Starting phenix.real_space_refine on Fri Aug 22 22:40:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cht_45601/08_2025/9cht_45601.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cht_45601/08_2025/9cht_45601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cht_45601/08_2025/9cht_45601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cht_45601/08_2025/9cht_45601.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cht_45601/08_2025/9cht_45601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cht_45601/08_2025/9cht_45601.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 59 5.16 5 C 5361 2.51 5 N 1445 2.21 5 O 1580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8445 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5664 Classifications: {'peptide': 692} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 663} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1565 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 184} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 1216 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 143, 1203 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 135} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Conformer: "B" Number of residues, atoms: 143, 1203 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 135} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 bond proxies already assigned to first conformer: 1215 Time building chain proxies: 2.69, per 1000 atoms: 0.32 Number of scatterers: 8445 At special positions: 0 Unit cell: (94.6, 117.82, 137.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 59 16.00 O 1580 8.00 N 1445 7.00 C 5361 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: 0.92 Conformation dependent library (CDL) restraints added in 402.7 milliseconds Enol-peptide restraints added in 1.4 microseconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 8 sheets defined 46.8% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 237 through 246 removed outlier: 4.516A pdb=" N TYR A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N THR A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 273 removed outlier: 4.162A pdb=" N THR A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Proline residue: A 265 - end of helix removed outlier: 4.220A pdb=" N TYR A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 279 No H-bonds generated for 'chain 'A' and resid 276 through 279' Processing helix chain 'A' and resid 281 through 292 removed outlier: 6.751A pdb=" N ASN A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N PHE A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 297 No H-bonds generated for 'chain 'A' and resid 294 through 297' Processing helix chain 'A' and resid 299 through 315 removed outlier: 4.279A pdb=" N GLU A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N MET A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Proline residue: A 307 - end of helix removed outlier: 4.261A pdb=" N LYS A 315 " --> pdb=" O LYS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 330 removed outlier: 3.885A pdb=" N GLY A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 327 " --> pdb=" O LYS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 353 Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 366 through 385 Processing helix chain 'A' and resid 405 through 412 removed outlier: 4.293A pdb=" N GLN A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU A 411 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 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 446 through 449 No H-bonds generated for 'chain 'A' and resid 446 through 449' Processing helix chain 'A' and resid 452 through 457 removed outlier: 4.064A pdb=" N VAL A 457 " --> pdb=" O PRO A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 468 removed outlier: 4.320A pdb=" N THR A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 479 No H-bonds generated for 'chain 'A' and resid 477 through 479' Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 486 through 515 removed outlier: 3.973A pdb=" N LEU A 510 " --> pdb=" O ARG A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 546 removed outlier: 7.671A pdb=" N ILE A 533 " --> pdb=" O ARG A 529 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N MET A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 552 removed outlier: 4.169A pdb=" N LYS A 552 " --> pdb=" O PRO A 548 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 548 through 552' Processing helix chain 'A' and resid 569 through 582 Processing helix chain 'A' and resid 609 through 624 removed outlier: 4.022A pdb=" N THR A 613 " --> pdb=" O GLU A 609 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 614 " --> pdb=" O GLY A 610 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE A 615 " --> pdb=" O GLN A 611 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLY A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 641 Processing helix chain 'A' and resid 648 through 654 removed outlier: 3.703A pdb=" N ASP A 653 " --> pdb=" O ARG A 649 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER A 654 " --> pdb=" O ASP A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 667 removed outlier: 3.861A pdb=" N GLU A 667 " --> pdb=" O LYS A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 700 through 702 No H-bonds generated for 'chain 'A' and resid 700 through 702' Processing helix chain 'A' and resid 710 through 724 removed outlier: 4.169A pdb=" N LEU A 722 " --> pdb=" O SER A 718 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LYS A 724 " --> pdb=" O TYR A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 741 Processing helix chain 'A' and resid 746 through 749 No H-bonds generated for 'chain 'A' and resid 746 through 749' Processing helix chain 'A' and resid 752 through 760 removed outlier: 4.644A pdb=" N GLU A 756 " --> pdb=" O PRO A 752 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LEU A 757 " --> pdb=" O GLU A 753 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 758 " --> pdb=" O GLU A 754 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A 759 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 773 Processing helix chain 'A' and resid 785 through 796 Processing helix chain 'A' and resid 799 through 810 Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 855 through 868 Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 278 through 291 removed outlier: 9.117A pdb=" N ARG B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N ARG B 283 " --> pdb=" O GLY B 279 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N THR B 284 " --> pdb=" O ARG B 280 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS B 291 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 18 removed outlier: 4.407A pdb=" N THR C 17 " --> pdb=" O PRO C 13 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLU C 18 " --> pdb=" O GLN C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'C' and resid 64 through 78 removed outlier: 5.269A pdb=" N LYS C 68 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N PHE C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR C 70 " --> pdb=" O CYS C 66 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LYS C 72 " --> pdb=" O LYS C 68 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE C 73 " --> pdb=" O PHE C 69 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N SER C 74 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N TYR C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ARG C 77 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N HIS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 64 through 78' Processing helix chain 'C' and resid 85 through 92 removed outlier: 5.514A pdb=" N GLU C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLN C 91 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 85 through 92' Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 112 through 120 removed outlier: 6.707A pdb=" N GLN C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ARG C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N HIS C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LEU C 119 " --> pdb=" O LYS C 115 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 590 through 593 removed outlier: 3.643A pdb=" N LEU A 598 " --> pdb=" O ASP A 593 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 775 through 777 removed outlier: 7.671A pdb=" N GLU A 775 " --> pdb=" O ILE A 827 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N LYS A 829 " --> pdb=" O GLU A 775 " (cutoff:3.500A) removed outlier: 9.439A pdb=" N ASP A 777 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 10.311A pdb=" N GLY A 831 " --> pdb=" O ASP A 777 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 204 through 207 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 204 through 207 current: chain 'B' and resid 214 through 219 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 214 through 219 current: chain 'B' and resid 230 through 236 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 55 removed outlier: 5.100A pdb=" N VAL C 53 " --> pdb=" O TYR C 60 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYR C 60 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 523 through 527 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 681 through 685 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 112 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 79 through 83 No H-bonds generated for sheet with id=AA8 226 hydrogen bonds defined for protein. 675 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: 1.21 Time building geometry restraints manager: 1.14 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: 2783 1.34 - 1.46: 1690 1.46 - 1.58: 4063 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 8624 Sorted by residual: bond pdb=" CA THR A 741 " pdb=" CB THR A 741 " ideal model delta sigma weight residual 1.524 1.564 -0.039 1.46e-02 4.69e+03 7.14e+00 bond pdb=" CA VAL B 147 " pdb=" CB VAL B 147 " ideal model delta sigma weight residual 1.551 1.537 0.014 1.08e-02 8.57e+03 1.67e+00 bond pdb=" CG LEU A 346 " pdb=" CD1 LEU A 346 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.50e+00 bond pdb=" CG GLU A 341 " pdb=" CD GLU A 341 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.41e+00 bond pdb=" CB PRO A 299 " pdb=" CG PRO A 299 " ideal model delta sigma weight residual 1.492 1.549 -0.057 5.00e-02 4.00e+02 1.31e+00 ... (remaining 8619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 11397 1.92 - 3.85: 201 3.85 - 5.77: 38 5.77 - 7.70: 10 7.70 - 9.62: 3 Bond angle restraints: 11649 Sorted by residual: angle pdb=" N GLU A 341 " pdb=" CA GLU A 341 " pdb=" CB GLU A 341 " ideal model delta sigma weight residual 110.28 117.59 -7.31 1.55e+00 4.16e-01 2.22e+01 angle pdb=" N ASP B 228 " pdb=" CA ASP B 228 " pdb=" C ASP B 228 " ideal model delta sigma weight residual 108.32 113.70 -5.38 1.64e+00 3.72e-01 1.08e+01 angle pdb=" C MET A 340 " pdb=" N GLU A 341 " pdb=" CA GLU A 341 " ideal model delta sigma weight residual 120.31 115.81 4.50 1.52e+00 4.33e-01 8.75e+00 angle pdb=" CA GLU A 341 " pdb=" CB GLU A 341 " pdb=" CG GLU A 341 " ideal model delta sigma weight residual 114.10 119.96 -5.86 2.00e+00 2.50e-01 8.58e+00 angle pdb=" C GLU A 341 " pdb=" N THR A 342 " pdb=" CA THR A 342 " ideal model delta sigma weight residual 120.29 116.15 4.14 1.42e+00 4.96e-01 8.48e+00 ... (remaining 11644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 4666 17.57 - 35.15: 495 35.15 - 52.72: 93 52.72 - 70.29: 20 70.29 - 87.87: 7 Dihedral angle restraints: 5281 sinusoidal: 2225 harmonic: 3056 Sorted by residual: dihedral pdb=" CA THR C 87 " pdb=" C THR C 87 " pdb=" N LEU C 88 " pdb=" CA LEU C 88 " ideal model delta harmonic sigma weight residual 180.00 160.03 19.97 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ARG A 418 " pdb=" C ARG A 418 " pdb=" N ASN A 419 " pdb=" CA ASN A 419 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASN A 419 " pdb=" C ASN A 419 " pdb=" N LYS A 420 " pdb=" CA LYS A 420 " ideal model delta harmonic sigma weight residual 180.00 -161.63 -18.37 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 5278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 878 0.040 - 0.080: 300 0.080 - 0.121: 78 0.121 - 0.161: 11 0.161 - 0.201: 3 Chirality restraints: 1270 Sorted by residual: chirality pdb=" CB THR B 150 " pdb=" CA THR B 150 " pdb=" OG1 THR B 150 " pdb=" CG2 THR B 150 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CG LEU A 346 " pdb=" CB LEU A 346 " pdb=" CD1 LEU A 346 " pdb=" CD2 LEU A 346 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CA GLU A 341 " pdb=" N GLU A 341 " pdb=" C GLU A 341 " pdb=" CB GLU A 341 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1267 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 298 " 0.056 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO A 299 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 299 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 299 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 584 " -0.043 5.00e-02 4.00e+02 6.60e-02 6.98e+00 pdb=" N PRO A 585 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 585 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 585 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 751 " 0.039 5.00e-02 4.00e+02 5.91e-02 5.59e+00 pdb=" N PRO A 752 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 752 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 752 " 0.033 5.00e-02 4.00e+02 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 715 2.74 - 3.28: 8837 3.28 - 3.82: 13788 3.82 - 4.36: 15949 4.36 - 4.90: 25870 Nonbonded interactions: 65159 Sorted by model distance: nonbonded pdb=" O TRP B 146 " pdb=" OG1 THR B 230 " model vdw 2.203 3.040 nonbonded pdb=" O LEU A 621 " pdb=" N ASN A 625 " model vdw 2.216 3.120 nonbonded pdb=" O LYS A 597 " pdb=" ND1 HIS A 632 " model vdw 2.251 3.120 nonbonded pdb=" O ARG A 763 " pdb=" NH2 ARG A 814 " model vdw 2.251 3.120 nonbonded pdb=" O GLY A 588 " pdb=" ND2 ASN A 602 " model vdw 2.251 3.120 ... (remaining 65154 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=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.470 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.420 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4686 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8624 Z= 0.135 Angle : 0.664 9.623 11649 Z= 0.336 Chirality : 0.043 0.201 1270 Planarity : 0.005 0.084 1514 Dihedral : 14.850 87.865 3311 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.94 % Favored : 89.96 % Rotamer: Outliers : 0.32 % Allowed : 0.21 % Favored : 99.47 % 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 aren not related in a simple way. whole: -1.62 (0.27), residues: 1028 helix: 0.33 (0.27), residues: 382 sheet: -2.08 (0.96), residues: 36 loop : -2.05 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 500 TYR 0.012 0.001 TYR C 81 PHE 0.016 0.001 PHE A 737 TRP 0.007 0.001 TRP B 146 HIS 0.015 0.001 HIS A 795 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8624) covalent geometry : angle 0.66375 (11649) hydrogen bonds : bond 0.06744 ( 226) hydrogen bonds : angle 4.97243 ( 675) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 313 MET cc_start: 0.3773 (tpt) cc_final: 0.2333 (tpt) REVERT: A 715 ASN cc_start: 0.4959 (t0) cc_final: 0.4739 (t0) REVERT: B 100 GLN cc_start: 0.6887 (mp-120) cc_final: 0.6521 (pp30) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.0944 time to fit residues: 13.9848 Evaluate side-chains 87 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.0980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS A 382 ASN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5160 r_free = 0.5160 target = 0.268041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.245631 restraints weight = 31596.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5000 r_free = 0.5000 target = 0.249319 restraints weight = 37222.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5020 r_free = 0.5020 target = 0.251951 restraints weight = 12074.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.5027 r_free = 0.5027 target = 0.252960 restraints weight = 7214.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.5029 r_free = 0.5029 target = 0.253201 restraints weight = 5339.999| |-----------------------------------------------------------------------------| r_work (final): 0.4996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4996 r_free = 0.4996 target_work(ls_wunit_k1) = 0.248 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4996 r_free = 0.4996 target_work(ls_wunit_k1) = 0.248 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4630 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8624 Z= 0.149 Angle : 0.637 7.589 11649 Z= 0.318 Chirality : 0.043 0.141 1270 Planarity : 0.005 0.061 1514 Dihedral : 4.677 22.059 1158 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.53 % Favored : 89.38 % Rotamer: Outliers : 0.85 % Allowed : 8.14 % Favored : 91.01 % 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 aren not related in a simple way. whole: -1.64 (0.27), residues: 1028 helix: 0.32 (0.27), residues: 386 sheet: -2.05 (0.99), residues: 36 loop : -2.08 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 102 TYR 0.022 0.001 TYR A 379 PHE 0.022 0.002 PHE A 713 TRP 0.011 0.001 TRP B 146 HIS 0.006 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8624) covalent geometry : angle 0.63705 (11649) hydrogen bonds : bond 0.03846 ( 226) hydrogen bonds : angle 4.77068 ( 675) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 715 ASN cc_start: 0.5508 (t0) cc_final: 0.5199 (t0) REVERT: B 100 GLN cc_start: 0.7212 (mp-120) cc_final: 0.6661 (pp30) REVERT: C 1 MET cc_start: 0.5357 (pmm) cc_final: 0.4136 (pmm) outliers start: 5 outliers final: 4 residues processed: 98 average time/residue: 0.0915 time to fit residues: 12.8647 Evaluate side-chains 90 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 31 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 78 optimal weight: 0.0570 chunk 57 optimal weight: 0.3980 chunk 48 optimal weight: 20.0000 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5182 r_free = 0.5182 target = 0.271332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5012 r_free = 0.5012 target = 0.249824 restraints weight = 27853.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5026 r_free = 0.5026 target = 0.252809 restraints weight = 33789.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5035 r_free = 0.5035 target = 0.253986 restraints weight = 12166.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.5042 r_free = 0.5042 target = 0.254979 restraints weight = 8629.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.5045 r_free = 0.5045 target = 0.255358 restraints weight = 6308.364| |-----------------------------------------------------------------------------| r_work (final): 0.5021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5020 r_free = 0.5020 target_work(ls_wunit_k1) = 0.251 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5020 r_free = 0.5020 target_work(ls_wunit_k1) = 0.251 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.5020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4534 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8624 Z= 0.108 Angle : 0.570 7.260 11649 Z= 0.286 Chirality : 0.041 0.142 1270 Planarity : 0.004 0.058 1514 Dihedral : 4.401 19.253 1158 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.75 % Favored : 90.16 % Rotamer: Outliers : 1.37 % Allowed : 10.78 % Favored : 87.84 % 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 aren not related in a simple way. whole: -1.42 (0.27), residues: 1028 helix: 0.55 (0.27), residues: 384 sheet: -1.93 (1.00), residues: 36 loop : -1.97 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 539 TYR 0.028 0.001 TYR A 379 PHE 0.020 0.001 PHE A 713 TRP 0.012 0.001 TRP B 146 HIS 0.002 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8624) covalent geometry : angle 0.56978 (11649) hydrogen bonds : bond 0.03413 ( 226) hydrogen bonds : angle 4.47141 ( 675) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 509 VAL cc_start: 0.7879 (p) cc_final: 0.7532 (t) REVERT: A 534 ASP cc_start: 0.5970 (OUTLIER) cc_final: 0.5495 (p0) REVERT: A 715 ASN cc_start: 0.5414 (t0) cc_final: 0.5062 (t0) REVERT: B 100 GLN cc_start: 0.7110 (mp-120) cc_final: 0.6646 (pp30) REVERT: C 1 MET cc_start: 0.5452 (pmm) cc_final: 0.4354 (pmm) outliers start: 10 outliers final: 5 residues processed: 101 average time/residue: 0.0870 time to fit residues: 12.7878 Evaluate side-chains 94 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain C residue 31 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 56 optimal weight: 0.1980 chunk 87 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 127 ASN ** 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 = 0.5169 r_free = 0.5169 target = 0.269677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4978 r_free = 0.4978 target = 0.246112 restraints weight = 36824.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4996 r_free = 0.4996 target = 0.250047 restraints weight = 41936.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5024 r_free = 0.5024 target = 0.253482 restraints weight = 12855.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5032 r_free = 0.5032 target = 0.254653 restraints weight = 6403.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5032 r_free = 0.5032 target = 0.254651 restraints weight = 4866.436| |-----------------------------------------------------------------------------| r_work (final): 0.4995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4996 r_free = 0.4996 target_work(ls_wunit_k1) = 0.248 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4996 r_free = 0.4996 target_work(ls_wunit_k1) = 0.248 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4595 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8624 Z= 0.121 Angle : 0.575 7.244 11649 Z= 0.288 Chirality : 0.042 0.142 1270 Planarity : 0.005 0.057 1514 Dihedral : 4.447 21.137 1158 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.14 % Favored : 89.77 % Rotamer: Outliers : 1.59 % Allowed : 13.64 % Favored : 84.78 % 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 aren not related in a simple way. whole: -1.40 (0.27), residues: 1028 helix: 0.54 (0.27), residues: 385 sheet: -1.95 (0.99), residues: 36 loop : -1.95 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 77 TYR 0.021 0.001 TYR A 379 PHE 0.013 0.001 PHE A 730 TRP 0.012 0.001 TRP B 146 HIS 0.004 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8624) covalent geometry : angle 0.57521 (11649) hydrogen bonds : bond 0.03326 ( 226) hydrogen bonds : angle 4.47897 ( 675) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 ASP cc_start: 0.5921 (OUTLIER) cc_final: 0.5506 (p0) REVERT: A 697 LYS cc_start: 0.5598 (OUTLIER) cc_final: 0.5214 (mmtt) REVERT: A 715 ASN cc_start: 0.5558 (t0) cc_final: 0.5166 (t0) REVERT: B 100 GLN cc_start: 0.7189 (mp-120) cc_final: 0.6662 (pp30) REVERT: C 1 MET cc_start: 0.5487 (pmm) cc_final: 0.4372 (pmm) outliers start: 12 outliers final: 6 residues processed: 98 average time/residue: 0.0905 time to fit residues: 12.9610 Evaluate side-chains 96 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 31 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 11 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 38 optimal weight: 20.0000 chunk 85 optimal weight: 0.0970 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 HIS ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5171 r_free = 0.5171 target = 0.269879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4975 r_free = 0.4975 target = 0.245774 restraints weight = 37464.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4996 r_free = 0.4996 target = 0.250087 restraints weight = 43282.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5024 r_free = 0.5024 target = 0.253548 restraints weight = 12984.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.5031 r_free = 0.5031 target = 0.254504 restraints weight = 6552.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.5035 r_free = 0.5035 target = 0.254956 restraints weight = 4871.331| |-----------------------------------------------------------------------------| r_work (final): 0.4997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4995 r_free = 0.4995 target_work(ls_wunit_k1) = 0.248 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4995 r_free = 0.4995 target_work(ls_wunit_k1) = 0.248 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4600 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8624 Z= 0.117 Angle : 0.568 7.409 11649 Z= 0.285 Chirality : 0.042 0.148 1270 Planarity : 0.004 0.058 1514 Dihedral : 4.403 20.799 1158 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.84 % Favored : 90.06 % Rotamer: Outliers : 1.59 % Allowed : 15.22 % Favored : 83.19 % 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 aren not related in a simple way. whole: -1.35 (0.27), residues: 1028 helix: 0.56 (0.27), residues: 386 sheet: -2.00 (0.98), residues: 36 loop : -1.90 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 213 TYR 0.023 0.001 TYR A 379 PHE 0.031 0.001 PHE A 805 TRP 0.009 0.001 TRP B 146 HIS 0.003 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8624) covalent geometry : angle 0.56805 (11649) hydrogen bonds : bond 0.03300 ( 226) hydrogen bonds : angle 4.42457 ( 675) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 VAL cc_start: 0.7908 (p) cc_final: 0.7553 (t) REVERT: A 534 ASP cc_start: 0.5912 (OUTLIER) cc_final: 0.5591 (p0) REVERT: A 697 LYS cc_start: 0.5511 (OUTLIER) cc_final: 0.5188 (mmtt) REVERT: A 715 ASN cc_start: 0.5535 (t0) cc_final: 0.5216 (t0) REVERT: B 100 GLN cc_start: 0.7175 (mp-120) cc_final: 0.6670 (pp30) REVERT: C 1 MET cc_start: 0.5495 (pmm) cc_final: 0.4394 (pmm) outliers start: 12 outliers final: 7 residues processed: 104 average time/residue: 0.0853 time to fit residues: 13.2226 Evaluate side-chains 101 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 31 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.0570 chunk 64 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 90 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 0.0010 chunk 5 optimal weight: 0.0060 overall best weight: 0.1920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5201 r_free = 0.5201 target = 0.274170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4999 r_free = 0.4999 target = 0.249324 restraints weight = 39977.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.254129 restraints weight = 41249.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5058 r_free = 0.5058 target = 0.258214 restraints weight = 12820.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.5065 r_free = 0.5065 target = 0.259280 restraints weight = 6022.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5065 r_free = 0.5065 target = 0.259281 restraints weight = 4462.618| |-----------------------------------------------------------------------------| r_work (final): 0.5032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5032 r_free = 0.5032 target_work(ls_wunit_k1) = 0.252 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5032 r_free = 0.5032 target_work(ls_wunit_k1) = 0.252 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.5032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4487 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8624 Z= 0.097 Angle : 0.535 7.214 11649 Z= 0.271 Chirality : 0.040 0.146 1270 Planarity : 0.004 0.057 1514 Dihedral : 4.159 17.918 1158 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.28 % Favored : 91.62 % Rotamer: Outliers : 1.48 % Allowed : 16.81 % Favored : 81.71 % 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 aren not related in a simple way. whole: -1.24 (0.27), residues: 1028 helix: 0.66 (0.28), residues: 390 sheet: -1.95 (0.97), residues: 36 loop : -1.86 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 213 TYR 0.025 0.001 TYR A 379 PHE 0.014 0.001 PHE A 730 TRP 0.009 0.001 TRP B 146 HIS 0.002 0.001 HIS A 795 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 8624) covalent geometry : angle 0.53520 (11649) hydrogen bonds : bond 0.03111 ( 226) hydrogen bonds : angle 4.22726 ( 675) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 VAL cc_start: 0.7871 (p) cc_final: 0.7517 (t) REVERT: A 697 LYS cc_start: 0.5483 (OUTLIER) cc_final: 0.5230 (mmtt) REVERT: A 715 ASN cc_start: 0.5586 (t0) cc_final: 0.5224 (t0) REVERT: B 100 GLN cc_start: 0.7194 (mp-120) cc_final: 0.6610 (pp30) REVERT: B 252 LEU cc_start: 0.4628 (OUTLIER) cc_final: 0.3398 (mm) REVERT: C 1 MET cc_start: 0.5631 (pmm) cc_final: 0.4563 (pmm) outliers start: 11 outliers final: 4 residues processed: 108 average time/residue: 0.0893 time to fit residues: 13.8791 Evaluate side-chains 94 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain C residue 31 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 42 optimal weight: 0.0870 chunk 52 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 27 optimal weight: 0.2980 chunk 67 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 738 HIS ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5159 r_free = 0.5159 target = 0.268374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.243946 restraints weight = 40285.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.248232 restraints weight = 42816.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5012 r_free = 0.5012 target = 0.252225 restraints weight = 12785.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.5015 r_free = 0.5015 target = 0.252674 restraints weight = 6849.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5015 r_free = 0.5015 target = 0.252674 restraints weight = 4500.215| |-----------------------------------------------------------------------------| r_work (final): 0.4970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4971 r_free = 0.4971 target_work(ls_wunit_k1) = 0.245 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4971 r_free = 0.4971 target_work(ls_wunit_k1) = 0.245 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4682 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8624 Z= 0.145 Angle : 0.611 7.293 11649 Z= 0.307 Chirality : 0.042 0.137 1270 Planarity : 0.005 0.057 1514 Dihedral : 4.431 22.226 1158 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.84 % Favored : 90.06 % Rotamer: Outliers : 1.80 % Allowed : 17.12 % Favored : 81.08 % 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 aren not related in a simple way. whole: -1.36 (0.27), residues: 1028 helix: 0.48 (0.27), residues: 386 sheet: -2.06 (0.97), residues: 36 loop : -1.85 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 77 TYR 0.022 0.001 TYR A 283 PHE 0.020 0.002 PHE A 737 TRP 0.010 0.001 TRP B 146 HIS 0.005 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8624) covalent geometry : angle 0.61098 (11649) hydrogen bonds : bond 0.03558 ( 226) hydrogen bonds : angle 4.49072 ( 675) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 ASN cc_start: 0.7370 (OUTLIER) cc_final: 0.6947 (t0) REVERT: A 697 LYS cc_start: 0.5546 (OUTLIER) cc_final: 0.5178 (mmtt) REVERT: A 715 ASN cc_start: 0.5532 (t0) cc_final: 0.5174 (t0) REVERT: B 100 GLN cc_start: 0.7158 (mp-120) cc_final: 0.6654 (pp30) outliers start: 14 outliers final: 9 residues processed: 100 average time/residue: 0.0686 time to fit residues: 10.4678 Evaluate side-chains 97 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain C residue 31 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 65 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 36 optimal weight: 0.0040 chunk 97 optimal weight: 0.8980 chunk 78 optimal weight: 0.0570 chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 85 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.3910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN A 738 HIS ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5189 r_free = 0.5189 target = 0.272323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5006 r_free = 0.5006 target = 0.248667 restraints weight = 31522.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5021 r_free = 0.5021 target = 0.252472 restraints weight = 38739.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5050 r_free = 0.5050 target = 0.256083 restraints weight = 13130.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.5056 r_free = 0.5056 target = 0.257256 restraints weight = 6977.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.5059 r_free = 0.5059 target = 0.257446 restraints weight = 5421.540| |-----------------------------------------------------------------------------| r_work (final): 0.5030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5028 r_free = 0.5028 target_work(ls_wunit_k1) = 0.252 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5028 r_free = 0.5028 target_work(ls_wunit_k1) = 0.252 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.5028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4510 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8624 Z= 0.102 Angle : 0.561 7.320 11649 Z= 0.283 Chirality : 0.041 0.144 1270 Planarity : 0.004 0.058 1514 Dihedral : 4.249 18.339 1158 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.58 % Favored : 91.33 % Rotamer: Outliers : 1.69 % Allowed : 18.08 % 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 aren not related in a simple way. whole: -1.23 (0.27), residues: 1028 helix: 0.59 (0.27), residues: 386 sheet: -2.01 (0.96), residues: 36 loop : -1.77 (0.27), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 213 TYR 0.020 0.001 TYR A 659 PHE 0.053 0.001 PHE A 648 TRP 0.009 0.001 TRP B 146 HIS 0.002 0.001 HIS A 795 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8624) covalent geometry : angle 0.56139 (11649) hydrogen bonds : bond 0.03169 ( 226) hydrogen bonds : angle 4.32324 ( 675) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 715 ASN cc_start: 0.5286 (t0) cc_final: 0.5016 (t0) REVERT: B 100 GLN cc_start: 0.7135 (mp-120) cc_final: 0.6583 (pp30) REVERT: B 252 LEU cc_start: 0.4213 (OUTLIER) cc_final: 0.2881 (mm) outliers start: 13 outliers final: 8 residues processed: 97 average time/residue: 0.0804 time to fit residues: 11.6792 Evaluate side-chains 95 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain C residue 31 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 3 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 93 optimal weight: 0.4980 chunk 60 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 91 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN A 382 ASN A 455 ASN A 738 HIS ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5153 r_free = 0.5153 target = 0.267213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.240536 restraints weight = 31423.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4902 r_free = 0.4902 target = 0.237542 restraints weight = 31481.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.235432 restraints weight = 18120.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4887 r_free = 0.4887 target = 0.237211 restraints weight = 16019.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.237384 restraints weight = 10684.828| |-----------------------------------------------------------------------------| r_work (final): 0.4841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4842 r_free = 0.4842 target_work(ls_wunit_k1) = 0.230 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4842 r_free = 0.4842 target_work(ls_wunit_k1) = 0.230 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4975 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8624 Z= 0.154 Angle : 0.634 8.512 11649 Z= 0.317 Chirality : 0.043 0.147 1270 Planarity : 0.005 0.058 1514 Dihedral : 4.537 22.994 1158 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.14 % Favored : 89.77 % Rotamer: Outliers : 1.69 % Allowed : 18.08 % 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 aren not related in a simple way. whole: -1.42 (0.27), residues: 1028 helix: 0.35 (0.27), residues: 387 sheet: -2.17 (0.94), residues: 36 loop : -1.81 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 77 TYR 0.021 0.001 TYR A 748 PHE 0.048 0.002 PHE A 648 TRP 0.011 0.001 TRP B 146 HIS 0.014 0.001 HIS A 795 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8624) covalent geometry : angle 0.63422 (11649) hydrogen bonds : bond 0.03618 ( 226) hydrogen bonds : angle 4.58860 ( 675) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 715 ASN cc_start: 0.6086 (t0) cc_final: 0.5872 (t0) REVERT: B 100 GLN cc_start: 0.7467 (mp-120) cc_final: 0.6781 (pp30) outliers start: 13 outliers final: 9 residues processed: 98 average time/residue: 0.0807 time to fit residues: 11.7735 Evaluate side-chains 98 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain C residue 31 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 54 optimal weight: 0.3980 chunk 96 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 738 HIS ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5124 r_free = 0.5124 target = 0.263351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.215097 restraints weight = 23972.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.221205 restraints weight = 15578.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.223039 restraints weight = 8879.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.223289 restraints weight = 6416.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.224241 restraints weight = 6467.883| |-----------------------------------------------------------------------------| r_work (final): 0.4775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4775 r_free = 0.4775 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4775 r_free = 0.4775 target_work(ls_wunit_k1) = 0.222 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5140 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 8624 Z= 0.186 Angle : 0.936 59.200 11649 Z= 0.534 Chirality : 0.044 0.444 1270 Planarity : 0.005 0.058 1514 Dihedral : 4.611 25.160 1158 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.14 % Favored : 89.77 % Rotamer: Outliers : 1.59 % Allowed : 19.03 % Favored : 79.39 % 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 aren not related in a simple way. whole: -1.43 (0.27), residues: 1028 helix: 0.34 (0.27), residues: 387 sheet: -2.18 (0.94), residues: 36 loop : -1.82 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 77 TYR 0.018 0.001 TYR A 748 PHE 0.044 0.002 PHE A 648 TRP 0.010 0.001 TRP B 146 HIS 0.012 0.001 HIS A 795 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8624) covalent geometry : angle 0.93551 (11649) hydrogen bonds : bond 0.03603 ( 226) hydrogen bonds : angle 4.59616 ( 675) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 363 ASN cc_start: 0.4781 (OUTLIER) cc_final: 0.4203 (p0) REVERT: A 715 ASN cc_start: 0.6166 (t0) cc_final: 0.5947 (t0) REVERT: B 100 GLN cc_start: 0.7484 (mp-120) cc_final: 0.6785 (pp30) outliers start: 12 outliers final: 9 residues processed: 95 average time/residue: 0.0804 time to fit residues: 11.4396 Evaluate side-chains 96 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain C residue 31 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 chunk 77 optimal weight: 30.0000 chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN A 738 HIS ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5123 r_free = 0.5123 target = 0.263207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.215423 restraints weight = 41334.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.220938 restraints weight = 27514.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.224791 restraints weight = 13021.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.224910 restraints weight = 9217.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.230658 restraints weight = 7876.421| |-----------------------------------------------------------------------------| r_work (final): 0.4828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4830 r_free = 0.4830 target_work(ls_wunit_k1) = 0.229 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4830 r_free = 0.4830 target_work(ls_wunit_k1) = 0.229 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5009 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 8624 Z= 0.186 Angle : 0.936 59.200 11649 Z= 0.534 Chirality : 0.044 0.444 1270 Planarity : 0.005 0.058 1514 Dihedral : 4.611 25.160 1158 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.14 % Favored : 89.77 % Rotamer: Outliers : 1.48 % Allowed : 19.34 % Favored : 79.18 % 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 aren not related in a simple way. whole: -1.43 (0.27), residues: 1028 helix: 0.34 (0.27), residues: 387 sheet: -2.18 (0.94), residues: 36 loop : -1.82 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 77 TYR 0.018 0.001 TYR A 748 PHE 0.044 0.002 PHE A 648 TRP 0.010 0.001 TRP B 146 HIS 0.012 0.001 HIS A 795 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 8624) covalent geometry : angle 0.93551 (11649) hydrogen bonds : bond 0.03603 ( 226) hydrogen bonds : angle 4.59616 ( 675) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2111.04 seconds wall clock time: 37 minutes 6.23 seconds (2226.23 seconds total)