Starting phenix.real_space_refine on Wed Mar 12 22:45:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cht_45601/03_2025/9cht_45601.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cht_45601/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cht_45601/03_2025/9cht_45601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cht_45601/03_2025/9cht_45601.map" model { file = "/net/cci-nas-00/data/ceres_data/9cht_45601/03_2025/9cht_45601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cht_45601/03_2025/9cht_45601.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.089 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.47, per 1000 atoms: 0.65 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: 2.39 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.94 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: 2.26 Time building geometry restraints manager: 2.81 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.470 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.420 ------------------------------------------------------------------------------- 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= 0.184 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 : 16.59 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.007 0.001 TRP B 146 HIS 0.015 0.001 HIS A 795 PHE 0.016 0.001 PHE A 737 TYR 0.012 0.001 TYR C 81 ARG 0.010 0.000 ARG A 500 *********************** 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 : 0.907 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: 0.1979 time to fit residues: 28.5260 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 : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 30.0000 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 0.3980 chunk 48 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5175 r_free = 0.5175 target = 0.269936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.246709 restraints weight = 40951.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5005 r_free = 0.5005 target = 0.250903 restraints weight = 41076.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.5027 r_free = 0.5027 target = 0.253574 restraints weight = 12393.937| |-----------------------------------------------------------------------------| r_work (final): 0.4990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4991 r_free = 0.4991 target_work(ls_wunit_k1) = 0.247 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4991 r_free = 0.4991 target_work(ls_wunit_k1) = 0.247 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4600 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8624 Z= 0.187 Angle : 0.612 7.414 11649 Z= 0.306 Chirality : 0.042 0.141 1270 Planarity : 0.005 0.061 1514 Dihedral : 4.546 20.542 1158 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.94 % Favored : 89.96 % Rotamer: Outliers : 0.85 % Allowed : 7.51 % Favored : 91.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.27), residues: 1028 helix: 0.44 (0.27), residues: 384 sheet: -2.04 (0.98), residues: 36 loop : -2.07 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 146 HIS 0.004 0.001 HIS C 78 PHE 0.022 0.002 PHE A 713 TYR 0.022 0.001 TYR A 379 ARG 0.004 0.000 ARG C 102 *********************** 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 100 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 715 ASN cc_start: 0.5521 (t0) cc_final: 0.5204 (t0) REVERT: B 100 GLN cc_start: 0.7100 (mp-120) cc_final: 0.6616 (pp30) REVERT: C 1 MET cc_start: 0.5249 (pmm) cc_final: 0.4047 (pmm) outliers start: 5 outliers final: 4 residues processed: 97 average time/residue: 0.1891 time to fit residues: 26.2918 Evaluate side-chains 91 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.0470 chunk 82 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 83 optimal weight: 0.2980 chunk 53 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 80 optimal weight: 0.1980 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 = 0.5191 r_free = 0.5191 target = 0.272450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4990 r_free = 0.4990 target = 0.247167 restraints weight = 36800.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5007 r_free = 0.5007 target = 0.251201 restraints weight = 42273.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5041 r_free = 0.5041 target = 0.255518 restraints weight = 14007.911| |-----------------------------------------------------------------------------| r_work (final): 0.5008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5010 r_free = 0.5010 target_work(ls_wunit_k1) = 0.249 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.5010 r_free = 0.5010 target_work(ls_wunit_k1) = 0.249 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.5010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4556 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8624 Z= 0.147 Angle : 0.553 7.301 11649 Z= 0.277 Chirality : 0.041 0.141 1270 Planarity : 0.004 0.058 1514 Dihedral : 4.321 19.211 1158 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.36 % Favored : 90.55 % Rotamer: Outliers : 1.27 % Allowed : 10.25 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.27), residues: 1028 helix: 0.54 (0.27), residues: 388 sheet: -1.90 (1.00), residues: 36 loop : -1.99 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 146 HIS 0.002 0.001 HIS A 655 PHE 0.020 0.001 PHE A 713 TYR 0.029 0.001 TYR A 379 ARG 0.002 0.000 ARG A 500 *********************** 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 106 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 VAL cc_start: 0.7868 (p) cc_final: 0.7516 (t) REVERT: A 534 ASP cc_start: 0.5831 (OUTLIER) cc_final: 0.5545 (p0) REVERT: A 715 ASN cc_start: 0.5462 (t0) cc_final: 0.5088 (t0) REVERT: B 100 GLN cc_start: 0.7017 (mp-120) cc_final: 0.6600 (pp30) REVERT: C 1 MET cc_start: 0.5439 (pmm) cc_final: 0.4333 (pmm) outliers start: 9 outliers final: 4 residues processed: 102 average time/residue: 0.2241 time to fit residues: 33.1327 Evaluate side-chains 93 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 1.393 ------------------------------------------------------------------------------- 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 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 44 optimal weight: 0.4980 chunk 77 optimal weight: 30.0000 chunk 45 optimal weight: 0.6980 chunk 87 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 70 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.5190 r_free = 0.5190 target = 0.272580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4961 r_free = 0.4961 target = 0.242637 restraints weight = 32874.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4939 r_free = 0.4939 target = 0.242238 restraints weight = 30491.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.239562 restraints weight = 15316.744| |-----------------------------------------------------------------------------| r_work (final): 0.4861 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4859 r_free = 0.4859 target_work(ls_wunit_k1) = 0.232 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4859 r_free = 0.4859 target_work(ls_wunit_k1) = 0.232 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4933 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8624 Z= 0.149 Angle : 0.546 7.261 11649 Z= 0.274 Chirality : 0.041 0.144 1270 Planarity : 0.004 0.056 1514 Dihedral : 4.251 19.377 1158 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.65 % Favored : 90.25 % Rotamer: Outliers : 1.27 % Allowed : 13.74 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.27), residues: 1028 helix: 0.63 (0.27), residues: 385 sheet: -1.81 (1.00), residues: 36 loop : -1.88 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 146 HIS 0.002 0.001 HIS A 655 PHE 0.013 0.001 PHE A 730 TYR 0.022 0.001 TYR A 379 ARG 0.002 0.000 ARG A 337 *********************** 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 105 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 VAL cc_start: 0.7964 (p) cc_final: 0.7652 (t) REVERT: A 697 LYS cc_start: 0.6219 (OUTLIER) cc_final: 0.5579 (mmtt) REVERT: A 715 ASN cc_start: 0.6054 (t0) cc_final: 0.5621 (t0) REVERT: B 100 GLN cc_start: 0.7366 (mp-120) cc_final: 0.6740 (pp30) REVERT: C 1 MET cc_start: 0.5125 (pmm) cc_final: 0.4074 (pmm) outliers start: 9 outliers final: 6 residues processed: 100 average time/residue: 0.2526 time to fit residues: 39.7227 Evaluate side-chains 93 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 741 THR Chi-restraints excluded: chain B residue 102 THR 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 18 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN C 24 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 = 0.5108 r_free = 0.5108 target = 0.261050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.217334 restraints weight = 33796.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.222971 restraints weight = 28646.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.224992 restraints weight = 12901.792| |-----------------------------------------------------------------------------| r_work (final): 0.4800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4800 r_free = 0.4800 target_work(ls_wunit_k1) = 0.224 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4800 r_free = 0.4800 target_work(ls_wunit_k1) = 0.224 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5108 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8624 Z= 0.310 Angle : 0.672 7.630 11649 Z= 0.339 Chirality : 0.044 0.169 1270 Planarity : 0.005 0.056 1514 Dihedral : 4.907 25.577 1158 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.21 % Favored : 88.69 % Rotamer: Outliers : 1.80 % Allowed : 15.43 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.26), residues: 1028 helix: 0.13 (0.26), residues: 387 sheet: -2.03 (0.98), residues: 36 loop : -2.03 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 146 HIS 0.006 0.001 HIS C 78 PHE 0.024 0.002 PHE A 737 TYR 0.031 0.002 TYR A 283 ARG 0.005 0.000 ARG C 77 *********************** 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 107 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 LYS cc_start: 0.5968 (OUTLIER) cc_final: 0.5318 (mmtt) REVERT: A 715 ASN cc_start: 0.6035 (t0) cc_final: 0.5603 (t0) REVERT: B 100 GLN cc_start: 0.7352 (mp-120) cc_final: 0.6710 (pp30) REVERT: C 1 MET cc_start: 0.5455 (pmm) cc_final: 0.4299 (pmm) outliers start: 14 outliers final: 6 residues processed: 103 average time/residue: 0.1831 time to fit residues: 27.7571 Evaluate side-chains 96 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 537 LEU 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 C residue 31 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 5 optimal weight: 9.9990 chunk 100 optimal weight: 0.2980 chunk 66 optimal weight: 40.0000 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 0.0370 chunk 34 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 = 0.5158 r_free = 0.5158 target = 0.268113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.220287 restraints weight = 37264.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.225640 restraints weight = 22798.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.229420 restraints weight = 11809.375| |-----------------------------------------------------------------------------| r_work (final): 0.4803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4803 r_free = 0.4803 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4803 r_free = 0.4803 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5039 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8624 Z= 0.152 Angle : 0.567 8.064 11649 Z= 0.288 Chirality : 0.042 0.160 1270 Planarity : 0.004 0.058 1514 Dihedral : 4.403 18.823 1158 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.77 % Favored : 91.13 % Rotamer: Outliers : 1.69 % Allowed : 16.28 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.27), residues: 1028 helix: 0.39 (0.27), residues: 387 sheet: -2.11 (0.95), residues: 36 loop : -1.88 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 146 HIS 0.002 0.001 HIS A 738 PHE 0.016 0.001 PHE A 730 TYR 0.020 0.001 TYR A 283 ARG 0.003 0.000 ARG A 418 *********************** 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 106 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 ASN cc_start: 0.7633 (OUTLIER) cc_final: 0.7384 (t0) REVERT: A 509 VAL cc_start: 0.8033 (p) cc_final: 0.7754 (t) REVERT: A 534 ASP cc_start: 0.5888 (m-30) cc_final: 0.5463 (p0) REVERT: A 697 LYS cc_start: 0.6637 (OUTLIER) cc_final: 0.5798 (mmtt) REVERT: A 715 ASN cc_start: 0.6352 (t0) cc_final: 0.5870 (t0) REVERT: B 100 GLN cc_start: 0.7347 (mp-120) cc_final: 0.6727 (pp30) REVERT: B 252 LEU cc_start: 0.5027 (OUTLIER) cc_final: 0.3865 (mm) REVERT: C 1 MET cc_start: 0.5012 (pmm) cc_final: 0.3893 (pmm) outliers start: 13 outliers final: 7 residues processed: 101 average time/residue: 0.1901 time to fit residues: 27.6525 Evaluate side-chains 101 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 537 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 ASN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 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 = 0.5081 r_free = 0.5081 target = 0.257841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.212518 restraints weight = 35893.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.217364 restraints weight = 30567.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.222131 restraints weight = 12245.060| |-----------------------------------------------------------------------------| r_work (final): 0.4763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4763 r_free = 0.4763 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4763 r_free = 0.4763 target_work(ls_wunit_k1) = 0.221 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5216 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 8624 Z= 0.386 Angle : 0.774 9.629 11649 Z= 0.390 Chirality : 0.048 0.270 1270 Planarity : 0.006 0.058 1514 Dihedral : 5.339 26.919 1158 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.70 % Favored : 88.11 % Rotamer: Outliers : 1.69 % Allowed : 17.12 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.26), residues: 1028 helix: -0.24 (0.26), residues: 388 sheet: -2.20 (0.92), residues: 36 loop : -2.15 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 146 HIS 0.008 0.001 HIS C 78 PHE 0.030 0.003 PHE A 805 TYR 0.033 0.002 TYR A 748 ARG 0.008 0.001 ARG A 418 *********************** 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 102 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 ILE cc_start: 0.5652 (OUTLIER) cc_final: 0.5383 (mm) REVERT: A 403 GLU cc_start: 0.3124 (pp20) cc_final: 0.2706 (pp20) REVERT: A 697 LYS cc_start: 0.6023 (OUTLIER) cc_final: 0.5288 (mmtt) REVERT: A 715 ASN cc_start: 0.6005 (t0) cc_final: 0.5529 (t0) REVERT: B 100 GLN cc_start: 0.7458 (mp-120) cc_final: 0.6766 (pp30) outliers start: 13 outliers final: 6 residues processed: 100 average time/residue: 0.1936 time to fit residues: 28.5303 Evaluate side-chains 91 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 537 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 84 optimal weight: 30.0000 chunk 42 optimal weight: 0.2980 chunk 19 optimal weight: 0.8980 chunk 59 optimal weight: 20.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5137 r_free = 0.5137 target = 0.265001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.216247 restraints weight = 25657.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.222551 restraints weight = 16087.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.224626 restraints weight = 8879.758| |-----------------------------------------------------------------------------| r_work (final): 0.4784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4784 r_free = 0.4784 target_work(ls_wunit_k1) = 0.223 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4784 r_free = 0.4784 target_work(ls_wunit_k1) = 0.223 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5110 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8624 Z= 0.167 Angle : 0.619 8.045 11649 Z= 0.312 Chirality : 0.043 0.215 1270 Planarity : 0.005 0.060 1514 Dihedral : 4.735 20.496 1158 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.67 % Favored : 91.23 % Rotamer: Outliers : 1.48 % Allowed : 18.39 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.27), residues: 1028 helix: 0.16 (0.27), residues: 392 sheet: -2.33 (0.89), residues: 36 loop : -1.93 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 146 HIS 0.004 0.001 HIS C 78 PHE 0.034 0.002 PHE A 805 TYR 0.028 0.001 TYR A 494 ARG 0.005 0.000 ARG A 418 *********************** 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 100 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 306 LEU cc_start: 0.4705 (tp) cc_final: 0.4394 (tp) REVERT: A 403 GLU cc_start: 0.2966 (pp20) cc_final: 0.2485 (pp20) REVERT: A 697 LYS cc_start: 0.6292 (OUTLIER) cc_final: 0.5495 (mmtt) REVERT: A 715 ASN cc_start: 0.6439 (t0) cc_final: 0.5973 (t0) REVERT: B 100 GLN cc_start: 0.7433 (mp-120) cc_final: 0.6750 (pp30) outliers start: 11 outliers final: 6 residues processed: 98 average time/residue: 0.1817 time to fit residues: 26.2345 Evaluate side-chains 96 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 577 LEU Chi-restraints excluded: chain A residue 619 LEU 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 C residue 31 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 98 optimal weight: 0.2980 chunk 57 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 HIS ** A 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5161 r_free = 0.5161 target = 0.268796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.246635 restraints weight = 30839.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.250444 restraints weight = 36451.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5025 r_free = 0.5025 target = 0.253107 restraints weight = 11439.621| |-----------------------------------------------------------------------------| r_work (final): 0.4992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4993 r_free = 0.4993 target_work(ls_wunit_k1) = 0.247 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4993 r_free = 0.4993 target_work(ls_wunit_k1) = 0.247 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4618 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8624 Z= 0.172 Angle : 0.612 7.490 11649 Z= 0.307 Chirality : 0.043 0.182 1270 Planarity : 0.005 0.061 1514 Dihedral : 4.588 21.449 1158 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.75 % Favored : 90.16 % Rotamer: Outliers : 1.16 % Allowed : 18.71 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.27), residues: 1028 helix: 0.23 (0.27), residues: 395 sheet: -3.32 (0.73), residues: 46 loop : -1.88 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 146 HIS 0.004 0.001 HIS C 78 PHE 0.037 0.002 PHE A 805 TYR 0.026 0.001 TYR A 494 ARG 0.004 0.000 ARG A 418 *********************** 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 98 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 488 THR cc_start: 0.5112 (OUTLIER) cc_final: 0.4790 (m) REVERT: A 697 LYS cc_start: 0.5288 (OUTLIER) cc_final: 0.4893 (mmtt) REVERT: A 715 ASN cc_start: 0.5684 (t0) cc_final: 0.5319 (t0) REVERT: B 100 GLN cc_start: 0.7154 (mp-120) cc_final: 0.6675 (pp30) outliers start: 8 outliers final: 4 residues processed: 95 average time/residue: 0.1906 time to fit residues: 26.5203 Evaluate side-chains 89 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 527 VAL 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 C residue 31 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 45 optimal weight: 0.2980 chunk 23 optimal weight: 0.0060 chunk 70 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 94 optimal weight: 0.0670 chunk 61 optimal weight: 20.0000 chunk 6 optimal weight: 0.0470 chunk 9 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 overall best weight: 0.6834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.5165 r_free = 0.5165 target = 0.269003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.244704 restraints weight = 45619.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4986 r_free = 0.4986 target = 0.249535 restraints weight = 41429.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.5011 r_free = 0.5011 target = 0.252642 restraints weight = 12424.263| |-----------------------------------------------------------------------------| r_work (final): 0.4967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4967 r_free = 0.4967 target_work(ls_wunit_k1) = 0.244 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4967 r_free = 0.4967 target_work(ls_wunit_k1) = 0.244 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4658 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8624 Z= 0.170 Angle : 0.632 8.435 11649 Z= 0.318 Chirality : 0.043 0.175 1270 Planarity : 0.005 0.060 1514 Dihedral : 4.527 20.283 1158 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.26 % Favored : 90.64 % Rotamer: Outliers : 1.37 % Allowed : 18.60 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.27), residues: 1028 helix: 0.29 (0.27), residues: 392 sheet: -3.33 (0.74), residues: 46 loop : -1.85 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 146 HIS 0.012 0.001 HIS A 795 PHE 0.038 0.001 PHE A 805 TYR 0.027 0.001 TYR A 494 ARG 0.004 0.000 ARG A 418 ********************** 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 96 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 488 THR cc_start: 0.5153 (OUTLIER) cc_final: 0.4809 (m) REVERT: A 697 LYS cc_start: 0.5620 (OUTLIER) cc_final: 0.5165 (mmtt) REVERT: A 715 ASN cc_start: 0.5689 (t0) cc_final: 0.5338 (t0) REVERT: A 720 TYR cc_start: 0.1183 (OUTLIER) cc_final: -0.0236 (t80) REVERT: B 100 GLN cc_start: 0.7134 (mp-120) cc_final: 0.6651 (pp30) outliers start: 10 outliers final: 4 residues processed: 92 average time/residue: 0.1905 time to fit residues: 25.5807 Evaluate side-chains 90 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 697 LYS Chi-restraints excluded: chain A residue 720 TYR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 155 THR 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 54 optimal weight: 0.9980 chunk 63 optimal weight: 0.1980 chunk 38 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 95 optimal weight: 0.0000 overall best weight: 0.6386 ------------------------------------------------------------------------------- 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** A 738 HIS ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5142 r_free = 0.5142 target = 0.265986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.219625 restraints weight = 46389.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.225139 restraints weight = 30695.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.229917 restraints weight = 13927.759| |-----------------------------------------------------------------------------| r_work (final): 0.4827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4827 r_free = 0.4827 target_work(ls_wunit_k1) = 0.228 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4827 r_free = 0.4827 target_work(ls_wunit_k1) = 0.228 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4970 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8624 Z= 0.164 Angle : 0.622 9.882 11649 Z= 0.311 Chirality : 0.042 0.160 1270 Planarity : 0.005 0.060 1514 Dihedral : 4.470 20.119 1158 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.65 % Favored : 90.25 % Rotamer: Outliers : 1.16 % Allowed : 18.71 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.27), residues: 1028 helix: 0.40 (0.27), residues: 391 sheet: -2.39 (0.89), residues: 36 loop : -1.84 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 146 HIS 0.010 0.001 HIS A 795 PHE 0.038 0.001 PHE A 805 TYR 0.032 0.001 TYR A 379 ARG 0.004 0.000 ARG A 418 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4235.53 seconds wall clock time: 75 minutes 25.22 seconds (4525.22 seconds total)