Starting phenix.real_space_refine on Thu Jul 2 17:03:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9x4c_66537/07_2026/9x4c_66537.cif Found real_map, /net/cci-nas-00/data/ceres_data/9x4c_66537/07_2026/9x4c_66537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9x4c_66537/07_2026/9x4c_66537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9x4c_66537/07_2026/9x4c_66537.map" model { file = "/net/cci-nas-00/data/ceres_data/9x4c_66537/07_2026/9x4c_66537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9x4c_66537/07_2026/9x4c_66537.cif" } resolution = 3.08 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= 0.000 sd= 0.034 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 P 3 5.49 5 Mg 1 5.21 5 S 40 5.16 5 C 5840 2.51 5 N 1529 2.21 5 O 1660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9073 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4514 Classifications: {'peptide': 572} Link IDs: {'PTRANS': 20, 'TRANS': 551} Chain: "B" Number of atoms: 4527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4527 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 13, 'TRANS': 556} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.16, per 1000 atoms: 0.24 Number of scatterers: 9073 At special positions: 0 Unit cell: (75.456, 99.56, 137.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 3 15.00 Mg 1 11.99 O 1660 8.00 N 1529 7.00 C 5840 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: 0.87 Conformation dependent library (CDL) restraints added in 317.0 milliseconds 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2154 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 7 sheets defined 72.6% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 removed outlier: 3.725A pdb=" N VAL A 6 " --> pdb=" O ALA A 3 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR A 7 " --> pdb=" O LEU A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 42 Proline residue: A 19 - end of helix Proline residue: A 33 - end of helix Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 48 through 98 Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'A' and resid 108 through 134 removed outlier: 4.195A pdb=" N ASP A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 152 Processing helix chain 'A' and resid 155 through 201 removed outlier: 3.886A pdb=" N PHE A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 210 through 237 removed outlier: 3.679A pdb=" N ILE A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 264 Processing helix chain 'A' and resid 268 through 281 Processing helix chain 'A' and resid 282 through 311 Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 437 through 448 Processing helix chain 'A' and resid 450 through 457 Processing helix chain 'A' and resid 459 through 462 removed outlier: 4.192A pdb=" N ASP A 462 " --> pdb=" O LEU A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 459 through 462' Processing helix chain 'A' and resid 473 through 487 Processing helix chain 'A' and resid 503 through 518 Processing helix chain 'A' and resid 552 through 560 Processing helix chain 'A' and resid 560 through 572 removed outlier: 3.658A pdb=" N GLN A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN A 572 " --> pdb=" O TYR A 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 19 Processing helix chain 'B' and resid 20 through 52 Proline residue: B 42 - end of helix Processing helix chain 'B' and resid 56 through 108 Proline residue: B 83 - end of helix Processing helix chain 'B' and resid 109 through 117 removed outlier: 3.557A pdb=" N GLY B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 161 removed outlier: 3.983A pdb=" N SER B 129 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE B 144 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 210 Proline residue: B 173 - end of helix Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'B' and resid 219 through 247 Processing helix chain 'B' and resid 247 through 273 Processing helix chain 'B' and resid 278 through 321 removed outlier: 4.286A pdb=" N THR B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Proline residue: B 295 - end of helix removed outlier: 4.497A pdb=" N SER B 304 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 389 Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 410 through 417 Processing helix chain 'B' and resid 431 through 437 Processing helix chain 'B' and resid 444 through 455 Processing helix chain 'B' and resid 457 through 464 Processing helix chain 'B' and resid 466 through 470 removed outlier: 3.503A pdb=" N ASP B 469 " --> pdb=" O LEU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 477 removed outlier: 3.645A pdb=" N ALA B 475 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 496 removed outlier: 3.644A pdb=" N ILE B 492 " --> pdb=" O THR B 488 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 525 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 559 through 567 Processing helix chain 'B' and resid 568 through 577 Processing sheet with id=AA1, first strand: chain 'A' and resid 350 through 358 removed outlier: 4.424A pdb=" N GLN A 351 " --> pdb=" O MET A 338 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N MET A 338 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE A 353 " --> pdb=" O ASP A 336 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP A 336 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N PHE A 355 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU A 334 " --> pdb=" O PHE A 355 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR A 357 " --> pdb=" O ALA A 332 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE A 335 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N THR A 392 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LYS A 337 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER A 390 " --> pdb=" O LYS A 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 410 through 413 removed outlier: 6.761A pdb=" N ALA A 411 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ASP A 496 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 413 " --> pdb=" O ASP A 496 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU A 493 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ILE A 526 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU A 495 " --> pdb=" O ILE A 526 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLY A 364 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU A 542 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE A 366 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY A 549 " --> pdb=" O VAL A 541 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 422 through 423 Processing sheet with id=AA4, first strand: chain 'B' and resid 342 through 343 Processing sheet with id=AA5, first strand: chain 'B' and resid 347 through 349 removed outlier: 6.140A pdb=" N VAL B 347 " --> pdb=" O ASP B 360 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP B 360 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 530 through 533 removed outlier: 6.832A pdb=" N THR B 370 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU B 547 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ALA B 372 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 418 through 419 630 hydrogen bonds defined for protein. 1860 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2929 1.34 - 1.46: 1639 1.46 - 1.58: 4583 1.58 - 1.69: 5 1.69 - 1.81: 77 Bond restraints: 9233 Sorted by residual: bond pdb=" O3A ANP A 701 " pdb=" PB ANP A 701 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.30e+01 bond pdb=" N3B ANP A 701 " pdb=" PG ANP A 701 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" O5' ANP A 701 " pdb=" PA ANP A 701 " ideal model delta sigma weight residual 1.655 1.576 0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" O3G ANP A 701 " pdb=" PG ANP A 701 " ideal model delta sigma weight residual 1.528 1.581 -0.053 2.00e-02 2.50e+03 6.90e+00 bond pdb=" O2B ANP A 701 " pdb=" PB ANP A 701 " ideal model delta sigma weight residual 1.508 1.553 -0.045 2.00e-02 2.50e+03 4.96e+00 ... (remaining 9228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.87: 12475 3.87 - 7.73: 33 7.73 - 11.60: 4 11.60 - 15.47: 0 15.47 - 19.33: 1 Bond angle restraints: 12513 Sorted by residual: angle pdb=" PB ANP A 701 " pdb=" N3B ANP A 701 " pdb=" PG ANP A 701 " ideal model delta sigma weight residual 126.95 107.62 19.33 3.00e+00 1.11e-01 4.15e+01 angle pdb=" O1B ANP A 701 " pdb=" PB ANP A 701 " pdb=" O2B ANP A 701 " ideal model delta sigma weight residual 120.08 109.53 10.55 3.00e+00 1.11e-01 1.24e+01 angle pdb=" N3B ANP A 701 " pdb=" PB ANP A 701 " pdb=" O3A ANP A 701 " ideal model delta sigma weight residual 101.56 110.32 -8.76 3.00e+00 1.11e-01 8.53e+00 angle pdb=" N3B ANP A 701 " pdb=" PG ANP A 701 " pdb=" O2G ANP A 701 " ideal model delta sigma weight residual 101.05 108.93 -7.88 3.00e+00 1.11e-01 6.89e+00 angle pdb=" CA GLN A 281 " pdb=" C GLN A 281 " pdb=" N ILE A 282 " ideal model delta sigma weight residual 117.96 121.04 -3.08 1.23e+00 6.61e-01 6.27e+00 ... (remaining 12508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5044 17.82 - 35.64: 435 35.64 - 53.46: 70 53.46 - 71.28: 27 71.28 - 89.10: 15 Dihedral angle restraints: 5591 sinusoidal: 2260 harmonic: 3331 Sorted by residual: dihedral pdb=" CA ILE A 380 " pdb=" C ILE A 380 " pdb=" N MET A 381 " pdb=" CA MET A 381 " ideal model delta harmonic sigma weight residual 180.00 160.51 19.49 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ILE B 532 " pdb=" C ILE B 532 " pdb=" N ILE B 533 " pdb=" CA ILE B 533 " ideal model delta harmonic sigma weight residual 180.00 163.37 16.63 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ILE B 533 " pdb=" C ILE B 533 " pdb=" N ALA B 534 " pdb=" CA ALA B 534 " ideal model delta harmonic sigma weight residual -180.00 -164.37 -15.63 0 5.00e+00 4.00e-02 9.77e+00 ... (remaining 5588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1313 0.058 - 0.116: 152 0.116 - 0.173: 11 0.173 - 0.231: 0 0.231 - 0.289: 1 Chirality restraints: 1477 Sorted by residual: chirality pdb=" C3' ANP A 701 " pdb=" C2' ANP A 701 " pdb=" C4' ANP A 701 " pdb=" O3' ANP A 701 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA ILE A 526 " pdb=" N ILE A 526 " pdb=" C ILE A 526 " pdb=" CB ILE A 526 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE B 365 " pdb=" N ILE B 365 " pdb=" C ILE B 365 " pdb=" CB ILE B 365 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 1474 not shown) Planarity restraints: 1571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 227 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C PHE B 227 " -0.035 2.00e-02 2.50e+03 pdb=" O PHE B 227 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN B 228 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 124 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C ARG B 124 " -0.026 2.00e-02 2.50e+03 pdb=" O ARG B 124 " 0.010 2.00e-02 2.50e+03 pdb=" N VAL B 125 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 18 " -0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO A 19 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 19 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 19 " -0.019 5.00e-02 4.00e+02 ... (remaining 1568 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 61 2.54 - 3.13: 7307 3.13 - 3.72: 14501 3.72 - 4.31: 19581 4.31 - 4.90: 33709 Nonbonded interactions: 75159 Sorted by model distance: nonbonded pdb=" O2G ANP A 701 " pdb="MG MG A 702 " model vdw 1.955 2.170 nonbonded pdb=" OE1 GLN A 415 " pdb="MG MG A 702 " model vdw 1.991 2.170 nonbonded pdb=" OG SER A 374 " pdb="MG MG A 702 " model vdw 2.001 2.170 nonbonded pdb=" O2B ANP A 701 " pdb="MG MG A 702 " model vdw 2.059 2.170 nonbonded pdb=" O GLU B 205 " pdb=" OG1 THR B 209 " model vdw 2.247 3.040 ... (remaining 75154 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.210 Find NCS groups from input model: 0.150 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 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 : 0.004 0.146 9233 Z= 0.194 Angle : 0.561 19.334 12513 Z= 0.271 Chirality : 0.038 0.289 1477 Planarity : 0.003 0.035 1571 Dihedral : 14.626 89.100 3437 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: 2.18 (0.26), residues: 1138 helix: 2.43 (0.19), residues: 784 sheet: -1.47 (0.68), residues: 62 loop : -0.66 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.009 0.001 TYR B 260 PHE 0.014 0.001 PHE B 493 TRP 0.010 0.001 TRP B 196 HIS 0.004 0.001 HIS B 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 ( 9233) covalent geometry : angle 0.56143 / 0.27 (12513) hydrogen bonds : bond 0.14163 / 9.84 ( 630) hydrogen bonds : angle 4.80052 / 3.51 ( 1860) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.214 Fit side-chains REVERT: A 154 ARG cc_start: 0.7670 (mtp180) cc_final: 0.7110 (ttt180) REVERT: A 256 TRP cc_start: 0.7196 (t60) cc_final: 0.6230 (t-100) REVERT: A 271 MET cc_start: 0.7458 (mmm) cc_final: 0.7200 (mmp) REVERT: A 325 LYS cc_start: 0.7426 (tppt) cc_final: 0.6270 (tptp) REVERT: A 428 LEU cc_start: 0.7795 (mp) cc_final: 0.7563 (mt) REVERT: A 543 ASP cc_start: 0.7854 (t0) cc_final: 0.7499 (t0) REVERT: A 568 TYR cc_start: 0.7422 (t80) cc_final: 0.6991 (m-10) REVERT: B 108 ILE cc_start: 0.7345 (mm) cc_final: 0.7053 (mt) REVERT: B 112 TYR cc_start: 0.7280 (t80) cc_final: 0.7003 (t80) REVERT: B 190 TYR cc_start: 0.7723 (t80) cc_final: 0.7065 (t80) REVERT: B 335 GLU cc_start: 0.6802 (tm-30) cc_final: 0.6481 (tt0) REVERT: B 389 MET cc_start: 0.7567 (mmm) cc_final: 0.7152 (mmt) REVERT: B 442 LYS cc_start: 0.7795 (mmtt) cc_final: 0.7080 (pttm) REVERT: B 518 GLN cc_start: 0.6631 (mt0) cc_final: 0.6272 (mm-40) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.0796 time to fit residues: 18.2959 Evaluate side-chains 123 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 572 GLN B 297 ASN B 307 GLN B 348 GLN B 518 GLN B 561 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.145354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.112608 restraints weight = 10261.689| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.45 r_work: 0.3108 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9233 Z= 0.155 Angle : 0.519 7.917 12513 Z= 0.270 Chirality : 0.039 0.143 1477 Planarity : 0.004 0.036 1571 Dihedral : 6.671 55.023 1265 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.21 % Allowed : 6.14 % Favored : 92.65 % 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: 2.04 (0.25), residues: 1138 helix: 2.27 (0.18), residues: 794 sheet: -0.63 (0.81), residues: 46 loop : -0.88 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 270 TYR 0.013 0.001 TYR B 112 PHE 0.020 0.001 PHE B 459 TRP 0.011 0.001 TRP B 196 HIS 0.003 0.001 HIS B 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 9233) covalent geometry : angle 0.51875 / 0.27 (12513) hydrogen bonds : bond 0.05147 / 3.30 ( 630) hydrogen bonds : angle 4.13372 / 3.01 ( 1860) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.282 Fit side-chains REVERT: A 154 ARG cc_start: 0.8324 (mtp180) cc_final: 0.7784 (ttt180) REVERT: A 325 LYS cc_start: 0.7435 (tppt) cc_final: 0.6415 (tttm) REVERT: A 381 MET cc_start: 0.7490 (mpp) cc_final: 0.7212 (mmm) REVERT: A 509 ARG cc_start: 0.8052 (mtm-85) cc_final: 0.7475 (mtm-85) REVERT: B 121 MET cc_start: 0.8558 (mmm) cc_final: 0.8255 (mmm) REVERT: B 190 TYR cc_start: 0.8185 (t80) cc_final: 0.7434 (t80) REVERT: B 335 GLU cc_start: 0.6884 (tm-30) cc_final: 0.6561 (tt0) REVERT: B 424 GLU cc_start: 0.7777 (pm20) cc_final: 0.7528 (pm20) REVERT: B 442 LYS cc_start: 0.8026 (mmtt) cc_final: 0.7300 (pttm) REVERT: B 462 LYS cc_start: 0.7642 (mmtt) cc_final: 0.7341 (mmtt) REVERT: B 518 GLN cc_start: 0.7264 (mt0) cc_final: 0.6989 (mm-40) REVERT: B 525 MET cc_start: 0.8434 (mtm) cc_final: 0.8231 (mtp) outliers start: 12 outliers final: 8 residues processed: 137 average time/residue: 0.0821 time to fit residues: 15.7322 Evaluate side-chains 131 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 538 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 50 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 34 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 51 optimal weight: 0.0060 chunk 72 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 297 ASN B 307 GLN B 348 GLN ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.144330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.109594 restraints weight = 10170.982| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.66 r_work: 0.3083 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9233 Z= 0.127 Angle : 0.463 6.444 12513 Z= 0.242 Chirality : 0.038 0.134 1477 Planarity : 0.003 0.035 1571 Dihedral : 5.258 55.818 1265 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.51 % Allowed : 8.26 % Favored : 90.23 % 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: 2.09 (0.25), residues: 1138 helix: 2.36 (0.18), residues: 793 sheet: -1.45 (0.72), residues: 56 loop : -0.82 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 536 TYR 0.009 0.001 TYR B 112 PHE 0.023 0.001 PHE B 227 TRP 0.009 0.001 TRP B 196 HIS 0.002 0.001 HIS B 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 ( 9233) covalent geometry : angle 0.46272 / 0.24 (12513) hydrogen bonds : bond 0.04815 / 3.09 ( 630) hydrogen bonds : angle 3.96504 / 2.90 ( 1860) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.274 Fit side-chains REVERT: A 54 MET cc_start: 0.8115 (ttp) cc_final: 0.7889 (ttp) REVERT: A 154 ARG cc_start: 0.8315 (mtp180) cc_final: 0.7787 (ttt180) REVERT: A 325 LYS cc_start: 0.7595 (tppt) cc_final: 0.6578 (tttm) REVERT: A 352 GLU cc_start: 0.7866 (mp0) cc_final: 0.7498 (mp0) REVERT: A 509 ARG cc_start: 0.8186 (mtm-85) cc_final: 0.7687 (mtm-85) REVERT: B 68 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.8007 (mtp) REVERT: B 103 MET cc_start: 0.8513 (mtm) cc_final: 0.8242 (mtm) REVERT: B 121 MET cc_start: 0.8515 (mmm) cc_final: 0.8274 (mmm) REVERT: B 190 TYR cc_start: 0.8164 (t80) cc_final: 0.7380 (t80) REVERT: B 335 GLU cc_start: 0.6753 (tm-30) cc_final: 0.6493 (tt0) REVERT: B 442 LYS cc_start: 0.8023 (mmtt) cc_final: 0.7340 (pttm) REVERT: B 462 LYS cc_start: 0.7686 (mmtt) cc_final: 0.7404 (mmtt) REVERT: B 492 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7131 (mp) REVERT: B 518 GLN cc_start: 0.7281 (mt0) cc_final: 0.6824 (mm-40) REVERT: B 525 MET cc_start: 0.8393 (mtm) cc_final: 0.8186 (mtp) outliers start: 15 outliers final: 12 residues processed: 135 average time/residue: 0.0800 time to fit residues: 15.1323 Evaluate side-chains 135 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 571 HIS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 538 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 7 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 307 GLN ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.144329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.110074 restraints weight = 10345.208| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.60 r_work: 0.3099 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9233 Z= 0.140 Angle : 0.477 8.170 12513 Z= 0.248 Chirality : 0.038 0.138 1477 Planarity : 0.003 0.037 1571 Dihedral : 4.937 59.621 1265 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.51 % Allowed : 9.97 % Favored : 88.52 % 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: 2.04 (0.25), residues: 1138 helix: 2.34 (0.18), residues: 791 sheet: -1.46 (0.72), residues: 56 loop : -0.89 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 536 TYR 0.009 0.001 TYR A 412 PHE 0.011 0.001 PHE B 227 TRP 0.009 0.001 TRP B 196 HIS 0.002 0.001 HIS B 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 9233) covalent geometry : angle 0.47711 / 0.25 (12513) hydrogen bonds : bond 0.04808 / 3.09 ( 630) hydrogen bonds : angle 3.95928 / 2.90 ( 1860) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.323 Fit side-chains REVERT: A 103 LYS cc_start: 0.7735 (mmtt) cc_final: 0.7484 (mmtt) REVERT: A 154 ARG cc_start: 0.8356 (mtp180) cc_final: 0.7857 (ttt180) REVERT: A 325 LYS cc_start: 0.7630 (tppt) cc_final: 0.6613 (tttm) REVERT: A 352 GLU cc_start: 0.7814 (mp0) cc_final: 0.7483 (mp0) REVERT: A 509 ARG cc_start: 0.8309 (mtm-85) cc_final: 0.7750 (mtm-85) REVERT: A 543 ASP cc_start: 0.7972 (t0) cc_final: 0.7740 (t0) REVERT: B 68 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7893 (mtp) REVERT: B 103 MET cc_start: 0.8469 (mtm) cc_final: 0.8180 (mtm) REVERT: B 121 MET cc_start: 0.8521 (mmm) cc_final: 0.8228 (mmm) REVERT: B 190 TYR cc_start: 0.8145 (t80) cc_final: 0.7350 (t80) REVERT: B 223 MET cc_start: 0.8954 (mmm) cc_final: 0.8747 (mmp) REVERT: B 335 GLU cc_start: 0.6732 (tm-30) cc_final: 0.6528 (tt0) REVERT: B 424 GLU cc_start: 0.7761 (pm20) cc_final: 0.7501 (pm20) REVERT: B 442 LYS cc_start: 0.8033 (mmtt) cc_final: 0.7390 (pttm) REVERT: B 462 LYS cc_start: 0.7566 (mmtt) cc_final: 0.7259 (mmtt) REVERT: B 463 GLN cc_start: 0.7571 (tt0) cc_final: 0.7257 (tt0) REVERT: B 477 GLN cc_start: 0.8157 (tp40) cc_final: 0.7947 (tp40) REVERT: B 492 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7018 (mp) REVERT: B 518 GLN cc_start: 0.7276 (mt0) cc_final: 0.6852 (mm-40) REVERT: B 525 MET cc_start: 0.8424 (mtm) cc_final: 0.8200 (mtp) outliers start: 15 outliers final: 11 residues processed: 135 average time/residue: 0.0864 time to fit residues: 16.2298 Evaluate side-chains 136 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 571 HIS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 538 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 97 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 104 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 GLN B 307 GLN ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.143343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.108310 restraints weight = 10304.565| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.67 r_work: 0.3074 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9233 Z= 0.139 Angle : 0.472 7.590 12513 Z= 0.247 Chirality : 0.038 0.136 1477 Planarity : 0.003 0.037 1571 Dihedral : 4.716 52.003 1265 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.91 % Allowed : 10.27 % Favored : 87.81 % 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: 2.00 (0.25), residues: 1138 helix: 2.31 (0.18), residues: 796 sheet: -1.46 (0.72), residues: 56 loop : -0.96 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 104 TYR 0.008 0.001 TYR B 260 PHE 0.011 0.001 PHE B 227 TRP 0.009 0.001 TRP B 196 HIS 0.002 0.001 HIS B 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 9233) covalent geometry : angle 0.47247 / 0.25 (12513) hydrogen bonds : bond 0.04758 / 3.05 ( 630) hydrogen bonds : angle 3.93015 / 2.87 ( 1860) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.247 Fit side-chains REVERT: A 103 LYS cc_start: 0.7749 (mmtt) cc_final: 0.7508 (mmtt) REVERT: A 154 ARG cc_start: 0.8355 (mtp180) cc_final: 0.7860 (ttt180) REVERT: A 325 LYS cc_start: 0.7693 (tppt) cc_final: 0.6713 (tttm) REVERT: A 352 GLU cc_start: 0.7828 (mp0) cc_final: 0.7455 (mp0) REVERT: A 509 ARG cc_start: 0.8316 (mtm-85) cc_final: 0.7762 (mtm-85) REVERT: A 543 ASP cc_start: 0.8008 (t0) cc_final: 0.7762 (t0) REVERT: B 50 ASP cc_start: 0.7835 (m-30) cc_final: 0.7625 (m-30) REVERT: B 68 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7962 (mtp) REVERT: B 103 MET cc_start: 0.8532 (mtm) cc_final: 0.8230 (mtm) REVERT: B 121 MET cc_start: 0.8494 (mmm) cc_final: 0.8201 (mmm) REVERT: B 190 TYR cc_start: 0.8137 (t80) cc_final: 0.7339 (t80) REVERT: B 335 GLU cc_start: 0.6740 (tm-30) cc_final: 0.6516 (tt0) REVERT: B 424 GLU cc_start: 0.7725 (pm20) cc_final: 0.7428 (pm20) REVERT: B 442 LYS cc_start: 0.8029 (mmtt) cc_final: 0.7398 (pttm) REVERT: B 462 LYS cc_start: 0.7556 (mmtt) cc_final: 0.7260 (mmtt) REVERT: B 477 GLN cc_start: 0.8137 (tp40) cc_final: 0.7896 (tp40) REVERT: B 492 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.6997 (mp) REVERT: B 518 GLN cc_start: 0.7286 (mt0) cc_final: 0.6845 (mm-40) REVERT: B 525 MET cc_start: 0.8427 (mtm) cc_final: 0.8181 (mtp) REVERT: B 549 MET cc_start: 0.8299 (mmt) cc_final: 0.8092 (mmm) outliers start: 19 outliers final: 13 residues processed: 134 average time/residue: 0.0808 time to fit residues: 14.8642 Evaluate side-chains 135 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 571 HIS Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 538 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 307 GLN ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.143922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.109946 restraints weight = 10153.943| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.57 r_work: 0.3057 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9233 Z= 0.158 Angle : 0.487 7.349 12513 Z= 0.254 Chirality : 0.039 0.138 1477 Planarity : 0.004 0.038 1571 Dihedral : 4.666 48.972 1265 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.71 % Allowed : 10.78 % Favored : 87.51 % 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: 1.97 (0.25), residues: 1138 helix: 2.30 (0.18), residues: 793 sheet: -1.83 (0.67), residues: 62 loop : -0.84 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 104 TYR 0.009 0.001 TYR B 260 PHE 0.011 0.001 PHE B 227 TRP 0.009 0.001 TRP B 196 HIS 0.002 0.001 HIS B 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 9233) covalent geometry : angle 0.48681 / 0.25 (12513) hydrogen bonds : bond 0.04890 / 3.14 ( 630) hydrogen bonds : angle 3.97294 / 2.91 ( 1860) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.241 Fit side-chains REVERT: A 41 ASP cc_start: 0.7887 (p0) cc_final: 0.7679 (p0) REVERT: A 97 MET cc_start: 0.9088 (mmp) cc_final: 0.8810 (mmm) REVERT: A 103 LYS cc_start: 0.7768 (mmtt) cc_final: 0.7529 (mmtt) REVERT: A 154 ARG cc_start: 0.8370 (mtp180) cc_final: 0.7871 (ttt180) REVERT: A 325 LYS cc_start: 0.7728 (tppt) cc_final: 0.6773 (tttp) REVERT: A 352 GLU cc_start: 0.7845 (mp0) cc_final: 0.7484 (mp0) REVERT: A 385 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7484 (mppt) REVERT: A 509 ARG cc_start: 0.8303 (mtm-85) cc_final: 0.7752 (mtm-85) REVERT: A 543 ASP cc_start: 0.8050 (t0) cc_final: 0.7801 (t0) REVERT: B 50 ASP cc_start: 0.7845 (m-30) cc_final: 0.7631 (m-30) REVERT: B 103 MET cc_start: 0.8525 (mtm) cc_final: 0.8244 (mtm) REVERT: B 121 MET cc_start: 0.8526 (mmm) cc_final: 0.8201 (mmm) REVERT: B 130 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: B 190 TYR cc_start: 0.8136 (t80) cc_final: 0.7325 (t80) REVERT: B 335 GLU cc_start: 0.6731 (tm-30) cc_final: 0.6521 (tt0) REVERT: B 339 GLN cc_start: 0.8107 (mt0) cc_final: 0.7775 (mt0) REVERT: B 424 GLU cc_start: 0.7727 (pm20) cc_final: 0.7349 (pm20) REVERT: B 442 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7427 (pttm) REVERT: B 477 GLN cc_start: 0.8187 (tp40) cc_final: 0.7956 (tp40) REVERT: B 492 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7028 (mp) REVERT: B 518 GLN cc_start: 0.7315 (mt0) cc_final: 0.6856 (mm-40) REVERT: B 525 MET cc_start: 0.8437 (mtm) cc_final: 0.8177 (mtp) REVERT: B 549 MET cc_start: 0.8334 (mmt) cc_final: 0.8102 (mmm) outliers start: 17 outliers final: 12 residues processed: 130 average time/residue: 0.0808 time to fit residues: 14.5134 Evaluate side-chains 136 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 571 HIS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 538 SER Chi-restraints excluded: chain B residue 564 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 48 optimal weight: 0.0970 chunk 88 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 GLN B 307 GLN ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.146053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.111727 restraints weight = 10200.075| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.60 r_work: 0.3060 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9233 Z= 0.132 Angle : 0.466 7.251 12513 Z= 0.244 Chirality : 0.038 0.136 1477 Planarity : 0.004 0.038 1571 Dihedral : 4.507 46.412 1265 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.91 % Allowed : 10.57 % Favored : 87.51 % 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: 2.02 (0.25), residues: 1138 helix: 2.34 (0.18), residues: 793 sheet: -1.81 (0.68), residues: 62 loop : -0.84 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 404 TYR 0.028 0.001 TYR B 408 PHE 0.010 0.001 PHE B 227 TRP 0.009 0.001 TRP B 196 HIS 0.002 0.001 HIS B 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 9233) covalent geometry : angle 0.46590 / 0.24 (12513) hydrogen bonds : bond 0.04679 / 3.00 ( 630) hydrogen bonds : angle 3.92116 / 2.87 ( 1860) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.229 Fit side-chains REVERT: A 97 MET cc_start: 0.9092 (mmp) cc_final: 0.8782 (mmm) REVERT: A 103 LYS cc_start: 0.7770 (mmtt) cc_final: 0.7468 (mmtt) REVERT: A 154 ARG cc_start: 0.8342 (mtp180) cc_final: 0.7847 (ttt180) REVERT: A 325 LYS cc_start: 0.7729 (tppt) cc_final: 0.6759 (tttp) REVERT: A 352 GLU cc_start: 0.7822 (mp0) cc_final: 0.7453 (mp0) REVERT: A 509 ARG cc_start: 0.8297 (mtm-85) cc_final: 0.7721 (mtm-85) REVERT: A 543 ASP cc_start: 0.8100 (t0) cc_final: 0.7863 (t0) REVERT: B 50 ASP cc_start: 0.7859 (m-30) cc_final: 0.7629 (m-30) REVERT: B 103 MET cc_start: 0.8528 (mtm) cc_final: 0.8240 (mtm) REVERT: B 121 MET cc_start: 0.8502 (mmm) cc_final: 0.8221 (mmm) REVERT: B 190 TYR cc_start: 0.8135 (t80) cc_final: 0.7326 (t80) REVERT: B 335 GLU cc_start: 0.6717 (tm-30) cc_final: 0.6443 (tt0) REVERT: B 424 GLU cc_start: 0.7727 (pm20) cc_final: 0.7320 (pm20) REVERT: B 442 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7420 (pttm) REVERT: B 462 LYS cc_start: 0.8365 (tppt) cc_final: 0.7241 (mmtt) REVERT: B 477 GLN cc_start: 0.8136 (tp40) cc_final: 0.7904 (tp40) REVERT: B 492 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.6942 (mp) REVERT: B 518 GLN cc_start: 0.7291 (mt0) cc_final: 0.6835 (mm-40) REVERT: B 525 MET cc_start: 0.8427 (mtm) cc_final: 0.8180 (mtp) REVERT: B 549 MET cc_start: 0.8299 (mmt) cc_final: 0.8098 (mmm) outliers start: 19 outliers final: 12 residues processed: 134 average time/residue: 0.0827 time to fit residues: 15.0598 Evaluate side-chains 134 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 571 HIS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 538 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.0670 chunk 25 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 100 optimal weight: 5.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 GLN B 307 GLN ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.145262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.113975 restraints weight = 10153.973| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.46 r_work: 0.3080 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9233 Z= 0.128 Angle : 0.466 7.186 12513 Z= 0.243 Chirality : 0.038 0.135 1477 Planarity : 0.003 0.037 1571 Dihedral : 4.413 45.125 1265 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.61 % Allowed : 11.28 % Favored : 87.11 % 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: 2.02 (0.25), residues: 1138 helix: 2.34 (0.18), residues: 793 sheet: -1.85 (0.68), residues: 62 loop : -0.87 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 404 TYR 0.022 0.001 TYR B 408 PHE 0.010 0.001 PHE B 227 TRP 0.010 0.001 TRP A 228 HIS 0.002 0.001 HIS B 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 9233) covalent geometry : angle 0.46552 / 0.24 (12513) hydrogen bonds : bond 0.04605 / 2.95 ( 630) hydrogen bonds : angle 3.89773 / 2.85 ( 1860) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.205 Fit side-chains REVERT: A 31 LEU cc_start: 0.8821 (tt) cc_final: 0.7398 (mt) REVERT: A 97 MET cc_start: 0.9091 (mmp) cc_final: 0.8805 (mmm) REVERT: A 103 LYS cc_start: 0.7790 (mmtt) cc_final: 0.7522 (mmtt) REVERT: A 154 ARG cc_start: 0.8326 (mtp180) cc_final: 0.7857 (ttt180) REVERT: A 325 LYS cc_start: 0.7778 (tppt) cc_final: 0.6826 (tttp) REVERT: A 352 GLU cc_start: 0.7846 (mp0) cc_final: 0.7491 (mp0) REVERT: A 509 ARG cc_start: 0.8223 (mtm-85) cc_final: 0.7664 (mtm-85) REVERT: A 543 ASP cc_start: 0.8114 (t0) cc_final: 0.7884 (t0) REVERT: B 50 ASP cc_start: 0.7865 (m-30) cc_final: 0.7626 (m-30) REVERT: B 103 MET cc_start: 0.8547 (mtm) cc_final: 0.8260 (mtm) REVERT: B 121 MET cc_start: 0.8533 (mmm) cc_final: 0.8259 (mmm) REVERT: B 190 TYR cc_start: 0.8134 (t80) cc_final: 0.7326 (t80) REVERT: B 335 GLU cc_start: 0.6718 (tm-30) cc_final: 0.6451 (tt0) REVERT: B 424 GLU cc_start: 0.7706 (pm20) cc_final: 0.7325 (pm20) REVERT: B 442 LYS cc_start: 0.8118 (mmtt) cc_final: 0.7440 (pttm) REVERT: B 492 ILE cc_start: 0.7264 (OUTLIER) cc_final: 0.6739 (mp) REVERT: B 518 GLN cc_start: 0.7328 (mt0) cc_final: 0.6866 (mm-40) REVERT: B 525 MET cc_start: 0.8438 (mtm) cc_final: 0.8193 (mtp) outliers start: 16 outliers final: 12 residues processed: 132 average time/residue: 0.0856 time to fit residues: 15.4831 Evaluate side-chains 130 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 571 HIS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 538 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 44 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 0.0370 chunk 25 optimal weight: 0.3980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 307 GLN ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.139541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.105258 restraints weight = 10594.250| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.56 r_work: 0.3013 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9233 Z= 0.123 Angle : 0.460 7.097 12513 Z= 0.242 Chirality : 0.038 0.135 1477 Planarity : 0.003 0.038 1571 Dihedral : 4.322 44.175 1265 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.41 % Allowed : 11.58 % Favored : 87.01 % 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: 2.03 (0.25), residues: 1138 helix: 2.36 (0.18), residues: 793 sheet: -1.87 (0.68), residues: 62 loop : -0.87 (0.36), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 12 TYR 0.021 0.001 TYR B 408 PHE 0.010 0.001 PHE B 227 TRP 0.009 0.001 TRP A 228 HIS 0.002 0.001 HIS B 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 9233) covalent geometry : angle 0.46026 / 0.24 (12513) hydrogen bonds : bond 0.04561 / 2.91 ( 630) hydrogen bonds : angle 3.88055 / 2.83 ( 1860) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 0.204 Fit side-chains REVERT: A 31 LEU cc_start: 0.8898 (tt) cc_final: 0.7574 (mt) REVERT: A 41 ASP cc_start: 0.7915 (p0) cc_final: 0.7667 (p0) REVERT: A 97 MET cc_start: 0.9112 (mmp) cc_final: 0.8863 (mmm) REVERT: A 103 LYS cc_start: 0.8047 (mmtt) cc_final: 0.7820 (mmtt) REVERT: A 154 ARG cc_start: 0.8417 (mtp180) cc_final: 0.7988 (ttt180) REVERT: A 325 LYS cc_start: 0.7862 (tppt) cc_final: 0.6970 (tttp) REVERT: A 352 GLU cc_start: 0.7907 (mp0) cc_final: 0.7608 (mp0) REVERT: A 509 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.7719 (mtm-85) REVERT: B 50 ASP cc_start: 0.7981 (m-30) cc_final: 0.7727 (m-30) REVERT: B 103 MET cc_start: 0.8692 (mtm) cc_final: 0.8430 (mtm) REVERT: B 121 MET cc_start: 0.8623 (mmm) cc_final: 0.8367 (mmm) REVERT: B 190 TYR cc_start: 0.8235 (t80) cc_final: 0.7466 (t80) REVERT: B 335 GLU cc_start: 0.6684 (tm-30) cc_final: 0.6420 (tt0) REVERT: B 339 GLN cc_start: 0.8031 (mt0) cc_final: 0.7815 (mt0) REVERT: B 424 GLU cc_start: 0.7766 (pm20) cc_final: 0.7407 (pm20) REVERT: B 442 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7526 (pttm) REVERT: B 462 LYS cc_start: 0.8564 (tppt) cc_final: 0.7248 (mttm) REVERT: B 492 ILE cc_start: 0.7493 (OUTLIER) cc_final: 0.6915 (mp) REVERT: B 518 GLN cc_start: 0.7523 (mt0) cc_final: 0.7075 (mm-40) REVERT: B 525 MET cc_start: 0.8529 (mtm) cc_final: 0.8296 (mtp) outliers start: 14 outliers final: 12 residues processed: 132 average time/residue: 0.0904 time to fit residues: 16.2341 Evaluate side-chains 132 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 571 HIS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 538 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 83 optimal weight: 0.2980 chunk 102 optimal weight: 0.7980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 ASN B 131 GLN B 307 GLN ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.135064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.100331 restraints weight = 10652.829| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.57 r_work: 0.2943 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9233 Z= 0.202 Angle : 0.538 7.283 12513 Z= 0.281 Chirality : 0.040 0.134 1477 Planarity : 0.004 0.038 1571 Dihedral : 4.630 45.864 1265 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.51 % Allowed : 11.68 % Favored : 86.81 % 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: 1.75 (0.25), residues: 1138 helix: 2.14 (0.18), residues: 795 sheet: -1.66 (0.73), residues: 56 loop : -1.07 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 104 TYR 0.019 0.001 TYR B 408 PHE 0.013 0.001 PHE B 255 TRP 0.009 0.001 TRP B 196 HIS 0.003 0.001 HIS B 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.20 ( 9233) covalent geometry : angle 0.53785 / 0.28 (12513) hydrogen bonds : bond 0.05168 / 3.32 ( 630) hydrogen bonds : angle 4.05319 / 2.96 ( 1860) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.280 Fit side-chains REVERT: A 41 ASP cc_start: 0.8150 (p0) cc_final: 0.7941 (p0) REVERT: A 97 MET cc_start: 0.9130 (mmp) cc_final: 0.8927 (mmm) REVERT: A 154 ARG cc_start: 0.8421 (mtp180) cc_final: 0.7942 (ttt180) REVERT: A 325 LYS cc_start: 0.7947 (tppt) cc_final: 0.6979 (tttp) REVERT: A 385 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7506 (mppt) REVERT: B 50 ASP cc_start: 0.7981 (m-30) cc_final: 0.7729 (m-30) REVERT: B 103 MET cc_start: 0.8672 (mtm) cc_final: 0.8376 (mtm) REVERT: B 130 ASP cc_start: 0.8393 (t0) cc_final: 0.8085 (m-30) REVERT: B 190 TYR cc_start: 0.8260 (t80) cc_final: 0.7505 (t80) REVERT: B 335 GLU cc_start: 0.6827 (tm-30) cc_final: 0.6539 (tt0) REVERT: B 424 GLU cc_start: 0.7788 (pm20) cc_final: 0.7439 (pm20) REVERT: B 492 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7240 (mp) REVERT: B 518 GLN cc_start: 0.7533 (mt0) cc_final: 0.7064 (mm-40) REVERT: B 525 MET cc_start: 0.8537 (mtm) cc_final: 0.8268 (mtp) outliers start: 15 outliers final: 12 residues processed: 129 average time/residue: 0.0813 time to fit residues: 14.6768 Evaluate side-chains 130 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 571 HIS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 492 ILE Chi-restraints excluded: chain B residue 538 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 14 optimal weight: 0.7980 chunk 76 optimal weight: 0.0980 chunk 51 optimal weight: 0.2980 chunk 62 optimal weight: 0.8980 chunk 111 optimal weight: 0.0670 chunk 92 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 GLN B 307 GLN ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.135461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.100814 restraints weight = 10568.124| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.57 r_work: 0.2950 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 9233 Z= 0.197 Angle : 0.857 59.190 12513 Z= 0.499 Chirality : 0.039 0.151 1477 Planarity : 0.004 0.038 1571 Dihedral : 4.641 45.815 1265 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.31 % Allowed : 12.19 % Favored : 86.51 % Cbeta Deviations : 0.09 % 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: 1.74 (0.25), residues: 1138 helix: 2.14 (0.18), residues: 795 sheet: -1.69 (0.73), residues: 56 loop : -1.08 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 12 TYR 0.018 0.001 TYR B 408 PHE 0.012 0.001 PHE B 255 TRP 0.010 0.001 TRP B 196 HIS 0.003 0.001 HIS B 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.20 ( 9233) covalent geometry : angle 0.85732 / 0.50 (12513) hydrogen bonds : bond 0.05066 / 3.27 ( 630) hydrogen bonds : angle 4.04979 / 2.96 ( 1860) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1925.61 seconds wall clock time: 33 minutes 37.20 seconds (2017.20 seconds total)