Starting phenix.real_space_refine on Wed Feb 12 21:42:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cht_45601/02_2025/9cht_45601.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cht_45601/02_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_45601/02_2025/9cht_45601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cht_45601/02_2025/9cht_45601.map" model { file = "/net/cci-nas-00/data/ceres_data/9cht_45601/02_2025/9cht_45601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cht_45601/02_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-5592/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: 5.65, per 1000 atoms: 0.67 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: 2.11 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: 0.71 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: 2.09 Time building geometry restraints manager: 2.45 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: 1.190 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.130 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.940 ------------------------------------------------------------------------------- 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 : 0.879 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: 0.2077 time to fit residues: 29.8593 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 : 0.907 ------------------------------------------------------------------------------- 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 = 0.246711 restraints weight = 40951.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5005 r_free = 0.5005 target = 0.250904 restraints weight = 41074.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.5027 r_free = 0.5027 target = 0.253574 restraints weight = 12393.128| |-----------------------------------------------------------------------------| 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 : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 715 ASN cc_start: 0.5520 (t0) cc_final: 0.5203 (t0) REVERT: B 100 GLN cc_start: 0.7100 (mp-120) cc_final: 0.6615 (pp30) REVERT: C 1 MET cc_start: 0.5250 (pmm) cc_final: 0.4048 (pmm) outliers start: 5 outliers final: 4 residues processed: 97 average time/residue: 0.2019 time to fit residues: 27.8411 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 : 0.952 ------------------------------------------------------------------------------- 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: 0.0010 chunk 55 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 65 optimal weight: 0.0170 chunk 83 optimal weight: 0.0870 chunk 53 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.2100 ------------------------------------------------------------------------------- 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 = 0.5204 r_free = 0.5204 target = 0.273774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.226734 restraints weight = 36029.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.231922 restraints weight = 20453.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.235420 restraints weight = 12123.687| |-----------------------------------------------------------------------------| r_work (final): 0.4843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4843 r_free = 0.4843 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 = 0.4843 r_free = 0.4843 target_work(ls_wunit_k1) = 0.229 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4957 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8624 Z= 0.138 Angle : 0.545 7.320 11649 Z= 0.273 Chirality : 0.041 0.143 1270 Planarity : 0.004 0.057 1514 Dihedral : 4.236 17.972 1158 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.67 % Favored : 91.23 % Rotamer: Outliers : 1.27 % Allowed : 10.57 % Favored : 88.16 % 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: -1.38 (0.27), residues: 1028 helix: 0.58 (0.27), residues: 388 sheet: -1.87 (1.00), residues: 36 loop : -1.98 (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 738 PHE 0.020 0.001 PHE A 713 TYR 0.028 0.001 TYR A 379 ARG 0.002 0.000 ARG A 539 *********************** 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 111 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 VAL cc_start: 0.7971 (p) cc_final: 0.7699 (t) REVERT: A 534 ASP cc_start: 0.5858 (OUTLIER) cc_final: 0.5582 (p0) REVERT: A 576 GLN cc_start: 0.7315 (pp30) cc_final: 0.6996 (pp30) REVERT: A 715 ASN cc_start: 0.6398 (t0) cc_final: 0.5889 (t0) REVERT: B 100 GLN cc_start: 0.7357 (mp-120) cc_final: 0.6716 (pp30) REVERT: B 147 VAL cc_start: 0.2426 (OUTLIER) cc_final: 0.2172 (p) REVERT: C 1 MET cc_start: 0.4751 (pmm) cc_final: 0.3690 (pmm) outliers start: 9 outliers final: 4 residues processed: 107 average time/residue: 0.2088 time to fit residues: 31.4107 Evaluate side-chains 96 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 B residue 147 VAL 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: 1.9990 chunk 77 optimal weight: 30.0000 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 chunk 40 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- 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 382 ASN ** C 24 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 = 0.5114 r_free = 0.5114 target = 0.261777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.214241 restraints weight = 32163.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.218442 restraints weight = 22571.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.220568 restraints weight = 13770.725| |-----------------------------------------------------------------------------| r_work (final): 0.4748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4748 r_free = 0.4748 target_work(ls_wunit_k1) = 0.219 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4748 r_free = 0.4748 target_work(ls_wunit_k1) = 0.219 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5212 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8624 Z= 0.307 Angle : 0.666 7.552 11649 Z= 0.334 Chirality : 0.044 0.157 1270 Planarity : 0.005 0.057 1514 Dihedral : 4.793 24.991 1158 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.82 % Favored : 89.08 % Rotamer: Outliers : 1.59 % Allowed : 14.27 % Favored : 84.14 % 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: 0.26 (0.26), residues: 387 sheet: -2.06 (0.98), residues: 36 loop : -2.02 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 146 HIS 0.008 0.001 HIS C 78 PHE 0.020 0.002 PHE A 737 TYR 0.024 0.002 TYR A 748 ARG 0.005 0.000 ARG C 77 *********************** 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 98 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 LYS cc_start: 0.6576 (OUTLIER) cc_final: 0.5748 (mmtt) REVERT: A 715 ASN cc_start: 0.6338 (t0) cc_final: 0.5852 (t0) REVERT: B 100 GLN cc_start: 0.7439 (mp-120) cc_final: 0.6732 (pp30) REVERT: B 147 VAL cc_start: 0.3059 (OUTLIER) cc_final: 0.2817 (p) REVERT: C 1 MET cc_start: 0.5204 (pmm) cc_final: 0.4066 (pmm) outliers start: 12 outliers final: 6 residues processed: 94 average time/residue: 0.2015 time to fit residues: 27.9549 Evaluate side-chains 90 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 B residue 102 THR Chi-restraints excluded: chain B residue 147 VAL 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 18 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 C 24 HIS ** 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 = 0.5133 r_free = 0.5133 target = 0.263488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.220612 restraints weight = 33777.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.227583 restraints weight = 26643.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.229439 restraints weight = 11324.200| |-----------------------------------------------------------------------------| r_work (final): 0.4854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4854 r_free = 0.4854 target_work(ls_wunit_k1) = 0.231 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4854 r_free = 0.4854 target_work(ls_wunit_k1) = 0.231 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4951 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8624 Z= 0.180 Angle : 0.582 7.519 11649 Z= 0.293 Chirality : 0.042 0.141 1270 Planarity : 0.005 0.059 1514 Dihedral : 4.534 20.576 1158 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.55 % Favored : 90.35 % Rotamer: Outliers : 1.69 % Allowed : 15.64 % Favored : 82.66 % 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: -1.47 (0.27), residues: 1028 helix: 0.39 (0.27), residues: 387 sheet: -2.16 (0.96), residues: 36 loop : -1.92 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 146 HIS 0.003 0.001 HIS C 78 PHE 0.016 0.001 PHE A 737 TYR 0.021 0.001 TYR A 379 ARG 0.003 0.000 ARG A 418 *********************** 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 101 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 LEU cc_start: 0.4991 (tp) cc_final: 0.4785 (tp) REVERT: A 534 ASP cc_start: 0.5854 (OUTLIER) cc_final: 0.5331 (p0) REVERT: A 697 LYS cc_start: 0.5929 (OUTLIER) cc_final: 0.5338 (mmtt) REVERT: A 715 ASN cc_start: 0.5946 (t0) cc_final: 0.5473 (t0) REVERT: B 100 GLN cc_start: 0.7286 (mp-120) cc_final: 0.6734 (pp30) REVERT: B 147 VAL cc_start: 0.3217 (OUTLIER) cc_final: 0.2860 (p) REVERT: C 1 MET cc_start: 0.5340 (pmm) cc_final: 0.4209 (pmm) outliers start: 13 outliers final: 6 residues processed: 96 average time/residue: 0.1883 time to fit residues: 26.2068 Evaluate side-chains 92 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 147 VAL 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: 0.0570 chunk 66 optimal weight: 40.0000 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 0.0770 chunk 34 optimal weight: 0.0770 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 2 optimal weight: 8.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.3414 ------------------------------------------------------------------------------- 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 = 0.5171 r_free = 0.5171 target = 0.269843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.230174 restraints weight = 36631.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.236699 restraints weight = 28415.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.237189 restraints weight = 9937.781| |-----------------------------------------------------------------------------| r_work (final): 0.4899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4901 r_free = 0.4901 target_work(ls_wunit_k1) = 0.236 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4901 r_free = 0.4901 target_work(ls_wunit_k1) = 0.236 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4824 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8624 Z= 0.140 Angle : 0.562 9.834 11649 Z= 0.283 Chirality : 0.042 0.283 1270 Planarity : 0.004 0.059 1514 Dihedral : 4.290 18.754 1158 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.06 % Favored : 90.84 % Rotamer: Outliers : 1.37 % Allowed : 17.44 % 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: -1.34 (0.27), residues: 1028 helix: 0.54 (0.27), residues: 384 sheet: -2.14 (0.95), residues: 36 loop : -1.85 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 146 HIS 0.002 0.001 HIS B 214 PHE 0.031 0.001 PHE A 805 TYR 0.026 0.001 TYR A 494 ARG 0.002 0.000 ARG A 803 *********************** 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 102 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 VAL cc_start: 0.7986 (p) cc_final: 0.7656 (t) REVERT: A 697 LYS cc_start: 0.5834 (OUTLIER) cc_final: 0.5359 (mmtt) REVERT: A 715 ASN cc_start: 0.5897 (t0) cc_final: 0.5445 (t0) REVERT: B 100 GLN cc_start: 0.7233 (mp-120) cc_final: 0.6692 (pp30) REVERT: B 147 VAL cc_start: 0.2920 (OUTLIER) cc_final: 0.2576 (p) REVERT: C 1 MET cc_start: 0.5298 (pmm) cc_final: 0.4186 (pmm) outliers start: 10 outliers final: 5 residues processed: 98 average time/residue: 0.1870 time to fit residues: 26.5627 Evaluate side-chains 95 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 147 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN ** A 738 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.5125 r_free = 0.5125 target = 0.263670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.217044 restraints weight = 36092.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.223776 restraints weight = 26349.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.226787 restraints weight = 11815.843| |-----------------------------------------------------------------------------| r_work (final): 0.4806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4806 r_free = 0.4806 target_work(ls_wunit_k1) = 0.226 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4806 r_free = 0.4806 target_work(ls_wunit_k1) = 0.226 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5065 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8624 Z= 0.240 Angle : 0.634 8.748 11649 Z= 0.317 Chirality : 0.044 0.359 1270 Planarity : 0.005 0.058 1514 Dihedral : 4.626 23.555 1158 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.04 % Favored : 89.86 % Rotamer: Outliers : 1.59 % Allowed : 17.44 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.52 (0.27), residues: 1028 helix: 0.30 (0.27), residues: 387 sheet: -2.25 (0.93), residues: 36 loop : -1.90 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 146 HIS 0.005 0.001 HIS C 78 PHE 0.023 0.002 PHE A 737 TYR 0.020 0.001 TYR A 748 ARG 0.003 0.000 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: 12 poor density : 90 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 LYS cc_start: 0.6107 (OUTLIER) cc_final: 0.5401 (mmtt) REVERT: A 715 ASN cc_start: 0.6170 (t0) cc_final: 0.5679 (t0) REVERT: B 100 GLN cc_start: 0.7399 (mp-120) cc_final: 0.6738 (pp30) REVERT: B 147 VAL cc_start: 0.3075 (OUTLIER) cc_final: 0.2780 (p) REVERT: C 1 MET cc_start: 0.5511 (pmm) cc_final: 0.4303 (pmm) outliers start: 12 outliers final: 6 residues processed: 98 average time/residue: 0.1870 time to fit residues: 26.7653 Evaluate side-chains 95 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 B residue 102 THR Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 155 THR 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: 6.9990 chunk 3 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 23 optimal weight: 0.0170 chunk 15 optimal weight: 4.9990 chunk 91 optimal weight: 0.3980 chunk 69 optimal weight: 10.0000 chunk 84 optimal weight: 0.3980 chunk 42 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 59 optimal weight: 20.0000 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5186 r_free = 0.5186 target = 0.272069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.5003 r_free = 0.5003 target = 0.248736 restraints weight = 25882.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5021 r_free = 0.5021 target = 0.252206 restraints weight = 33028.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5029 r_free = 0.5029 target = 0.253281 restraints weight = 11943.756| |-----------------------------------------------------------------------------| r_work (final): 0.5003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5002 r_free = 0.5002 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 = 0.5002 r_free = 0.5002 target_work(ls_wunit_k1) = 0.249 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.5002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4569 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8624 Z= 0.146 Angle : 0.584 9.188 11649 Z= 0.293 Chirality : 0.042 0.302 1270 Planarity : 0.004 0.059 1514 Dihedral : 4.311 18.721 1158 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.28 % Favored : 91.62 % Rotamer: Outliers : 1.90 % Allowed : 17.97 % 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: -1.26 (0.27), residues: 1028 helix: 0.52 (0.27), residues: 393 sheet: -2.23 (0.91), residues: 36 loop : -1.76 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 146 HIS 0.002 0.001 HIS A 795 PHE 0.019 0.001 PHE A 648 TYR 0.021 0.001 TYR A 659 ARG 0.002 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 107 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 VAL cc_start: 0.7824 (p) cc_final: 0.7464 (t) REVERT: A 697 LYS cc_start: 0.5150 (OUTLIER) cc_final: 0.4910 (mmtt) REVERT: A 715 ASN cc_start: 0.5295 (t0) cc_final: 0.4974 (t0) REVERT: B 100 GLN cc_start: 0.7076 (mp-120) cc_final: 0.6578 (pp30) REVERT: B 147 VAL cc_start: 0.3287 (OUTLIER) cc_final: 0.2960 (p) outliers start: 15 outliers final: 9 residues processed: 103 average time/residue: 0.1880 time to fit residues: 27.9468 Evaluate side-chains 96 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 619 LEU Chi-restraints excluded: chain A residue 621 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 147 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 98 optimal weight: 0.0040 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- 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 = 0.5173 r_free = 0.5173 target = 0.270017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4997 r_free = 0.4997 target = 0.247925 restraints weight = 30925.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5014 r_free = 0.5014 target = 0.251437 restraints weight = 38011.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5037 r_free = 0.5037 target = 0.254334 restraints weight = 12734.463| |-----------------------------------------------------------------------------| r_work (final): 0.5010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.5010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.5010 r_free = 0.5010 target_work(ls_wunit_k1) = 0.250 | | 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) = 0.250 | | 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: 0.4563 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8624 Z= 0.166 Angle : 0.597 9.169 11649 Z= 0.300 Chirality : 0.043 0.336 1270 Planarity : 0.005 0.059 1514 Dihedral : 4.319 20.316 1158 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.06 % Favored : 90.84 % Rotamer: Outliers : 1.48 % Allowed : 18.50 % 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: -1.28 (0.27), residues: 1028 helix: 0.49 (0.27), residues: 392 sheet: -2.29 (0.90), residues: 36 loop : -1.75 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 146 HIS 0.011 0.001 HIS A 795 PHE 0.035 0.002 PHE A 805 TYR 0.029 0.001 TYR A 379 ARG 0.002 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: 11 poor density : 87 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 697 LYS cc_start: 0.5288 (OUTLIER) cc_final: 0.5018 (mmtt) REVERT: A 715 ASN cc_start: 0.5316 (t0) cc_final: 0.4986 (t0) REVERT: B 100 GLN cc_start: 0.7138 (mp-120) cc_final: 0.6595 (pp30) REVERT: B 147 VAL cc_start: 0.3307 (OUTLIER) cc_final: 0.2972 (p) outliers start: 11 outliers final: 7 residues processed: 94 average time/residue: 0.1920 time to fit residues: 26.3738 Evaluate side-chains 93 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 621 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 147 VAL 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: 10.0000 chunk 38 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 94 optimal weight: 0.0170 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 84 optimal weight: 0.0060 overall best weight: 0.5236 ------------------------------------------------------------------------------- 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 ** 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 = 0.271153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4986 r_free = 0.4986 target = 0.247458 restraints weight = 45604.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5008 r_free = 0.5008 target = 0.251989 restraints weight = 41731.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.5026 r_free = 0.5026 target = 0.254105 restraints weight = 12544.958| |-----------------------------------------------------------------------------| r_work (final): 0.4986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4987 r_free = 0.4987 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 = 0.4987 r_free = 0.4987 target_work(ls_wunit_k1) = 0.247 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4577 moved from start: 0.2236 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 : 0.581 9.816 11649 Z= 0.293 Chirality : 0.042 0.310 1270 Planarity : 0.004 0.058 1514 Dihedral : 4.225 19.096 1158 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.87 % Favored : 91.03 % Rotamer: Outliers : 1.48 % Allowed : 19.03 % Favored : 79.49 % 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: -1.22 (0.27), residues: 1028 helix: 0.56 (0.27), residues: 392 sheet: -2.29 (0.89), residues: 36 loop : -1.73 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 146 HIS 0.010 0.001 HIS A 795 PHE 0.035 0.001 PHE A 805 TYR 0.028 0.001 TYR A 379 ARG 0.002 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 95 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 697 LYS cc_start: 0.5582 (OUTLIER) cc_final: 0.5213 (mmtt) REVERT: A 715 ASN cc_start: 0.5402 (t0) cc_final: 0.5106 (t0) REVERT: A 720 TYR cc_start: 0.1329 (OUTLIER) cc_final: -0.0145 (t80) REVERT: B 100 GLN cc_start: 0.7099 (mp-120) cc_final: 0.6585 (pp30) REVERT: B 147 VAL cc_start: 0.3166 (OUTLIER) cc_final: 0.2839 (p) outliers start: 11 outliers final: 6 residues processed: 90 average time/residue: 0.2064 time to fit residues: 26.9226 Evaluate side-chains 90 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 720 TYR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 147 VAL 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: 3.9990 chunk 63 optimal weight: 0.5980 chunk 38 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 69 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 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 = 0.5138 r_free = 0.5138 target = 0.265265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.224805 restraints weight = 46322.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4853 r_free = 0.4853 target = 0.231643 restraints weight = 34236.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.233874 restraints weight = 12588.135| |-----------------------------------------------------------------------------| r_work (final): 0.4872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4872 r_free = 0.4872 target_work(ls_wunit_k1) = 0.233 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4872 r_free = 0.4872 target_work(ls_wunit_k1) = 0.233 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.4872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4901 moved from start: 0.2276 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= 0.190 Angle : 0.619 7.940 11649 Z= 0.311 Chirality : 0.043 0.276 1270 Planarity : 0.005 0.058 1514 Dihedral : 4.366 21.330 1158 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.45 % Favored : 90.45 % Rotamer: Outliers : 1.16 % Allowed : 19.45 % 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 (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: -1.31 (0.27), residues: 1028 helix: 0.45 (0.27), residues: 392 sheet: -2.30 (0.89), residues: 36 loop : -1.76 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 146 HIS 0.011 0.001 HIS A 795 PHE 0.035 0.002 PHE A 805 TYR 0.033 0.001 TYR A 379 ARG 0.002 0.000 ARG C 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3918.13 seconds wall clock time: 70 minutes 36.79 seconds (4236.79 seconds total)