Starting phenix.real_space_refine on Sat Jul 4 11:53:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8eks_28212/07_2026/8eks_28212.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eks_28212/07_2026/8eks_28212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eks_28212/07_2026/8eks_28212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eks_28212/07_2026/8eks_28212.map" model { file = "/net/cci-nas-00/data/ceres_data/8eks_28212/07_2026/8eks_28212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eks_28212/07_2026/8eks_28212.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8eks_28212/07_2026/8eks_28212.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8eks_28212/07_2026/8eks_28212.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.065 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 112 5.16 5 C 13364 2.51 5 N 3440 2.21 5 O 3564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20484 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 5086 Classifications: {'peptide': 626} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 601} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PEX': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 5.18, per 1000 atoms: 0.25 Number of scatterers: 20484 At special positions: 0 Unit cell: (138.03, 138.03, 110.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 112 16.00 P 4 15.00 O 3564 8.00 N 3440 7.00 C 13364 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: 1.70 Conformation dependent library (CDL) restraints added in 806.4 milliseconds 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4728 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 65.5% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 88 through 93 removed outlier: 3.682A pdb=" N GLU A 91 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 93 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.644A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.507A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 257 removed outlier: 3.591A pdb=" N VAL A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.602A pdb=" N ARG A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.567A pdb=" N GLU A 289 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 286 through 290' Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.902A pdb=" N VAL A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 389 Processing helix chain 'A' and resid 389 through 413 Processing helix chain 'A' and resid 429 through 459 Processing helix chain 'A' and resid 459 through 466 removed outlier: 3.797A pdb=" N ILE A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 492 removed outlier: 4.048A pdb=" N ILE A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 511 removed outlier: 4.043A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 518 removed outlier: 3.799A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 524 Processing helix chain 'A' and resid 530 through 562 removed outlier: 3.779A pdb=" N LEU A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 605 Processing helix chain 'A' and resid 618 through 651 Processing helix chain 'A' and resid 655 through 674 removed outlier: 3.837A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 674 " --> pdb=" O GLU A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 719 removed outlier: 3.642A pdb=" N LYS A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 88 through 93 removed outlier: 3.682A pdb=" N GLU B 91 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 93 " --> pdb=" O GLU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.644A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 186 removed outlier: 3.507A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 257 removed outlier: 3.591A pdb=" N VAL B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.602A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.567A pdb=" N GLU B 289 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 286 through 290' Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.902A pdb=" N VAL B 373 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 389 Processing helix chain 'B' and resid 389 through 413 Processing helix chain 'B' and resid 429 through 459 Processing helix chain 'B' and resid 459 through 466 removed outlier: 3.797A pdb=" N ILE B 463 " --> pdb=" O ARG B 459 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 492 removed outlier: 4.048A pdb=" N ILE B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 511 removed outlier: 4.043A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 518 removed outlier: 3.799A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B 518 " --> pdb=" O TYR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 524 Processing helix chain 'B' and resid 530 through 562 removed outlier: 3.779A pdb=" N LEU B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 554 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 605 Processing helix chain 'B' and resid 618 through 651 Processing helix chain 'B' and resid 655 through 674 removed outlier: 3.837A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY B 674 " --> pdb=" O GLU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 719 removed outlier: 3.642A pdb=" N LYS B 717 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 718 " --> pdb=" O ALA B 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 88 through 93 removed outlier: 3.682A pdb=" N GLU C 91 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR C 93 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 146 Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.644A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 186 removed outlier: 3.507A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 257 removed outlier: 3.591A pdb=" N VAL C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.602A pdb=" N ARG C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 removed outlier: 3.567A pdb=" N GLU C 289 " --> pdb=" O GLN C 286 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE C 290 " --> pdb=" O LEU C 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 286 through 290' Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.902A pdb=" N VAL C 373 " --> pdb=" O ARG C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 389 Processing helix chain 'C' and resid 389 through 413 Processing helix chain 'C' and resid 429 through 459 Processing helix chain 'C' and resid 459 through 466 removed outlier: 3.797A pdb=" N ILE C 463 " --> pdb=" O ARG C 459 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP C 464 " --> pdb=" O ARG C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 492 removed outlier: 4.048A pdb=" N ILE C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 511 removed outlier: 4.043A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 518 removed outlier: 3.799A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 518 " --> pdb=" O TYR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 524 Processing helix chain 'C' and resid 530 through 562 removed outlier: 3.779A pdb=" N LEU C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA C 554 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 605 Processing helix chain 'C' and resid 618 through 651 Processing helix chain 'C' and resid 655 through 674 removed outlier: 3.837A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY C 674 " --> pdb=" O GLU C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 719 removed outlier: 3.642A pdb=" N LYS C 717 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 88 through 93 removed outlier: 3.682A pdb=" N GLU D 91 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 93 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 146 Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.644A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 186 removed outlier: 3.507A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 248 through 257 removed outlier: 3.591A pdb=" N VAL D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.602A pdb=" N ARG D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.567A pdb=" N GLU D 289 " --> pdb=" O GLN D 286 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE D 290 " --> pdb=" O LEU D 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 286 through 290' Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.902A pdb=" N VAL D 373 " --> pdb=" O ARG D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 389 through 413 Processing helix chain 'D' and resid 429 through 459 Processing helix chain 'D' and resid 459 through 466 removed outlier: 3.797A pdb=" N ILE D 463 " --> pdb=" O ARG D 459 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP D 464 " --> pdb=" O ARG D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 492 removed outlier: 4.048A pdb=" N ILE D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 511 removed outlier: 4.043A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 518 removed outlier: 3.799A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY D 518 " --> pdb=" O TYR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 524 Processing helix chain 'D' and resid 530 through 562 removed outlier: 3.779A pdb=" N LEU D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL D 543 " --> pdb=" O ARG D 539 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA D 554 " --> pdb=" O GLY D 550 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 605 Processing helix chain 'D' and resid 618 through 651 Processing helix chain 'D' and resid 655 through 674 removed outlier: 3.837A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY D 674 " --> pdb=" O GLU D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 719 removed outlier: 3.642A pdb=" N LYS D 717 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR D 718 " --> pdb=" O ALA D 714 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335 removed outlier: 6.978A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG A 702 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS A 690 " --> pdb=" O ARG A 702 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS A 704 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU A 688 " --> pdb=" O CYS A 704 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 335 removed outlier: 6.978A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG B 702 " --> pdb=" O LYS B 690 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS B 690 " --> pdb=" O ARG B 702 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS B 704 " --> pdb=" O LEU B 688 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU B 688 " --> pdb=" O CYS B 704 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.978A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG C 702 " --> pdb=" O LYS C 690 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS C 690 " --> pdb=" O ARG C 702 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS C 704 " --> pdb=" O LEU C 688 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU C 688 " --> pdb=" O CYS C 704 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 335 removed outlier: 6.978A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG D 702 " --> pdb=" O LYS D 690 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS D 690 " --> pdb=" O ARG D 702 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS D 704 " --> pdb=" O LEU D 688 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU D 688 " --> pdb=" O CYS D 704 " (cutoff:3.500A) 1116 hydrogen bonds defined for protein. 3264 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: 3.27 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3192 1.31 - 1.44: 5876 1.44 - 1.56: 11736 1.56 - 1.69: 8 1.69 - 1.82: 172 Bond restraints: 20984 Sorted by residual: bond pdb=" C4 PEX A 801 " pdb=" O4 PEX A 801 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C4 PEX B 801 " pdb=" O4 PEX B 801 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C4 PEX D 801 " pdb=" O4 PEX D 801 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C4 PEX C 801 " pdb=" O4 PEX C 801 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C14 PEX D 801 " pdb=" O6 PEX D 801 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.17e+01 ... (remaining 20979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 28236 3.25 - 6.50: 168 6.50 - 9.75: 20 9.75 - 12.99: 0 12.99 - 16.24: 4 Bond angle restraints: 28428 Sorted by residual: angle pdb=" O3 PEX C 801 " pdb=" P1 PEX C 801 " pdb=" O8 PEX C 801 " ideal model delta sigma weight residual 93.74 109.98 -16.24 3.00e+00 1.11e-01 2.93e+01 angle pdb=" O3 PEX B 801 " pdb=" P1 PEX B 801 " pdb=" O8 PEX B 801 " ideal model delta sigma weight residual 93.74 109.98 -16.24 3.00e+00 1.11e-01 2.93e+01 angle pdb=" O3 PEX D 801 " pdb=" P1 PEX D 801 " pdb=" O8 PEX D 801 " ideal model delta sigma weight residual 93.74 109.98 -16.24 3.00e+00 1.11e-01 2.93e+01 angle pdb=" O3 PEX A 801 " pdb=" P1 PEX A 801 " pdb=" O8 PEX A 801 " ideal model delta sigma weight residual 93.74 109.98 -16.24 3.00e+00 1.11e-01 2.93e+01 angle pdb=" N VAL B 190 " pdb=" CA VAL B 190 " pdb=" C VAL B 190 " ideal model delta sigma weight residual 113.07 107.22 5.85 1.37e+00 5.33e-01 1.82e+01 ... (remaining 28423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 11328 17.99 - 35.98: 904 35.98 - 53.97: 116 53.97 - 71.96: 20 71.96 - 89.95: 20 Dihedral angle restraints: 12388 sinusoidal: 5080 harmonic: 7308 Sorted by residual: dihedral pdb=" CA ASP A 130 " pdb=" CB ASP A 130 " pdb=" CG ASP A 130 " pdb=" OD1 ASP A 130 " ideal model delta sinusoidal sigma weight residual -30.00 -86.67 56.67 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASP D 130 " pdb=" CB ASP D 130 " pdb=" CG ASP D 130 " pdb=" OD1 ASP D 130 " ideal model delta sinusoidal sigma weight residual -30.00 -86.67 56.67 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASP C 130 " pdb=" CB ASP C 130 " pdb=" CG ASP C 130 " pdb=" OD1 ASP C 130 " ideal model delta sinusoidal sigma weight residual -30.00 -86.67 56.67 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 12385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2668 0.049 - 0.098: 456 0.098 - 0.147: 40 0.147 - 0.196: 4 0.196 - 0.245: 4 Chirality restraints: 3172 Sorted by residual: chirality pdb=" CA ARG D 490 " pdb=" N ARG D 490 " pdb=" C ARG D 490 " pdb=" CB ARG D 490 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ARG B 490 " pdb=" N ARG B 490 " pdb=" C ARG B 490 " pdb=" CB ARG B 490 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA ARG C 490 " pdb=" N ARG C 490 " pdb=" C ARG C 490 " pdb=" CB ARG C 490 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 3169 not shown) Planarity restraints: 3536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 414 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO D 415 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 415 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 415 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 414 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO C 415 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 415 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 415 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 414 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO A 415 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " -0.021 5.00e-02 4.00e+02 ... (remaining 3533 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2508 2.75 - 3.29: 19704 3.29 - 3.83: 33144 3.83 - 4.36: 41072 4.36 - 4.90: 70664 Nonbonded interactions: 167092 Sorted by model distance: nonbonded pdb=" OG SER C 592 " pdb=" OD2 ASP C 595 " model vdw 2.215 3.040 nonbonded pdb=" OG SER A 592 " pdb=" OD2 ASP A 595 " model vdw 2.215 3.040 nonbonded pdb=" OG SER D 592 " pdb=" OD2 ASP D 595 " model vdw 2.215 3.040 nonbonded pdb=" OG SER B 592 " pdb=" OD2 ASP B 595 " model vdw 2.215 3.040 nonbonded pdb=" O GLY D 131 " pdb=" OG SER D 176 " model vdw 2.293 3.040 ... (remaining 167087 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.840 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 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 0.072 20984 Z= 0.146 Angle : 0.617 16.243 28428 Z= 0.309 Chirality : 0.035 0.245 3172 Planarity : 0.004 0.039 3536 Dihedral : 13.011 89.955 7660 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.13), residues: 2464 helix: -1.74 (0.09), residues: 1436 sheet: -0.79 (0.48), residues: 120 loop : -0.90 (0.18), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 687 TYR 0.005 0.001 TYR C 514 PHE 0.010 0.001 PHE D 405 TRP 0.011 0.001 TRP D 101 HIS 0.004 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (20984) covalent geometry : angle 0.61745 / 0.31 (28428) hydrogen bonds : bond 0.26234 / 17.86 ( 1116) hydrogen bonds : angle 7.21755 / 5.12 ( 3264) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.770 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1336 time to fit residues: 40.7652 Evaluate side-chains 156 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 247 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 4.9990 overall best weight: 2.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.139746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.114764 restraints weight = 24224.632| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.28 r_work: 0.2950 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20984 Z= 0.217 Angle : 0.564 5.921 28428 Z= 0.284 Chirality : 0.039 0.163 3172 Planarity : 0.005 0.036 3536 Dihedral : 5.385 45.855 2820 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.72 % Allowed : 6.34 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.16), residues: 2464 helix: 0.68 (0.13), residues: 1512 sheet: 0.03 (0.59), residues: 84 loop : -0.85 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 687 TYR 0.013 0.002 TYR A 271 PHE 0.015 0.002 PHE A 472 TRP 0.015 0.002 TRP C 509 HIS 0.007 0.002 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.22 (20984) covalent geometry : angle 0.56409 / 0.28 (28428) hydrogen bonds : bond 0.04894 / 3.29 ( 1116) hydrogen bonds : angle 4.27066 / 2.97 ( 3264) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.768 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 184 average time/residue: 0.1390 time to fit residues: 40.6371 Evaluate side-chains 168 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 6.9990 chunk 236 optimal weight: 2.9990 chunk 127 optimal weight: 0.0020 chunk 77 optimal weight: 0.5980 chunk 183 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 211 optimal weight: 0.8980 chunk 232 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 164 optimal weight: 0.9980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.142812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114076 restraints weight = 23948.628| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.58 r_work: 0.2943 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20984 Z= 0.096 Angle : 0.429 5.221 28428 Z= 0.216 Chirality : 0.035 0.129 3172 Planarity : 0.004 0.037 3536 Dihedral : 4.949 49.687 2820 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.09 % Allowed : 7.61 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.17), residues: 2464 helix: 1.71 (0.14), residues: 1492 sheet: 0.38 (0.60), residues: 84 loop : -0.71 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 687 TYR 0.009 0.001 TYR A 271 PHE 0.007 0.001 PHE A 705 TRP 0.009 0.001 TRP C 509 HIS 0.003 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (20984) covalent geometry : angle 0.42944 / 0.22 (28428) hydrogen bonds : bond 0.03689 / 2.49 ( 1116) hydrogen bonds : angle 3.82830 / 2.67 ( 3264) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.752 Fit side-chains REVERT: A 433 MET cc_start: 0.7319 (tpt) cc_final: 0.7072 (tpt) REVERT: A 538 LEU cc_start: 0.8225 (mm) cc_final: 0.7829 (mm) REVERT: B 433 MET cc_start: 0.7316 (tpt) cc_final: 0.7069 (tpt) REVERT: B 538 LEU cc_start: 0.8223 (mm) cc_final: 0.7827 (mm) REVERT: C 433 MET cc_start: 0.7309 (tpt) cc_final: 0.7063 (tpt) REVERT: C 538 LEU cc_start: 0.8226 (mm) cc_final: 0.7829 (mm) REVERT: D 433 MET cc_start: 0.7325 (tpt) cc_final: 0.7079 (tpt) REVERT: D 538 LEU cc_start: 0.8226 (mm) cc_final: 0.7829 (mm) outliers start: 24 outliers final: 16 residues processed: 200 average time/residue: 0.1443 time to fit residues: 45.0584 Evaluate side-chains 176 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 233 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 222 optimal weight: 8.9990 chunk 168 optimal weight: 3.9990 chunk 203 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.125635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.092955 restraints weight = 25685.313| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.88 r_work: 0.2910 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20984 Z= 0.156 Angle : 0.470 5.278 28428 Z= 0.236 Chirality : 0.037 0.115 3172 Planarity : 0.004 0.038 3536 Dihedral : 5.214 56.972 2820 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.81 % Allowed : 7.43 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.17), residues: 2464 helix: 1.89 (0.14), residues: 1492 sheet: 0.33 (0.60), residues: 84 loop : -0.66 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 684 TYR 0.011 0.001 TYR A 271 PHE 0.011 0.001 PHE B 319 TRP 0.010 0.001 TRP C 677 HIS 0.006 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (20984) covalent geometry : angle 0.47000 / 0.24 (28428) hydrogen bonds : bond 0.03740 / 2.51 ( 1116) hydrogen bonds : angle 3.76099 / 2.62 ( 3264) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 160 time to evaluate : 1.070 Fit side-chains REVERT: A 433 MET cc_start: 0.7316 (tpt) cc_final: 0.7085 (tpt) REVERT: A 538 LEU cc_start: 0.8259 (mm) cc_final: 0.8059 (mt) REVERT: B 433 MET cc_start: 0.7313 (tpt) cc_final: 0.7082 (tpt) REVERT: B 538 LEU cc_start: 0.8256 (mm) cc_final: 0.8055 (mt) REVERT: C 433 MET cc_start: 0.7312 (tpt) cc_final: 0.7082 (tpt) REVERT: D 433 MET cc_start: 0.7305 (tpt) cc_final: 0.7075 (tpt) outliers start: 40 outliers final: 24 residues processed: 192 average time/residue: 0.1530 time to fit residues: 45.5783 Evaluate side-chains 176 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 78 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 98 optimal weight: 0.0020 chunk 80 optimal weight: 4.9990 chunk 229 optimal weight: 0.6980 chunk 123 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.128192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.095625 restraints weight = 25179.125| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.87 r_work: 0.2955 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20984 Z= 0.092 Angle : 0.411 5.161 28428 Z= 0.208 Chirality : 0.034 0.120 3172 Planarity : 0.003 0.039 3536 Dihedral : 4.740 44.974 2820 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.45 % Allowed : 7.88 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.17), residues: 2464 helix: 2.17 (0.14), residues: 1500 sheet: 0.59 (0.61), residues: 84 loop : -0.62 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 687 TYR 0.008 0.001 TYR A 271 PHE 0.006 0.001 PHE C 705 TRP 0.008 0.001 TRP C 677 HIS 0.003 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.09 (20984) covalent geometry : angle 0.41113 / 0.21 (28428) hydrogen bonds : bond 0.03134 / 2.11 ( 1116) hydrogen bonds : angle 3.56144 / 2.49 ( 3264) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.892 Fit side-chains REVERT: A 159 ASP cc_start: 0.7560 (t0) cc_final: 0.7342 (t70) REVERT: A 538 LEU cc_start: 0.8264 (mm) cc_final: 0.8049 (mt) REVERT: B 159 ASP cc_start: 0.7547 (t0) cc_final: 0.7327 (t70) REVERT: B 538 LEU cc_start: 0.8261 (mm) cc_final: 0.8045 (mt) REVERT: C 159 ASP cc_start: 0.7543 (t0) cc_final: 0.7325 (t70) REVERT: D 159 ASP cc_start: 0.7562 (t0) cc_final: 0.7346 (t70) outliers start: 32 outliers final: 20 residues processed: 192 average time/residue: 0.1452 time to fit residues: 44.2586 Evaluate side-chains 184 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 211 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 200 optimal weight: 0.5980 chunk 147 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 155 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.126635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.093970 restraints weight = 25273.247| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.87 r_work: 0.3001 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20984 Z= 0.131 Angle : 0.440 5.257 28428 Z= 0.222 Chirality : 0.036 0.115 3172 Planarity : 0.004 0.039 3536 Dihedral : 4.720 45.711 2820 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.18 % Allowed : 7.97 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.17), residues: 2464 helix: 2.21 (0.13), residues: 1500 sheet: 0.51 (0.61), residues: 84 loop : -0.62 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 687 TYR 0.009 0.001 TYR A 271 PHE 0.008 0.001 PHE A 319 TRP 0.009 0.001 TRP B 677 HIS 0.005 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 (20984) covalent geometry : angle 0.44040 / 0.22 (28428) hydrogen bonds : bond 0.03327 / 2.24 ( 1116) hydrogen bonds : angle 3.59683 / 2.51 ( 3264) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.801 Fit side-chains REVERT: A 538 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8163 (mt) REVERT: B 538 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8158 (mt) outliers start: 26 outliers final: 16 residues processed: 184 average time/residue: 0.1443 time to fit residues: 42.2548 Evaluate side-chains 178 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 102 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 210 optimal weight: 0.9990 chunk 214 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 217 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 231 optimal weight: 6.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.126355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.093522 restraints weight = 25529.537| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.89 r_work: 0.2886 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20984 Z= 0.127 Angle : 0.439 5.259 28428 Z= 0.221 Chirality : 0.036 0.118 3172 Planarity : 0.004 0.039 3536 Dihedral : 4.690 45.831 2820 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.00 % Allowed : 8.97 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.17), residues: 2464 helix: 2.23 (0.13), residues: 1500 sheet: 0.49 (0.62), residues: 84 loop : -0.59 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 687 TYR 0.009 0.001 TYR A 271 PHE 0.008 0.001 PHE B 319 TRP 0.009 0.001 TRP C 677 HIS 0.005 0.001 HIS B 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (20984) covalent geometry : angle 0.43866 / 0.22 (28428) hydrogen bonds : bond 0.03285 / 2.21 ( 1116) hydrogen bonds : angle 3.58793 / 2.50 ( 3264) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.752 Fit side-chains REVERT: A 538 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7930 (mt) REVERT: B 538 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7926 (mt) outliers start: 22 outliers final: 16 residues processed: 188 average time/residue: 0.1459 time to fit residues: 43.0611 Evaluate side-chains 182 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 220 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 219 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 62 optimal weight: 0.0980 chunk 238 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.127566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.094811 restraints weight = 25299.340| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.89 r_work: 0.2894 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 20984 Z= 0.096 Angle : 0.412 5.198 28428 Z= 0.207 Chirality : 0.035 0.119 3172 Planarity : 0.003 0.039 3536 Dihedral : 4.552 45.907 2820 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.18 % Allowed : 9.15 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.17), residues: 2464 helix: 2.40 (0.13), residues: 1496 sheet: 0.52 (0.62), residues: 84 loop : -0.54 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 687 TYR 0.008 0.001 TYR D 544 PHE 0.006 0.001 PHE D 705 TRP 0.007 0.001 TRP B 677 HIS 0.004 0.001 HIS C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (20984) covalent geometry : angle 0.41220 / 0.21 (28428) hydrogen bonds : bond 0.03024 / 2.03 ( 1116) hydrogen bonds : angle 3.48044 / 2.43 ( 3264) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.617 Fit side-chains REVERT: A 37 SER cc_start: 0.8078 (t) cc_final: 0.7820 (p) REVERT: A 538 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7894 (mt) REVERT: A 651 HIS cc_start: 0.6452 (m90) cc_final: 0.6079 (m90) REVERT: B 37 SER cc_start: 0.8086 (t) cc_final: 0.7828 (p) REVERT: B 538 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7893 (mt) REVERT: B 651 HIS cc_start: 0.6455 (m90) cc_final: 0.6083 (m90) REVERT: C 37 SER cc_start: 0.8078 (t) cc_final: 0.7821 (p) REVERT: C 651 HIS cc_start: 0.6455 (m90) cc_final: 0.6085 (m90) REVERT: D 37 SER cc_start: 0.8081 (t) cc_final: 0.7825 (p) REVERT: D 651 HIS cc_start: 0.6459 (m90) cc_final: 0.6089 (m90) outliers start: 26 outliers final: 20 residues processed: 204 average time/residue: 0.1428 time to fit residues: 45.7284 Evaluate side-chains 202 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 221 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.125150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.092434 restraints weight = 25344.782| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.88 r_work: 0.2906 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 20984 Z= 0.155 Angle : 0.478 5.693 28428 Z= 0.239 Chirality : 0.037 0.153 3172 Planarity : 0.004 0.039 3536 Dihedral : 4.772 46.553 2820 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.36 % Allowed : 9.33 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.17), residues: 2464 helix: 2.23 (0.13), residues: 1496 sheet: 0.34 (0.62), residues: 84 loop : -0.56 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 687 TYR 0.011 0.001 TYR A 544 PHE 0.009 0.001 PHE C 705 TRP 0.010 0.001 TRP A 677 HIS 0.006 0.001 HIS C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.15 (20984) covalent geometry : angle 0.47805 / 0.24 (28428) hydrogen bonds : bond 0.03512 / 2.36 ( 1116) hydrogen bonds : angle 3.62870 / 2.53 ( 3264) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.872 Fit side-chains REVERT: A 490 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7044 (ttt-90) REVERT: A 538 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7939 (mm) REVERT: A 651 HIS cc_start: 0.6521 (m90) cc_final: 0.6142 (m90) REVERT: B 490 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7037 (ttt-90) REVERT: B 538 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7938 (mm) REVERT: B 651 HIS cc_start: 0.6523 (m90) cc_final: 0.6145 (m90) REVERT: C 490 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7040 (ttt-90) REVERT: C 651 HIS cc_start: 0.6526 (m90) cc_final: 0.6152 (m90) REVERT: D 490 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.7048 (ttt-90) REVERT: D 651 HIS cc_start: 0.6533 (m90) cc_final: 0.6157 (m90) outliers start: 30 outliers final: 16 residues processed: 204 average time/residue: 0.1505 time to fit residues: 47.6548 Evaluate side-chains 198 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 490 ARG Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 194 optimal weight: 0.9980 chunk 199 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 246 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.126930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.096712 restraints weight = 25303.732| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.65 r_work: 0.2910 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20984 Z= 0.105 Angle : 0.445 8.698 28428 Z= 0.221 Chirality : 0.036 0.149 3172 Planarity : 0.004 0.039 3536 Dihedral : 4.626 45.712 2820 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.00 % Allowed : 9.96 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.17), residues: 2464 helix: 2.34 (0.14), residues: 1496 sheet: 0.40 (0.63), residues: 84 loop : -0.49 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 687 TYR 0.008 0.001 TYR B 544 PHE 0.007 0.001 PHE D 705 TRP 0.009 0.001 TRP B 223 HIS 0.004 0.001 HIS C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (20984) covalent geometry : angle 0.44507 / 0.22 (28428) hydrogen bonds : bond 0.03134 / 2.11 ( 1116) hydrogen bonds : angle 3.52019 / 2.46 ( 3264) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.790 Fit side-chains REVERT: A 490 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7099 (ttt-90) REVERT: A 538 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7975 (mm) REVERT: A 651 HIS cc_start: 0.6558 (m90) cc_final: 0.6166 (m90) REVERT: B 159 ASP cc_start: 0.7463 (t70) cc_final: 0.7240 (t70) REVERT: B 490 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7094 (ttt-90) REVERT: B 538 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7970 (mm) REVERT: B 651 HIS cc_start: 0.6558 (m90) cc_final: 0.6166 (m90) REVERT: C 159 ASP cc_start: 0.7461 (t70) cc_final: 0.7235 (t70) REVERT: C 490 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7102 (ttt-90) REVERT: C 651 HIS cc_start: 0.6556 (m90) cc_final: 0.6167 (m90) REVERT: D 159 ASP cc_start: 0.7471 (t70) cc_final: 0.7251 (t70) REVERT: D 490 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7100 (ttt-90) REVERT: D 651 HIS cc_start: 0.6565 (m90) cc_final: 0.6174 (m90) outliers start: 22 outliers final: 16 residues processed: 204 average time/residue: 0.1517 time to fit residues: 47.6703 Evaluate side-chains 206 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 490 ARG Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 490 ARG Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 88 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 186 optimal weight: 0.0020 chunk 79 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 214 optimal weight: 4.9990 chunk 217 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.125865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.095620 restraints weight = 25308.651| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.64 r_work: 0.2892 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20984 Z= 0.140 Angle : 0.462 6.065 28428 Z= 0.231 Chirality : 0.036 0.150 3172 Planarity : 0.004 0.039 3536 Dihedral : 4.705 46.006 2820 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.18 % Allowed : 9.78 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.17), residues: 2464 helix: 2.28 (0.13), residues: 1496 sheet: 0.33 (0.62), residues: 84 loop : -0.47 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 687 TYR 0.010 0.001 TYR B 271 PHE 0.008 0.001 PHE D 705 TRP 0.009 0.001 TRP A 677 HIS 0.005 0.001 HIS A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 (20984) covalent geometry : angle 0.46237 / 0.23 (28428) hydrogen bonds : bond 0.03351 / 2.26 ( 1116) hydrogen bonds : angle 3.57654 / 2.50 ( 3264) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4759.85 seconds wall clock time: 82 minutes 24.74 seconds (4944.74 seconds total)