05e-02 9.07e+03 1.13e+00 bond pdb=" CG1 ILE B 56 " pdb=" CD1 ILE B 56 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.11e+00 bond pdb=" CA LEU B 76 " pdb=" C LEU B 76 " ideal model delta sigma weight residual 1.521 1.533 -0.011 1.08e-02 8.57e+03 1.11e+00 bond pdb=" CA ILE A 395 " pdb=" CB ILE A 395 " ideal model delta sigma weight residual 1.537 1.524 0.014 1.29e-02 6.01e+03 1.10e+00 ... (remaining 7009 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 9273 1.62 - 3.24: 245 3.24 - 4.86: 44 4.86 - 6.48: 7 6.48 - 8.10: 5 Bond angle restraints: 9574 Sorted by residual: angle pdb=" CA PRO A 160 " pdb=" N PRO A 160 " pdb=" CD PRO A 160 " ideal model delta sigma weight residual 112.00 107.47 4.53 1.40e+00 5.10e-01 1.05e+01 angle pdb=" CA GLY A 264 " pdb=" C GLY A 264 " pdb=" N TRP A 265 " ideal model delta sigma weight residual 114.23 116.86 -2.63 8.80e-01 1.29e+00 8.91e+00 angle pdb=" CB ARG A 302 " pdb=" CG ARG A 302 " pdb=" CD ARG A 302 " ideal model delta sigma weight residual 111.30 118.16 -6.86 2.30e+00 1.89e-01 8.89e+00 angle pdb=" CB MET B 384 " pdb=" CG MET B 384 " pdb=" SD MET B 384 " ideal model delta sigma weight residual 112.70 120.12 -7.42 3.00e+00 1.11e-01 6.12e+00 angle pdb=" C LEU B 76 " pdb=" CA LEU B 76 " pdb=" CB LEU B 76 " ideal model delta sigma weight residual 113.57 109.70 3.87 1.57e+00 4.06e-01 6.08e+00 ... (remaining 9569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 3717 17.55 - 35.10: 264 35.10 - 52.65: 47 52.65 - 70.20: 2 70.20 - 87.75: 6 Dihedral angle restraints: 4036 sinusoidal: 1418 harmonic: 2618 Sorted by residual: dihedral pdb=" CA ASN A 476 " pdb=" C ASN A 476 " pdb=" N ASP A 477 " pdb=" CA ASP A 477 " ideal model delta harmonic sigma weight residual -180.00 -163.62 -16.38 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB GLU A 288 " pdb=" CG GLU A 288 " pdb=" CD GLU A 288 " pdb=" OE1 GLU A 288 " ideal model delta sinusoidal sigma weight residual 0.00 87.75 -87.75 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CB GLU B 288 " pdb=" CG GLU B 288 " pdb=" CD GLU B 288 " pdb=" OE1 GLU B 288 " ideal model delta sinusoidal sigma weight residual 0.00 87.66 -87.66 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 4033 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 674 0.028 - 0.057: 313 0.057 - 0.085: 135 0.085 - 0.113: 47 0.113 - 0.142: 15 Chirality restraints: 1184 Sorted by residual: chirality pdb=" CA MET A 353 " pdb=" N MET A 353 " pdb=" C MET A 353 " pdb=" CB MET A 353 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CB VAL A 427 " pdb=" CA VAL A 427 " pdb=" CG1 VAL A 427 " pdb=" CG2 VAL A 427 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA PRO A 448 " pdb=" N PRO A 448 " pdb=" C PRO A 448 " pdb=" CB PRO A 448 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 1181 not shown) Planarity restraints: 1192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 159 " -0.073 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO A 160 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO A 160 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 160 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 214 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.30e+00 pdb=" N PRO A 215 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 347 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO B 348 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 348 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 348 " -0.028 5.00e-02 4.00e+02 ... (remaining 1189 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 372 2.73 - 3.27: 7265 3.27 - 3.81: 11245 3.81 - 4.36: 11601 4.36 - 4.90: 21354 Nonbonded interactions: 51837 Sorted by model distance: nonbonded pdb=" O ILE B 115 " pdb=" NH1 ARG B 119 " model vdw 2.187 3.120 nonbonded pdb=" ND2 ASN A 305 " pdb=" O ILE A 508 " model vdw 2.215 3.120 nonbonded pdb=" NZ LYS A 78 " pdb=" O THR A 202 " model vdw 2.282 3.120 nonbonded pdb=" ND2 ASN B 305 " pdb=" O ILE B 508 " model vdw 2.313 3.120 nonbonded pdb=" OG SER A 48 " pdb=" N TRP A 49 " model vdw 2.327 3.120 ... (remaining 51832 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.780 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.610 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 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 : 0.003 0.041 7014 Z= 0.165 Angle : 0.640 8.102 9574 Z= 0.351 Chirality : 0.041 0.142 1184 Planarity : 0.006 0.108 1192 Dihedral : 12.871 87.751 2380 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.28), residues: 940 helix: 2.59 (0.19), residues: 738 sheet: None (None), residues: 0 loop : -0.56 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 302 TYR 0.023 0.002 TYR A 487 PHE 0.016 0.002 PHE A 314 TRP 0.005 0.001 TRP A 206 HIS 0.003 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 ( 7014) covalent geometry : angle 0.64013 / 0.35 ( 9574) hydrogen bonds : bond 0.12828 / 8.73 ( 569) hydrogen bonds : angle 4.56431 / 3.35 ( 1689) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: B 257 PHE cc_start: 0.7354 (t80) cc_final: 0.7026 (t80) REVERT: B 314 PHE cc_start: 0.8494 (t80) cc_final: 0.8007 (t80) REVERT: B 462 THR cc_start: 0.8029 (m) cc_final: 0.7780 (m) REVERT: A 115 ILE cc_start: 0.7872 (mm) cc_final: 0.7592 (tt) REVERT: A 130 ILE cc_start: 0.8050 (mm) cc_final: 0.7684 (mm) REVERT: A 214 VAL cc_start: 0.8359 (t) cc_final: 0.8109 (t) REVERT: A 322 THR cc_start: 0.8369 (m) cc_final: 0.8130 (t) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.0760 time to fit residues: 18.9683 Evaluate side-chains 158 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.2980 chunk 74 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 GLN B 362 GLN B 400 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.141916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119256 restraints weight = 10281.301| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.01 r_work: 0.3431 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7014 Z= 0.180 Angle : 0.627 10.492 9574 Z= 0.326 Chirality : 0.041 0.137 1184 Planarity : 0.005 0.076 1192 Dihedral : 4.126 17.276 1002 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.47 % Allowed : 12.21 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.98 (0.27), residues: 940 helix: 2.62 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -0.63 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 393 TYR 0.018 0.002 TYR A 489 PHE 0.017 0.002 PHE B 349 TRP 0.004 0.001 TRP B 206 HIS 0.002 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 ( 7014) covalent geometry : angle 0.62652 / 0.33 ( 9574) hydrogen bonds : bond 0.07092 / 4.64 ( 569) hydrogen bonds : angle 3.85819 / 2.84 ( 1689) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: B 61 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7627 (tpp) REVERT: B 67 MET cc_start: 0.8083 (ttt) cc_final: 0.7683 (ttp) REVERT: B 192 VAL cc_start: 0.8806 (p) cc_final: 0.8571 (t) REVERT: B 193 MET cc_start: 0.8453 (tmm) cc_final: 0.8212 (tmm) REVERT: B 251 THR cc_start: 0.8556 (m) cc_final: 0.8287 (m) REVERT: A 99 LEU cc_start: 0.7976 (tt) cc_final: 0.7770 (tp) REVERT: A 115 ILE cc_start: 0.8003 (mm) cc_final: 0.7631 (tt) REVERT: A 126 MET cc_start: 0.7519 (tmm) cc_final: 0.7229 (tmm) REVERT: A 330 TYR cc_start: 0.8803 (t80) cc_final: 0.8427 (t80) REVERT: A 393 ARG cc_start: 0.7694 (mtp85) cc_final: 0.7470 (mtp85) REVERT: A 396 PRO cc_start: 0.7820 (Cg_exo) cc_final: 0.7596 (Cg_endo) REVERT: A 431 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.7785 (mtm-85) outliers start: 17 outliers final: 12 residues processed: 166 average time/residue: 0.0830 time to fit residues: 18.6328 Evaluate side-chains 166 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 511 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 0.0020 chunk 20 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.141905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119669 restraints weight = 10129.801| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.97 r_work: 0.3439 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7014 Z= 0.154 Angle : 0.585 8.791 9574 Z= 0.301 Chirality : 0.040 0.135 1184 Planarity : 0.005 0.062 1192 Dihedral : 4.041 16.348 1002 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.05 % Allowed : 16.13 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.12 (0.28), residues: 940 helix: 2.73 (0.19), residues: 740 sheet: None (None), residues: 0 loop : -0.64 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 119 TYR 0.013 0.002 TYR A 489 PHE 0.015 0.001 PHE B 398 TRP 0.006 0.000 TRP B 206 HIS 0.002 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 ( 7014) covalent geometry : angle 0.58470 / 0.30 ( 9574) hydrogen bonds : bond 0.06287 / 4.12 ( 569) hydrogen bonds : angle 3.72019 / 2.75 ( 1689) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 192 VAL cc_start: 0.8721 (p) cc_final: 0.8489 (t) REVERT: B 226 THR cc_start: 0.8865 (t) cc_final: 0.8627 (t) REVERT: B 248 LEU cc_start: 0.8235 (mm) cc_final: 0.8007 (mm) REVERT: B 251 THR cc_start: 0.8590 (m) cc_final: 0.8319 (m) REVERT: B 314 PHE cc_start: 0.8741 (t80) cc_final: 0.8511 (t80) REVERT: A 99 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7753 (tp) REVERT: A 115 ILE cc_start: 0.7894 (mm) cc_final: 0.7512 (tt) REVERT: A 126 MET cc_start: 0.7599 (tmm) cc_final: 0.7103 (tmm) REVERT: A 322 THR cc_start: 0.8605 (m) cc_final: 0.8322 (t) REVERT: A 332 GLN cc_start: 0.8248 (tp40) cc_final: 0.7672 (tp40) REVERT: A 346 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.8262 (m-80) REVERT: A 396 PRO cc_start: 0.8018 (Cg_exo) cc_final: 0.7782 (Cg_endo) outliers start: 21 outliers final: 13 residues processed: 168 average time/residue: 0.0841 time to fit residues: 18.9849 Evaluate side-chains 172 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 186 MET Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 511 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 76 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 GLN B 290 ASN B 362 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.137314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.115097 restraints weight = 10348.809| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.99 r_work: 0.3373 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7014 Z= 0.176 Angle : 0.593 7.510 9574 Z= 0.312 Chirality : 0.040 0.144 1184 Planarity : 0.005 0.057 1192 Dihedral : 4.098 15.725 1002 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.92 % Allowed : 19.04 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.97 (0.28), residues: 940 helix: 2.69 (0.19), residues: 736 sheet: None (None), residues: 0 loop : -0.89 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 306 TYR 0.021 0.002 TYR B 386 PHE 0.018 0.002 PHE B 398 TRP 0.006 0.001 TRP B 206 HIS 0.002 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 ( 7014) covalent geometry : angle 0.59334 / 0.31 ( 9574) hydrogen bonds : bond 0.07302 / 4.78 ( 569) hydrogen bonds : angle 3.82081 / 2.83 ( 1689) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7637 (mp) REVERT: B 226 THR cc_start: 0.8946 (t) cc_final: 0.8708 (t) REVERT: B 248 LEU cc_start: 0.8265 (mm) cc_final: 0.8016 (mm) REVERT: B 314 PHE cc_start: 0.8789 (t80) cc_final: 0.8575 (t80) REVERT: A 56 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8169 (mp) REVERT: A 99 LEU cc_start: 0.8140 (tt) cc_final: 0.7895 (tp) REVERT: A 115 ILE cc_start: 0.7899 (mm) cc_final: 0.7478 (tt) REVERT: A 332 GLN cc_start: 0.8272 (tp40) cc_final: 0.7743 (tp40) REVERT: A 341 ARG cc_start: 0.7512 (mpt-90) cc_final: 0.7242 (mpt-90) REVERT: A 346 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.8400 (m-80) outliers start: 27 outliers final: 19 residues processed: 179 average time/residue: 0.0838 time to fit residues: 20.1347 Evaluate side-chains 186 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 511 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 11 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 0.0980 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 290 ASN B 362 GLN A 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.135084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113038 restraints weight = 10488.345| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.03 r_work: 0.3343 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7014 Z= 0.180 Angle : 0.593 7.194 9574 Z= 0.311 Chirality : 0.040 0.142 1184 Planarity : 0.005 0.052 1192 Dihedral : 4.102 16.095 1002 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.07 % Allowed : 20.20 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.96 (0.28), residues: 940 helix: 2.70 (0.19), residues: 736 sheet: None (None), residues: 0 loop : -0.96 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 370 TYR 0.015 0.002 TYR B 386 PHE 0.017 0.001 PHE B 398 TRP 0.007 0.001 TRP A 92 HIS 0.002 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 ( 7014) covalent geometry : angle 0.59274 / 0.31 ( 9574) hydrogen bonds : bond 0.07339 / 4.81 ( 569) hydrogen bonds : angle 3.84657 / 2.86 ( 1689) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7604 (mp) REVERT: B 226 THR cc_start: 0.8955 (t) cc_final: 0.8750 (t) REVERT: B 248 LEU cc_start: 0.8238 (mm) cc_final: 0.7984 (mm) REVERT: B 314 PHE cc_start: 0.8797 (t80) cc_final: 0.8590 (t80) REVERT: B 353 MET cc_start: 0.8356 (mtp) cc_final: 0.7938 (ttm) REVERT: A 56 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8128 (mp) REVERT: A 115 ILE cc_start: 0.7831 (mm) cc_final: 0.7416 (tt) REVERT: A 293 ASN cc_start: 0.8781 (m110) cc_final: 0.8528 (m-40) REVERT: A 341 ARG cc_start: 0.7596 (mpt-90) cc_final: 0.7246 (mpt-90) REVERT: A 346 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8404 (m-80) outliers start: 28 outliers final: 20 residues processed: 178 average time/residue: 0.0855 time to fit residues: 20.4560 Evaluate side-chains 187 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 511 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 85 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 22 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 0.0570 chunk 39 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 GLN B 362 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.136728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.114968 restraints weight = 10493.804| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.03 r_work: 0.3364 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7014 Z= 0.159 Angle : 0.577 8.957 9574 Z= 0.299 Chirality : 0.039 0.133 1184 Planarity : 0.005 0.053 1192 Dihedral : 4.089 20.023 1002 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.94 % Allowed : 21.37 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.05 (0.28), residues: 940 helix: 2.80 (0.19), residues: 730 sheet: None (None), residues: 0 loop : -0.98 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 117 TYR 0.014 0.002 TYR B 386 PHE 0.018 0.001 PHE B 398 TRP 0.007 0.001 TRP B 206 HIS 0.002 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 ( 7014) covalent geometry : angle 0.57739 / 0.30 ( 9574) hydrogen bonds : bond 0.06743 / 4.42 ( 569) hydrogen bonds : angle 3.77066 / 2.80 ( 1689) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7639 (mp) REVERT: B 226 THR cc_start: 0.8947 (t) cc_final: 0.8733 (t) REVERT: B 229 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7286 (mp10) REVERT: B 248 LEU cc_start: 0.8227 (mm) cc_final: 0.7980 (mm) REVERT: A 56 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8098 (mp) REVERT: A 61 MET cc_start: 0.7710 (tpp) cc_final: 0.7509 (tpt) REVERT: A 115 ILE cc_start: 0.7789 (mm) cc_final: 0.7408 (tt) REVERT: A 293 ASN cc_start: 0.8784 (m110) cc_final: 0.8527 (m-40) REVERT: A 332 GLN cc_start: 0.8280 (tp40) cc_final: 0.7768 (tp40) REVERT: A 346 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8340 (m-80) outliers start: 34 outliers final: 23 residues processed: 174 average time/residue: 0.0848 time to fit residues: 19.8884 Evaluate side-chains 186 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 511 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 62 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.134913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113266 restraints weight = 10363.109| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.97 r_work: 0.3347 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7014 Z= 0.170 Angle : 0.597 10.946 9574 Z= 0.307 Chirality : 0.040 0.143 1184 Planarity : 0.005 0.053 1192 Dihedral : 4.068 17.431 1002 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.92 % Allowed : 22.53 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.28), residues: 940 helix: 2.78 (0.19), residues: 730 sheet: None (None), residues: 0 loop : -1.03 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 370 TYR 0.013 0.002 TYR B 386 PHE 0.030 0.001 PHE B 314 TRP 0.007 0.001 TRP B 92 HIS 0.002 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 ( 7014) covalent geometry : angle 0.59713 / 0.31 ( 9574) hydrogen bonds : bond 0.07088 / 4.64 ( 569) hydrogen bonds : angle 3.83276 / 2.85 ( 1689) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7722 (mp) REVERT: B 193 MET cc_start: 0.8515 (tmm) cc_final: 0.8313 (tmm) REVERT: B 226 THR cc_start: 0.8984 (t) cc_final: 0.8760 (t) REVERT: B 229 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7374 (tp40) REVERT: B 248 LEU cc_start: 0.8311 (mm) cc_final: 0.8054 (mm) REVERT: B 314 PHE cc_start: 0.8767 (t80) cc_final: 0.8241 (t80) REVERT: B 353 MET cc_start: 0.8403 (mtp) cc_final: 0.8095 (ttp) REVERT: A 56 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8113 (mp) REVERT: A 111 LEU cc_start: 0.8375 (tt) cc_final: 0.8144 (pp) REVERT: A 115 ILE cc_start: 0.7798 (mm) cc_final: 0.7436 (tt) REVERT: A 293 ASN cc_start: 0.8813 (m110) cc_final: 0.8527 (m-40) REVERT: A 332 GLN cc_start: 0.8313 (tp40) cc_final: 0.7801 (tp40) REVERT: A 341 ARG cc_start: 0.7541 (mpt-90) cc_final: 0.7278 (mpt-90) REVERT: A 346 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8361 (m-80) outliers start: 27 outliers final: 22 residues processed: 169 average time/residue: 0.0879 time to fit residues: 19.8280 Evaluate side-chains 181 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 229 GLN Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 511 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 37 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 290 ASN B 362 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.134381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.112820 restraints weight = 10572.545| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.99 r_work: 0.3334 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7014 Z= 0.174 Angle : 0.604 12.368 9574 Z= 0.311 Chirality : 0.040 0.135 1184 Planarity : 0.005 0.053 1192 Dihedral : 4.080 16.741 1002 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.65 % Allowed : 22.53 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.99 (0.28), residues: 940 helix: 2.78 (0.19), residues: 726 sheet: None (None), residues: 0 loop : -1.02 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 370 TYR 0.013 0.002 TYR A 489 PHE 0.026 0.001 PHE B 314 TRP 0.007 0.001 TRP B 92 HIS 0.002 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 7014) covalent geometry : angle 0.60418 / 0.31 ( 9574) hydrogen bonds : bond 0.07213 / 4.73 ( 569) hydrogen bonds : angle 3.85120 / 2.86 ( 1689) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7733 (mp) REVERT: B 226 THR cc_start: 0.9000 (t) cc_final: 0.8786 (t) REVERT: B 244 LEU cc_start: 0.8636 (tt) cc_final: 0.8234 (tt) REVERT: B 248 LEU cc_start: 0.8266 (mm) cc_final: 0.8033 (mm) REVERT: B 314 PHE cc_start: 0.8785 (t80) cc_final: 0.8256 (t80) REVERT: B 353 MET cc_start: 0.8388 (mtp) cc_final: 0.8086 (ttp) REVERT: A 56 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8141 (mp) REVERT: A 111 LEU cc_start: 0.8357 (tt) cc_final: 0.8137 (pp) REVERT: A 115 ILE cc_start: 0.7811 (mm) cc_final: 0.7452 (tt) REVERT: A 151 GLN cc_start: 0.8450 (mt0) cc_final: 0.8224 (mt0) REVERT: A 332 GLN cc_start: 0.8326 (tp40) cc_final: 0.8011 (tt0) REVERT: A 341 ARG cc_start: 0.7586 (mpt-90) cc_final: 0.7270 (mpt-90) REVERT: A 346 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8348 (m-80) REVERT: A 353 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7826 (ttt) outliers start: 32 outliers final: 25 residues processed: 174 average time/residue: 0.0942 time to fit residues: 21.7127 Evaluate side-chains 189 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 511 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 70 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 290 ASN B 362 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.131764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.110368 restraints weight = 10446.272| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.93 r_work: 0.3310 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7014 Z= 0.194 Angle : 0.619 8.580 9574 Z= 0.323 Chirality : 0.041 0.138 1184 Planarity : 0.005 0.054 1192 Dihedral : 4.141 17.959 1002 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.65 % Allowed : 22.38 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.92 (0.28), residues: 940 helix: 2.72 (0.19), residues: 726 sheet: None (None), residues: 0 loop : -1.03 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 370 TYR 0.014 0.002 TYR B 97 PHE 0.026 0.002 PHE B 314 TRP 0.006 0.001 TRP B 206 HIS 0.002 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 ( 7014) covalent geometry : angle 0.61884 / 0.32 ( 9574) hydrogen bonds : bond 0.07798 / 5.11 ( 569) hydrogen bonds : angle 3.95165 / 2.93 ( 1689) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7747 (mp) REVERT: B 203 GLU cc_start: 0.6514 (mm-30) cc_final: 0.6283 (mp0) REVERT: B 226 THR cc_start: 0.9023 (t) cc_final: 0.8820 (t) REVERT: B 244 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8203 (tt) REVERT: B 248 LEU cc_start: 0.8256 (mm) cc_final: 0.8004 (mm) REVERT: B 314 PHE cc_start: 0.8807 (t80) cc_final: 0.8271 (t80) REVERT: B 353 MET cc_start: 0.8421 (mtp) cc_final: 0.8112 (ttp) REVERT: A 56 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8190 (mp) REVERT: A 111 LEU cc_start: 0.8395 (tt) cc_final: 0.8191 (pp) REVERT: A 115 ILE cc_start: 0.7870 (mm) cc_final: 0.7496 (tt) REVERT: A 151 GLN cc_start: 0.8452 (mt0) cc_final: 0.8235 (mt0) REVERT: A 341 ARG cc_start: 0.7551 (mpt-90) cc_final: 0.7295 (mpt-90) REVERT: A 346 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8352 (m-80) REVERT: A 353 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7850 (ttt) REVERT: A 390 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7715 (m-80) outliers start: 32 outliers final: 23 residues processed: 170 average time/residue: 0.0934 time to fit residues: 20.9622 Evaluate side-chains 184 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 105 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 511 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 45 optimal weight: 0.0670 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 93 optimal weight: 0.0020 chunk 87 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 4 optimal weight: 0.0050 overall best weight: 0.2940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 290 ASN B 362 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.138634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.117382 restraints weight = 10445.743| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.02 r_work: 0.3408 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7014 Z= 0.133 Angle : 0.576 12.035 9574 Z= 0.290 Chirality : 0.038 0.134 1184 Planarity : 0.005 0.052 1192 Dihedral : 4.015 17.913 1002 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.07 % Allowed : 23.26 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.19 (0.28), residues: 940 helix: 2.89 (0.19), residues: 734 sheet: None (None), residues: 0 loop : -0.96 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 207 TYR 0.013 0.001 TYR B 386 PHE 0.026 0.001 PHE B 314 TRP 0.007 0.000 TRP B 206 HIS 0.002 0.001 HIS B 392 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 ( 7014) covalent geometry : angle 0.57557 / 0.29 ( 9574) hydrogen bonds : bond 0.05437 / 3.59 ( 569) hydrogen bonds : angle 3.66903 / 2.72 ( 1689) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1880 Ramachandran restraints generated. 940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.242 Fit side-chains revert: symmetry clash REVERT: B 56 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7583 (mp) REVERT: B 226 THR cc_start: 0.8933 (t) cc_final: 0.8706 (t) REVERT: B 244 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8197 (tt) REVERT: B 248 LEU cc_start: 0.8258 (mm) cc_final: 0.7896 (mm) REVERT: B 251 THR cc_start: 0.8408 (m) cc_final: 0.8140 (p) REVERT: B 314 PHE cc_start: 0.8643 (t80) cc_final: 0.8380 (t80) REVERT: B 353 MET cc_start: 0.8321 (mtp) cc_final: 0.8037 (ttp) REVERT: A 56 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.8026 (mp) REVERT: A 111 LEU cc_start: 0.8247 (tt) cc_final: 0.8005 (pp) REVERT: A 115 ILE cc_start: 0.7763 (mm) cc_final: 0.7448 (tt) REVERT: A 220 MET cc_start: 0.6005 (tpp) cc_final: 0.5730 (mpp) REVERT: A 293 ASN cc_start: 0.8741 (m110) cc_final: 0.8444 (m110) REVERT: A 332 GLN cc_start: 0.8173 (tp40) cc_final: 0.7858 (tt0) REVERT: A 346 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.8237 (m-80) REVERT: A 353 MET cc_start: 0.8063 (mtp) cc_final: 0.7788 (ttt) REVERT: A 390 PHE cc_start: 0.7643 (OUTLIER) cc_final: 0.7399 (m-80) REVERT: A 396 PRO cc_start: 0.8155 (Cg_exo) cc_final: 0.7909 (Cg_endo) outliers start: 28 outliers final: 20 residues processed: 168 average time/residue: 0.0894 time to fit residues: 19.9385 Evaluate side-chains 179 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 366 ARG Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 444 ASN Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 517 HIS Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 305 ASN Chi-restraints excluded: chain A residue 346 PHE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 511 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 290 ASN B 362 GLN A 444 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.134213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.112899 restraints weight = 10422.081| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.99 r_work: 0.3344 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7014 Z= 0.173 Angle : 0.618 9.491 9574 Z= 0.314 Chirality : 0.040 0.134 1184 Planarity : 0.005 0.054 1192 Dihedral : 4.047 17.470 1002 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.92 % Allowed : 23.84 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.28), residues: 940 helix: 2.84 (0.19), residues: 726 sheet: None (None), residues: 0 loop : -0.98 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 370 TYR 0.012 0.002 TYR B 386 PHE 0.026 0.001 PHE B 314 TRP 0.007 0.001 TRP B 206 HIS 0.002 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 7014) covalent geometry : angle 0.61770 / 0.31 ( 9574) hydrogen bonds : bond 0.06812 / 4.48 ( 569) hydrogen bonds : angle 3.81681 / 2.83 ( 1689) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1858.89 seconds wall clock time: 32 minutes 31.29 seconds (1951.29 seconds total)