Starting phenix.real_space_refine on Wed Feb 4 04:03:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u9y_63972/02_2026/9u9y_63972_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u9y_63972/02_2026/9u9y_63972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u9y_63972/02_2026/9u9y_63972_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u9y_63972/02_2026/9u9y_63972_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u9y_63972/02_2026/9u9y_63972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u9y_63972/02_2026/9u9y_63972.map" } resolution = 2.7 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= 0.024 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 Zn 1 6.06 5 P 3 5.49 5 S 31 5.16 5 C 5433 2.51 5 N 1489 2.21 5 O 1628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8585 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3377 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 15, 'TRANS': 405} Chain breaks: 5 Chain: "B" Number of atoms: 3507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3507 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 14, 'TRANS': 421} Chain breaks: 5 Chain: "H" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1669 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7234 SG CYS H 43 49.198 50.387 73.676 1.00160.70 S ATOM 7257 SG CYS H 46 47.142 52.706 71.453 1.00162.10 S ATOM 7528 SG CYS H 78 48.163 49.161 70.148 1.00176.46 S ATOM 7569 SG CYS H 90 50.613 51.801 70.451 1.00162.44 S Time building chain proxies: 2.00, per 1000 atoms: 0.23 Number of scatterers: 8585 At special positions: 0 Unit cell: (78.57, 105.3, 106.92, 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) Zn 1 29.99 S 31 16.00 P 3 15.00 O 1628 8.00 N 1489 7.00 C 5433 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: 0.67 Conformation dependent library (CDL) restraints added in 303.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 90 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 78 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 46 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 43 " Number of angles added : 6 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2002 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 10 sheets defined 51.5% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 removed outlier: 3.786A pdb=" N TYR A 46 " --> pdb=" O MET A 42 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 47 " --> pdb=" O CYS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 119 removed outlier: 4.642A pdb=" N LYS A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TRP A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 189 removed outlier: 4.025A pdb=" N LEU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 removed outlier: 3.556A pdb=" N ARG A 207 " --> pdb=" O ASN A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 228 Processing helix chain 'A' and resid 231 through 235 removed outlier: 4.197A pdb=" N GLY A 235 " --> pdb=" O THR A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 253 Processing helix chain 'A' and resid 311 through 326 Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 358 through 379 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.666A pdb=" N GLY A 388 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 417 removed outlier: 4.039A pdb=" N GLU A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE A 410 " --> pdb=" O GLN A 406 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LEU A 411 " --> pdb=" O GLN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 433 Processing helix chain 'A' and resid 434 through 435 No H-bonds generated for 'chain 'A' and resid 434 through 435' Processing helix chain 'A' and resid 436 through 438 No H-bonds generated for 'chain 'A' and resid 436 through 438' Processing helix chain 'A' and resid 465 through 473 Processing helix chain 'A' and resid 488 through 500 Processing helix chain 'A' and resid 508 through 516 Processing helix chain 'A' and resid 522 through 546 removed outlier: 3.900A pdb=" N ALA A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 530 " --> pdb=" O LYS A 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 43 through 49 removed outlier: 3.876A pdb=" N ILE B 47 " --> pdb=" O CYS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 119 removed outlier: 3.977A pdb=" N LEU B 103 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TRP B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 193 Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 224 through 230 Processing helix chain 'B' and resid 238 through 253 Processing helix chain 'B' and resid 311 through 326 removed outlier: 3.639A pdb=" N VAL B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 360 through 379 Processing helix chain 'B' and resid 384 through 388 Processing helix chain 'B' and resid 402 through 417 removed outlier: 4.303A pdb=" N GLU B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE B 410 " --> pdb=" O GLN B 406 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LEU B 411 " --> pdb=" O GLN B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 434 through 435 No H-bonds generated for 'chain 'B' and resid 434 through 435' Processing helix chain 'B' and resid 436 through 438 No H-bonds generated for 'chain 'B' and resid 436 through 438' Processing helix chain 'B' and resid 465 through 473 Processing helix chain 'B' and resid 483 through 486 Processing helix chain 'B' and resid 487 through 499 removed outlier: 3.996A pdb=" N ASN B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 519 Processing helix chain 'B' and resid 522 through 547 removed outlier: 3.649A pdb=" N GLU B 547 " --> pdb=" O LYS B 543 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 16 removed outlier: 3.628A pdb=" N GLN H 15 " --> pdb=" O ILE H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 26 Processing helix chain 'H' and resid 27 through 30 Processing helix chain 'H' and resid 31 through 40 removed outlier: 3.642A pdb=" N LEU H 35 " --> pdb=" O VAL H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 68 Processing helix chain 'H' and resid 70 through 72 No H-bonds generated for 'chain 'H' and resid 70 through 72' Processing helix chain 'H' and resid 89 through 97 removed outlier: 3.644A pdb=" N TYR H 93 " --> pdb=" O ARG H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 106 Processing helix chain 'H' and resid 113 through 116 Processing helix chain 'H' and resid 134 through 147 removed outlier: 3.621A pdb=" N PHE H 147 " --> pdb=" O THR H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 166 removed outlier: 3.879A pdb=" N ILE H 166 " --> pdb=" O ALA H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 176 removed outlier: 3.616A pdb=" N TYR H 174 " --> pdb=" O VAL H 170 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU H 176 " --> pdb=" O TYR H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 196 removed outlier: 3.630A pdb=" N TRP H 185 " --> pdb=" O ASP H 181 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE H 196 " --> pdb=" O GLU H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 199 No H-bonds generated for 'chain 'H' and resid 197 through 199' Processing helix chain 'H' and resid 201 through 210 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 83 removed outlier: 6.657A pdb=" N SER A 78 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU A 66 " --> pdb=" O PHE A 149 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N PHE A 149 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N PHE A 150 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LYS A 155 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 203 removed outlier: 6.161A pdb=" N THR A 199 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU A 393 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA A 201 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLY A 390 " --> pdb=" O GLN A 421 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE A 423 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL A 392 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N THR A 425 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE A 394 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ARG A 441 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL A 90 " --> pdb=" O ARG A 441 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 335 removed outlier: 4.256A pdb=" N ASN A 331 " --> pdb=" O THR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 50 through 52 Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 83 removed outlier: 6.698A pdb=" N LEU B 79 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LYS B 72 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLU B 81 " --> pdb=" O THR B 70 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR B 70 " --> pdb=" O GLU B 81 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LYS B 83 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ARG B 68 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU B 66 " --> pdb=" O PHE B 149 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE B 149 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG B 68 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N PHE B 74 " --> pdb=" O TYR B 141 " (cutoff:3.500A) removed outlier: 10.873A pdb=" N TYR B 141 " --> pdb=" O PHE B 74 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 199 through 203 removed outlier: 6.070A pdb=" N THR B 199 " --> pdb=" O ILE B 391 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU B 393 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ALA B 201 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ASP B 395 " --> pdb=" O ALA B 201 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TYR B 203 " --> pdb=" O ASP B 395 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N THR B 89 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ARG B 441 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL B 90 " --> pdb=" O ARG B 441 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 329 through 333 removed outlier: 4.027A pdb=" N ASN B 331 " --> pdb=" O THR B 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 57 Processing sheet with id=AB1, first strand: chain 'H' and resid 118 through 120 383 hydrogen bonds defined for protein. 1047 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: 1.29 Time building geometry restraints manager: 0.90 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: 2863 1.34 - 1.46: 1870 1.46 - 1.58: 3959 1.58 - 1.70: 3 1.70 - 1.82: 50 Bond restraints: 8745 Sorted by residual: bond pdb=" C TRP A 488 " pdb=" N LEU A 489 " ideal model delta sigma weight residual 1.335 1.273 0.062 1.31e-02 5.83e+03 2.23e+01 bond pdb=" C HIS A 487 " pdb=" N TRP A 488 " ideal model delta sigma weight residual 1.331 1.286 0.045 1.23e-02 6.61e+03 1.35e+01 bond pdb=" N PHE A 443 " pdb=" CA PHE A 443 " ideal model delta sigma weight residual 1.462 1.426 0.036 1.26e-02 6.30e+03 8.22e+00 bond pdb=" CA PHE A 443 " pdb=" C PHE A 443 " ideal model delta sigma weight residual 1.524 1.489 0.035 1.27e-02 6.20e+03 7.69e+00 bond pdb=" CA ALA A 100 " pdb=" C ALA A 100 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.27e-02 6.20e+03 4.21e+00 ... (remaining 8740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 11537 2.35 - 4.70: 229 4.70 - 7.06: 35 7.06 - 9.41: 7 9.41 - 11.76: 6 Bond angle restraints: 11814 Sorted by residual: angle pdb=" N ARG A 140 " pdb=" CA ARG A 140 " pdb=" C ARG A 140 " ideal model delta sigma weight residual 111.54 105.12 6.42 1.36e+00 5.41e-01 2.23e+01 angle pdb=" N GLY A 519 " pdb=" CA GLY A 519 " pdb=" C GLY A 519 " ideal model delta sigma weight residual 114.90 108.01 6.89 1.54e+00 4.22e-01 2.00e+01 angle pdb=" C CYS H 90 " pdb=" CA CYS H 90 " pdb=" CB CYS H 90 " ideal model delta sigma weight residual 116.34 110.53 5.81 1.40e+00 5.10e-01 1.72e+01 angle pdb=" N ALA A 100 " pdb=" CA ALA A 100 " pdb=" C ALA A 100 " ideal model delta sigma weight residual 111.07 106.66 4.41 1.07e+00 8.73e-01 1.70e+01 angle pdb=" CA GLU A 442 " pdb=" CB GLU A 442 " pdb=" CG GLU A 442 " ideal model delta sigma weight residual 114.10 122.08 -7.98 2.00e+00 2.50e-01 1.59e+01 ... (remaining 11809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 4689 17.46 - 34.92: 464 34.92 - 52.38: 102 52.38 - 69.84: 34 69.84 - 87.30: 9 Dihedral angle restraints: 5298 sinusoidal: 2222 harmonic: 3076 Sorted by residual: dihedral pdb=" CA VAL A 188 " pdb=" C VAL A 188 " pdb=" N ILE A 189 " pdb=" CA ILE A 189 " ideal model delta harmonic sigma weight residual 180.00 158.90 21.10 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA ILE A 189 " pdb=" C ILE A 189 " pdb=" N ASN A 190 " pdb=" CA ASN A 190 " ideal model delta harmonic sigma weight residual -180.00 -160.35 -19.65 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASP A 227 " pdb=" C ASP A 227 " pdb=" N ALA A 228 " pdb=" CA ALA A 228 " ideal model delta harmonic sigma weight residual 180.00 160.78 19.22 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 5295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1104 0.070 - 0.139: 197 0.139 - 0.209: 6 0.209 - 0.279: 0 0.279 - 0.348: 2 Chirality restraints: 1309 Sorted by residual: chirality pdb=" CG LEU H 173 " pdb=" CB LEU H 173 " pdb=" CD1 LEU H 173 " pdb=" CD2 LEU H 173 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CB ILE B 322 " pdb=" CA ILE B 322 " pdb=" CG1 ILE B 322 " pdb=" CG2 ILE B 322 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB ILE B 520 " pdb=" CA ILE B 520 " pdb=" CG1 ILE B 520 " pdb=" CG2 ILE B 520 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.18e-01 ... (remaining 1306 not shown) Planarity restraints: 1525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 402 " 0.043 5.00e-02 4.00e+02 6.54e-02 6.85e+00 pdb=" N PRO B 403 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 403 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 403 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 129 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.79e+00 pdb=" C GLU A 129 " 0.045 2.00e-02 2.50e+03 pdb=" O GLU A 129 " -0.017 2.00e-02 2.50e+03 pdb=" N MET A 130 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 442 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.41e+00 pdb=" C GLU A 442 " 0.044 2.00e-02 2.50e+03 pdb=" O GLU A 442 " -0.016 2.00e-02 2.50e+03 pdb=" N PHE A 443 " -0.015 2.00e-02 2.50e+03 ... (remaining 1522 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 425 2.72 - 3.26: 9172 3.26 - 3.81: 14245 3.81 - 4.35: 17589 4.35 - 4.90: 29874 Nonbonded interactions: 71305 Sorted by model distance: nonbonded pdb=" OH TYR H 174 " pdb=" O TRP H 209 " model vdw 2.173 3.040 nonbonded pdb=" O ASN B 475 " pdb=" ND2 ASN B 475 " model vdw 2.253 3.120 nonbonded pdb=" OH TYR A 46 " pdb=" O PHE A 150 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR B 46 " pdb=" O PHE B 150 " model vdw 2.299 3.040 nonbonded pdb=" OH TYR A 104 " pdb=" OD2 ASP A 132 " model vdw 2.302 3.040 ... (remaining 71300 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 42 through 209 or resid 221 through 335 or resid 342 throu \ gh 546)) selection = (chain 'B' and (resid 42 through 162 or resid 176 through 501 or resid 507 throu \ gh 546)) } 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.120 Find NCS groups from input model: 0.120 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:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 0.076 8749 Z= 0.226 Angle : 0.845 11.761 11820 Z= 0.447 Chirality : 0.050 0.348 1309 Planarity : 0.005 0.065 1525 Dihedral : 15.257 87.300 3296 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.29 % Favored : 96.52 % Rotamer: Outliers : 0.74 % Allowed : 19.02 % Favored : 80.23 % 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: 0.01 (0.27), residues: 1034 helix: 0.39 (0.25), residues: 441 sheet: -0.63 (0.48), residues: 126 loop : 0.01 (0.31), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 222 TYR 0.023 0.002 TYR A 104 PHE 0.018 0.002 PHE A 74 TRP 0.023 0.002 TRP A 245 HIS 0.006 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 8745) covalent geometry : angle 0.84063 (11814) hydrogen bonds : bond 0.17269 ( 383) hydrogen bonds : angle 6.88650 ( 1047) metal coordination : bond 0.00900 ( 4) metal coordination : angle 3.97801 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 MET cc_start: 0.8712 (ttm) cc_final: 0.8441 (ttm) REVERT: H 195 LYS cc_start: 0.8827 (tppp) cc_final: 0.8564 (tppt) outliers start: 7 outliers final: 4 residues processed: 106 average time/residue: 0.5385 time to fit residues: 61.3454 Evaluate side-chains 95 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain H residue 133 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 30.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN ** B 402 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 = 0.3666 r_free = 0.3666 target = 0.083576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.066801 restraints weight = 23314.775| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 4.03 r_work: 0.3150 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8749 Z= 0.194 Angle : 0.634 7.889 11820 Z= 0.327 Chirality : 0.045 0.234 1309 Planarity : 0.004 0.068 1525 Dihedral : 7.496 59.751 1179 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.76 % Allowed : 16.37 % Favored : 80.87 % 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: 0.13 (0.27), residues: 1034 helix: 0.74 (0.24), residues: 449 sheet: -0.81 (0.47), residues: 127 loop : -0.17 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 222 TYR 0.018 0.002 TYR A 104 PHE 0.020 0.002 PHE H 156 TRP 0.015 0.001 TRP A 245 HIS 0.005 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 8745) covalent geometry : angle 0.63045 (11814) hydrogen bonds : bond 0.04449 ( 383) hydrogen bonds : angle 5.38915 ( 1047) metal coordination : bond 0.01133 ( 4) metal coordination : angle 3.23208 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8716 (mtm110) cc_final: 0.8414 (mtm110) REVERT: A 222 ARG cc_start: 0.7092 (mpt180) cc_final: 0.6349 (mmt90) REVERT: A 483 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.7541 (tp) REVERT: B 42 MET cc_start: 0.5063 (OUTLIER) cc_final: 0.4615 (mtm) REVERT: B 136 ASP cc_start: 0.9166 (m-30) cc_final: 0.8177 (p0) REVERT: B 231 GLN cc_start: 0.8656 (mp10) cc_final: 0.8303 (mp10) REVERT: B 375 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6397 (tmt) outliers start: 26 outliers final: 6 residues processed: 111 average time/residue: 0.5182 time to fit residues: 62.0739 Evaluate side-chains 97 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain H residue 130 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 22 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 0.0070 chunk 73 optimal weight: 0.6980 overall best weight: 2.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 402 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.083101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.066307 restraints weight = 23241.399| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 4.08 r_work: 0.3139 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8749 Z= 0.172 Angle : 0.617 7.870 11820 Z= 0.316 Chirality : 0.044 0.161 1309 Planarity : 0.004 0.068 1525 Dihedral : 7.215 58.322 1177 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.51 % Allowed : 17.32 % Favored : 79.17 % 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: 0.26 (0.27), residues: 1034 helix: 0.97 (0.24), residues: 441 sheet: -0.88 (0.47), residues: 127 loop : -0.16 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 222 TYR 0.015 0.001 TYR A 104 PHE 0.014 0.002 PHE B 492 TRP 0.014 0.001 TRP A 245 HIS 0.005 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 8745) covalent geometry : angle 0.61278 (11814) hydrogen bonds : bond 0.04020 ( 383) hydrogen bonds : angle 5.15933 ( 1047) metal coordination : bond 0.00987 ( 4) metal coordination : angle 3.20660 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8725 (mtm110) cc_final: 0.8443 (mtm110) REVERT: A 140 ARG cc_start: 0.7059 (tpt90) cc_final: 0.6856 (tpt90) REVERT: A 224 GLU cc_start: 0.8602 (pt0) cc_final: 0.8227 (pm20) REVERT: A 317 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8799 (mp) REVERT: A 375 MET cc_start: 0.8724 (ttm) cc_final: 0.8521 (ttm) REVERT: A 465 GLU cc_start: 0.8817 (tp30) cc_final: 0.8567 (tp30) REVERT: A 483 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.7634 (tp) REVERT: A 529 ASP cc_start: 0.7838 (m-30) cc_final: 0.7533 (p0) REVERT: B 136 ASP cc_start: 0.9205 (m-30) cc_final: 0.8212 (p0) REVERT: B 142 SER cc_start: 0.9068 (OUTLIER) cc_final: 0.8245 (m) REVERT: B 155 LYS cc_start: 0.9090 (mmmm) cc_final: 0.8738 (mmmm) REVERT: B 231 GLN cc_start: 0.8662 (mp10) cc_final: 0.8371 (mp10) REVERT: B 375 MET cc_start: 0.7048 (OUTLIER) cc_final: 0.6417 (tmt) REVERT: H 171 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8333 (tp30) outliers start: 33 outliers final: 10 residues processed: 117 average time/residue: 0.4983 time to fit residues: 62.9819 Evaluate side-chains 108 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 488 TRP Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 171 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 81 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 64 optimal weight: 0.0770 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 10 optimal weight: 10.0000 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 GLN B 250 HIS H 164 GLN ** H 207 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 = 0.3708 r_free = 0.3708 target = 0.087001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.069778 restraints weight = 23002.706| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 4.12 r_work: 0.3196 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8749 Z= 0.114 Angle : 0.579 8.120 11820 Z= 0.290 Chirality : 0.043 0.200 1309 Planarity : 0.004 0.064 1525 Dihedral : 6.978 57.163 1176 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.40 % Allowed : 17.64 % Favored : 78.96 % 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: 0.52 (0.27), residues: 1034 helix: 1.16 (0.25), residues: 436 sheet: -0.82 (0.47), residues: 127 loop : 0.04 (0.31), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 222 TYR 0.016 0.001 TYR A 104 PHE 0.016 0.001 PHE B 453 TRP 0.010 0.001 TRP B 333 HIS 0.004 0.001 HIS A 427 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8745) covalent geometry : angle 0.57672 (11814) hydrogen bonds : bond 0.03319 ( 383) hydrogen bonds : angle 4.89160 ( 1047) metal coordination : bond 0.00575 ( 4) metal coordination : angle 2.41382 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8721 (mtm110) cc_final: 0.8276 (ttm-80) REVERT: A 140 ARG cc_start: 0.7157 (tpt90) cc_final: 0.6732 (tpt90) REVERT: A 224 GLU cc_start: 0.8519 (pt0) cc_final: 0.8180 (pm20) REVERT: A 317 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8713 (mp) REVERT: A 408 GLU cc_start: 0.8960 (tt0) cc_final: 0.8709 (tt0) REVERT: A 483 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.7541 (tp) REVERT: B 85 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7763 (mp0) REVERT: B 136 ASP cc_start: 0.9175 (m-30) cc_final: 0.8189 (p0) REVERT: B 142 SER cc_start: 0.9061 (t) cc_final: 0.8235 (m) REVERT: B 155 LYS cc_start: 0.9079 (mmmm) cc_final: 0.8650 (mmmm) REVERT: B 375 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6329 (tmt) REVERT: B 465 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: H 15 GLN cc_start: 0.8958 (mp10) cc_final: 0.8719 (mp10) REVERT: H 172 TYR cc_start: 0.8596 (t80) cc_final: 0.8287 (t80) REVERT: H 190 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7395 (mpp-170) outliers start: 32 outliers final: 12 residues processed: 128 average time/residue: 0.5040 time to fit residues: 69.4592 Evaluate side-chains 115 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 164 GLN Chi-restraints excluded: chain H residue 190 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS B 475 ASN H 164 GLN ** H 207 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 = 0.3688 r_free = 0.3688 target = 0.085801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.068618 restraints weight = 22799.183| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 4.13 r_work: 0.3172 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8749 Z= 0.135 Angle : 0.593 9.365 11820 Z= 0.296 Chirality : 0.043 0.179 1309 Planarity : 0.004 0.065 1525 Dihedral : 6.965 55.775 1176 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.72 % Allowed : 18.49 % Favored : 77.79 % 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: 0.56 (0.27), residues: 1034 helix: 1.17 (0.25), residues: 433 sheet: -0.80 (0.47), residues: 127 loop : 0.10 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 374 TYR 0.014 0.001 TYR A 104 PHE 0.011 0.001 PHE H 156 TRP 0.011 0.001 TRP A 245 HIS 0.004 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8745) covalent geometry : angle 0.59108 (11814) hydrogen bonds : bond 0.03375 ( 383) hydrogen bonds : angle 4.83523 ( 1047) metal coordination : bond 0.00686 ( 4) metal coordination : angle 2.38826 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8702 (mtm110) cc_final: 0.8265 (ttm-80) REVERT: A 140 ARG cc_start: 0.7127 (tpt90) cc_final: 0.6735 (tpt90) REVERT: A 222 ARG cc_start: 0.6693 (mmt90) cc_final: 0.6488 (mmt90) REVERT: A 317 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8727 (mp) REVERT: A 375 MET cc_start: 0.8605 (ttm) cc_final: 0.8212 (ttt) REVERT: A 408 GLU cc_start: 0.8988 (tt0) cc_final: 0.8741 (tt0) REVERT: A 483 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.7763 (pt) REVERT: B 42 MET cc_start: 0.5290 (OUTLIER) cc_final: 0.4791 (mtt) REVERT: B 85 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7867 (mp0) REVERT: B 136 ASP cc_start: 0.9201 (m-30) cc_final: 0.8222 (p0) REVERT: B 142 SER cc_start: 0.9091 (t) cc_final: 0.8243 (m) REVERT: B 155 LYS cc_start: 0.9082 (mmmm) cc_final: 0.8678 (mmmm) REVERT: B 375 MET cc_start: 0.6902 (OUTLIER) cc_final: 0.6397 (tmt) REVERT: B 453 PHE cc_start: 0.8875 (m-80) cc_final: 0.8596 (t80) REVERT: B 474 MET cc_start: 0.9160 (mmm) cc_final: 0.8779 (mmm) REVERT: H 15 GLN cc_start: 0.8979 (mp10) cc_final: 0.8759 (mp10) REVERT: H 172 TYR cc_start: 0.8786 (t80) cc_final: 0.8348 (t80) REVERT: H 190 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7370 (mpp-170) outliers start: 35 outliers final: 11 residues processed: 119 average time/residue: 0.4645 time to fit residues: 59.6224 Evaluate side-chains 114 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 488 TRP Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 190 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 91 optimal weight: 2.9990 chunk 44 optimal weight: 0.0670 chunk 12 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS B 402 HIS B 475 ASN H 164 GLN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.084139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.068107 restraints weight = 23761.689| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 4.11 r_work: 0.3116 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8749 Z= 0.220 Angle : 0.651 9.743 11820 Z= 0.328 Chirality : 0.045 0.162 1309 Planarity : 0.004 0.067 1525 Dihedral : 7.122 53.758 1176 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.51 % Allowed : 19.02 % Favored : 77.47 % 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: 0.26 (0.27), residues: 1034 helix: 1.02 (0.25), residues: 438 sheet: -0.99 (0.47), residues: 127 loop : -0.18 (0.31), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 222 TYR 0.011 0.001 TYR H 117 PHE 0.014 0.002 PHE B 226 TRP 0.011 0.001 TRP H 209 HIS 0.005 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 8745) covalent geometry : angle 0.64752 (11814) hydrogen bonds : bond 0.03916 ( 383) hydrogen bonds : angle 4.94456 ( 1047) metal coordination : bond 0.01180 ( 4) metal coordination : angle 3.18981 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8733 (mtm110) cc_final: 0.8512 (mtp-110) REVERT: A 222 ARG cc_start: 0.6771 (mmt90) cc_final: 0.6555 (mmt90) REVERT: A 317 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8784 (mp) REVERT: B 42 MET cc_start: 0.5551 (OUTLIER) cc_final: 0.5020 (mtt) REVERT: B 136 ASP cc_start: 0.9207 (m-30) cc_final: 0.8227 (p0) REVERT: B 142 SER cc_start: 0.9105 (OUTLIER) cc_final: 0.8247 (m) REVERT: B 155 LYS cc_start: 0.9111 (mmmm) cc_final: 0.8684 (mmmm) REVERT: B 375 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6460 (tmt) REVERT: B 442 GLU cc_start: 0.8638 (pt0) cc_final: 0.8426 (pt0) REVERT: H 15 GLN cc_start: 0.9034 (mp10) cc_final: 0.8767 (mp10) REVERT: H 190 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7504 (mpp-170) outliers start: 33 outliers final: 12 residues processed: 119 average time/residue: 0.4189 time to fit residues: 53.5937 Evaluate side-chains 113 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 459 MET Chi-restraints excluded: chain A residue 488 TRP Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 164 GLN Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain H residue 190 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 99 optimal weight: 0.4980 chunk 66 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS B 475 ASN H 141 GLN H 164 GLN H 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.085965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.069844 restraints weight = 23448.358| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 4.15 r_work: 0.3158 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8749 Z= 0.136 Angle : 0.631 11.553 11820 Z= 0.316 Chirality : 0.043 0.164 1309 Planarity : 0.004 0.065 1525 Dihedral : 6.944 54.964 1176 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.98 % Allowed : 20.19 % Favored : 76.83 % 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: 0.47 (0.27), residues: 1034 helix: 1.18 (0.25), residues: 426 sheet: -0.91 (0.47), residues: 127 loop : -0.00 (0.31), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 374 TYR 0.024 0.001 TYR H 172 PHE 0.025 0.001 PHE H 147 TRP 0.009 0.001 TRP B 333 HIS 0.004 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8745) covalent geometry : angle 0.62793 (11814) hydrogen bonds : bond 0.03403 ( 383) hydrogen bonds : angle 4.84955 ( 1047) metal coordination : bond 0.00689 ( 4) metal coordination : angle 2.80237 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8667 (mtm110) cc_final: 0.8202 (ttm-80) REVERT: A 142 SER cc_start: 0.8446 (t) cc_final: 0.8053 (t) REVERT: A 222 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.6376 (mmt90) REVERT: A 317 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8739 (mp) REVERT: B 42 MET cc_start: 0.5458 (OUTLIER) cc_final: 0.5257 (mtm) REVERT: B 136 ASP cc_start: 0.9204 (m-30) cc_final: 0.8229 (p0) REVERT: B 142 SER cc_start: 0.9049 (OUTLIER) cc_final: 0.8223 (m) REVERT: B 155 LYS cc_start: 0.9099 (mmmm) cc_final: 0.8674 (mmmm) REVERT: B 224 GLU cc_start: 0.8211 (tp30) cc_final: 0.7787 (mp0) REVERT: B 375 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6367 (tmt) REVERT: H 15 GLN cc_start: 0.9027 (mp10) cc_final: 0.8786 (mp10) REVERT: H 164 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8223 (mp10) REVERT: H 172 TYR cc_start: 0.8600 (t80) cc_final: 0.8133 (t80) REVERT: H 190 ARG cc_start: 0.7643 (mpp-170) cc_final: 0.7390 (mpp-170) outliers start: 28 outliers final: 11 residues processed: 122 average time/residue: 0.4692 time to fit residues: 61.8684 Evaluate side-chains 116 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 488 TRP Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 164 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 59 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 1 optimal weight: 0.0980 chunk 13 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS H 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.086123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.069639 restraints weight = 23237.638| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 4.22 r_work: 0.3162 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8749 Z= 0.142 Angle : 0.662 11.162 11820 Z= 0.328 Chirality : 0.044 0.179 1309 Planarity : 0.004 0.062 1525 Dihedral : 6.917 54.513 1176 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.76 % Allowed : 20.83 % Favored : 76.41 % 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: 0.41 (0.27), residues: 1034 helix: 1.09 (0.25), residues: 432 sheet: -1.09 (0.50), residues: 114 loop : 0.01 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 140 TYR 0.020 0.001 TYR H 172 PHE 0.014 0.001 PHE H 147 TRP 0.009 0.001 TRP A 245 HIS 0.004 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8745) covalent geometry : angle 0.66032 (11814) hydrogen bonds : bond 0.03357 ( 383) hydrogen bonds : angle 4.77928 ( 1047) metal coordination : bond 0.00565 ( 4) metal coordination : angle 2.04114 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8718 (mtm110) cc_final: 0.8271 (ttm-80) REVERT: A 375 MET cc_start: 0.8600 (ttm) cc_final: 0.8321 (ttt) REVERT: B 85 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8286 (tp30) REVERT: B 136 ASP cc_start: 0.9184 (m-30) cc_final: 0.8239 (p0) REVERT: B 142 SER cc_start: 0.9094 (OUTLIER) cc_final: 0.8282 (m) REVERT: B 155 LYS cc_start: 0.9108 (mmmm) cc_final: 0.8715 (mmmm) REVERT: B 375 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6445 (tmt) REVERT: B 471 GLU cc_start: 0.9090 (tt0) cc_final: 0.8843 (tt0) REVERT: H 15 GLN cc_start: 0.9023 (mp10) cc_final: 0.8782 (mp10) REVERT: H 164 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8327 (mp10) REVERT: H 190 ARG cc_start: 0.7653 (mpp-170) cc_final: 0.7421 (mpp-170) outliers start: 26 outliers final: 9 residues processed: 113 average time/residue: 0.4657 time to fit residues: 56.6216 Evaluate side-chains 107 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 488 TRP Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 164 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS H 164 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.085320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.068686 restraints weight = 23435.920| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 4.33 r_work: 0.3148 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8749 Z= 0.150 Angle : 0.678 9.888 11820 Z= 0.334 Chirality : 0.044 0.182 1309 Planarity : 0.004 0.062 1525 Dihedral : 6.896 54.753 1176 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.02 % Allowed : 21.47 % Favored : 76.51 % 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: 0.43 (0.27), residues: 1034 helix: 1.12 (0.25), residues: 432 sheet: -1.12 (0.50), residues: 114 loop : 0.02 (0.31), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 140 TYR 0.021 0.001 TYR H 172 PHE 0.012 0.001 PHE B 453 TRP 0.009 0.001 TRP A 245 HIS 0.004 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8745) covalent geometry : angle 0.67733 (11814) hydrogen bonds : bond 0.03331 ( 383) hydrogen bonds : angle 4.78390 ( 1047) metal coordination : bond 0.00619 ( 4) metal coordination : angle 1.86972 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8670 (mtm110) cc_final: 0.8151 (ttm110) REVERT: A 222 ARG cc_start: 0.6640 (mmt90) cc_final: 0.6260 (mmp80) REVERT: A 375 MET cc_start: 0.8567 (ttm) cc_final: 0.8342 (ttt) REVERT: B 42 MET cc_start: 0.4797 (mtm) cc_final: 0.4442 (mtp) REVERT: B 85 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8261 (tp30) REVERT: B 136 ASP cc_start: 0.9218 (m-30) cc_final: 0.8258 (p0) REVERT: B 142 SER cc_start: 0.9093 (OUTLIER) cc_final: 0.8270 (m) REVERT: B 155 LYS cc_start: 0.9087 (mmmm) cc_final: 0.8689 (mmmm) REVERT: B 375 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6415 (tmt) REVERT: B 407 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: B 471 GLU cc_start: 0.9085 (tt0) cc_final: 0.8863 (tt0) REVERT: H 15 GLN cc_start: 0.9023 (mp10) cc_final: 0.8757 (mp10) REVERT: H 190 ARG cc_start: 0.7625 (mpp-170) cc_final: 0.7381 (mpp-170) outliers start: 19 outliers final: 12 residues processed: 106 average time/residue: 0.5175 time to fit residues: 58.9872 Evaluate side-chains 107 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 488 TRP Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 164 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 HIS B 468 GLN H 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.082755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.065781 restraints weight = 23270.530| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 4.11 r_work: 0.3116 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8749 Z= 0.203 Angle : 0.714 10.103 11820 Z= 0.354 Chirality : 0.045 0.206 1309 Planarity : 0.004 0.063 1525 Dihedral : 7.047 55.152 1176 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.91 % Allowed : 22.00 % Favored : 76.09 % 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: 0.28 (0.27), residues: 1034 helix: 1.02 (0.25), residues: 432 sheet: -1.22 (0.50), residues: 115 loop : -0.09 (0.31), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 140 TYR 0.029 0.002 TYR H 172 PHE 0.011 0.002 PHE B 492 TRP 0.012 0.001 TRP A 245 HIS 0.005 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 8745) covalent geometry : angle 0.71186 (11814) hydrogen bonds : bond 0.03679 ( 383) hydrogen bonds : angle 4.87190 ( 1047) metal coordination : bond 0.00900 ( 4) metal coordination : angle 2.32053 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8706 (mtm110) cc_final: 0.8299 (mtm-85) REVERT: B 42 MET cc_start: 0.4855 (mtm) cc_final: 0.4514 (mtp) REVERT: B 80 LEU cc_start: 0.8879 (tt) cc_final: 0.8658 (tp) REVERT: B 85 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8265 (tp30) REVERT: B 136 ASP cc_start: 0.9192 (m-30) cc_final: 0.8244 (p0) REVERT: B 142 SER cc_start: 0.9116 (OUTLIER) cc_final: 0.8296 (m) REVERT: B 155 LYS cc_start: 0.9099 (mmmm) cc_final: 0.8710 (mmmm) REVERT: B 231 GLN cc_start: 0.8536 (mp10) cc_final: 0.8286 (mp10) REVERT: B 375 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6549 (tmt) REVERT: B 407 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: B 471 GLU cc_start: 0.9090 (tt0) cc_final: 0.8844 (tt0) REVERT: H 15 GLN cc_start: 0.9047 (mp10) cc_final: 0.8774 (mp10) REVERT: H 164 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8269 (mp10) REVERT: H 190 ARG cc_start: 0.7644 (mpp-170) cc_final: 0.7436 (mpp-170) outliers start: 18 outliers final: 9 residues processed: 102 average time/residue: 0.5200 time to fit residues: 56.9805 Evaluate side-chains 104 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 488 TRP Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain H residue 54 HIS Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 164 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 63 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 HIS ** H 164 GLN ** 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 = 0.3650 r_free = 0.3650 target = 0.084236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.068302 restraints weight = 23575.884| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 4.11 r_work: 0.3134 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8749 Z= 0.164 Angle : 0.696 10.453 11820 Z= 0.343 Chirality : 0.044 0.233 1309 Planarity : 0.004 0.062 1525 Dihedral : 6.986 55.693 1176 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.70 % Allowed : 22.21 % Favored : 76.09 % 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: 0.36 (0.27), residues: 1034 helix: 1.11 (0.25), residues: 426 sheet: -1.23 (0.50), residues: 115 loop : -0.05 (0.31), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 140 TYR 0.025 0.002 TYR H 172 PHE 0.010 0.001 PHE H 64 TRP 0.010 0.001 TRP A 245 HIS 0.004 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8745) covalent geometry : angle 0.69459 (11814) hydrogen bonds : bond 0.03493 ( 383) hydrogen bonds : angle 4.83539 ( 1047) metal coordination : bond 0.00757 ( 4) metal coordination : angle 2.24134 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2877.89 seconds wall clock time: 49 minutes 56.44 seconds (2996.44 seconds total)