Starting phenix.real_space_refine on Sun Aug 24 14:41:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eks_28212/08_2025/8eks_28212.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eks_28212/08_2025/8eks_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_28212/08_2025/8eks_28212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eks_28212/08_2025/8eks_28212.map" model { file = "/net/cci-nas-00/data/ceres_data/8eks_28212/08_2025/8eks_28212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eks_28212/08_2025/8eks_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-2.0-5787/lib/python3.9/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: 4.80, per 1000 atoms: 0.23 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: 1.65 Conformation dependent library (CDL) restraints added in 647.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.63 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: 3.55 Time building geometry restraints manager: 2.17 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 - 26.25: 11896 26.25 - 52.50: 476 52.50 - 78.74: 28 78.74 - 104.99: 20 104.99 - 131.24: 4 Dihedral angle restraints: 12424 sinusoidal: 5116 harmonic: 7308 Sorted by residual: dihedral pdb=" O4 PEX D 801 " pdb=" C2 PEX D 801 " pdb=" C3 PEX D 801 " pdb=" O6 PEX D 801 " ideal model delta sinusoidal sigma weight residual 52.53 -176.23 -131.24 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" O4 PEX C 801 " pdb=" C2 PEX C 801 " pdb=" C3 PEX C 801 " pdb=" O6 PEX C 801 " ideal model delta sinusoidal sigma weight residual 52.53 -176.23 -131.24 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" O4 PEX A 801 " pdb=" C2 PEX A 801 " pdb=" C3 PEX A 801 " pdb=" O6 PEX A 801 " ideal model delta sinusoidal sigma weight residual 52.53 -176.23 -131.24 1 3.00e+01 1.11e-03 1.77e+01 ... (remaining 12421 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: 1.440 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.440 Find NCS groups from input model: 0.170 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 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 : 13.549 131.241 7696 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 aren 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 covalent geometry : bond 0.00274 (20984) covalent geometry : angle 0.61745 (28428) hydrogen bonds : bond 0.26234 ( 1116) hydrogen bonds : angle 7.21755 ( 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 : 0.853 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1529 time to fit residues: 45.7498 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 : 0.844 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3625 r_free = 0.3625 target = 0.139888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.114939 restraints weight = 24210.616| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.29 r_work: 0.2951 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20984 Z= 0.216 Angle : 0.557 5.892 28428 Z= 0.281 Chirality : 0.039 0.159 3172 Planarity : 0.005 0.035 3536 Dihedral : 7.762 137.254 2856 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.91 % Allowed : 6.16 % 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 aren not related in a simple way. whole: 0.08 (0.16), residues: 2464 helix: 0.63 (0.13), residues: 1512 sheet: 0.04 (0.59), residues: 84 loop : -0.84 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 684 TYR 0.014 0.002 TYR A 271 PHE 0.015 0.002 PHE A 319 TRP 0.015 0.002 TRP C 509 HIS 0.007 0.002 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00532 (20984) covalent geometry : angle 0.55726 (28428) hydrogen bonds : bond 0.05213 ( 1116) hydrogen bonds : angle 4.28155 ( 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 196 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.522 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 188 average time/residue: 0.1506 time to fit residues: 44.5623 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 : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 434 LEU 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 434 LEU 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 434 LEU 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 434 LEU 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: 5.9990 chunk 236 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 211 optimal weight: 0.6980 chunk 232 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 164 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3651 r_free = 0.3651 target = 0.142153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.117309 restraints weight = 24002.269| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.30 r_work: 0.2986 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20984 Z= 0.107 Angle : 0.438 5.250 28428 Z= 0.221 Chirality : 0.035 0.130 3172 Planarity : 0.004 0.037 3536 Dihedral : 7.511 136.153 2856 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.91 % Allowed : 7.61 % Favored : 91.49 % 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 aren not related in a simple way. whole: 1.15 (0.17), residues: 2464 helix: 1.66 (0.14), residues: 1492 sheet: 0.33 (0.60), residues: 84 loop : -0.72 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 687 TYR 0.010 0.001 TYR B 271 PHE 0.007 0.001 PHE C 705 TRP 0.010 0.001 TRP B 509 HIS 0.004 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00251 (20984) covalent geometry : angle 0.43777 (28428) hydrogen bonds : bond 0.03784 ( 1116) hydrogen bonds : angle 3.84041 ( 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 208 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.809 Fit side-chains REVERT: A 433 MET cc_start: 0.7547 (tpt) cc_final: 0.7273 (tpt) REVERT: B 433 MET cc_start: 0.7545 (tpt) cc_final: 0.7268 (tpt) REVERT: C 433 MET cc_start: 0.7550 (tpt) cc_final: 0.7277 (tpt) REVERT: D 433 MET cc_start: 0.7553 (tpt) cc_final: 0.7275 (tpt) outliers start: 20 outliers final: 16 residues processed: 204 average time/residue: 0.1631 time to fit residues: 50.4972 Evaluate side-chains 172 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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: 5.9990 chunk 116 optimal weight: 2.9990 chunk 233 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 222 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 chunk 203 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3636 r_free = 0.3636 target = 0.140519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114624 restraints weight = 24064.069| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.36 r_work: 0.2955 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20984 Z= 0.131 Angle : 0.444 5.211 28428 Z= 0.223 Chirality : 0.036 0.115 3172 Planarity : 0.004 0.038 3536 Dihedral : 7.491 134.245 2856 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.63 % Allowed : 7.25 % Favored : 91.12 % 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 aren not related in a simple way. whole: 1.43 (0.17), residues: 2464 helix: 1.90 (0.14), residues: 1492 sheet: 0.44 (0.60), residues: 84 loop : -0.63 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 687 TYR 0.010 0.001 TYR A 271 PHE 0.009 0.001 PHE A 319 TRP 0.009 0.001 TRP B 677 HIS 0.005 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00321 (20984) covalent geometry : angle 0.44366 (28428) hydrogen bonds : bond 0.03577 ( 1116) hydrogen bonds : angle 3.73676 ( 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 204 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 0.875 Fit side-chains REVERT: A 159 ASP cc_start: 0.7627 (t0) cc_final: 0.7424 (t70) REVERT: A 433 MET cc_start: 0.7491 (tpt) cc_final: 0.7266 (tpt) REVERT: B 159 ASP cc_start: 0.7617 (t0) cc_final: 0.7414 (t70) REVERT: B 433 MET cc_start: 0.7486 (tpt) cc_final: 0.7260 (tpt) REVERT: C 159 ASP cc_start: 0.7619 (t0) cc_final: 0.7415 (t70) REVERT: C 433 MET cc_start: 0.7486 (tpt) cc_final: 0.7262 (tpt) REVERT: D 159 ASP cc_start: 0.7625 (t0) cc_final: 0.7424 (t70) REVERT: D 433 MET cc_start: 0.7483 (tpt) cc_final: 0.7259 (tpt) outliers start: 36 outliers final: 24 residues processed: 196 average time/residue: 0.1483 time to fit residues: 45.9807 Evaluate side-chains 184 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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: 2.9990 chunk 142 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 223 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 chunk 98 optimal weight: 0.0060 chunk 80 optimal weight: 0.5980 chunk 229 optimal weight: 0.5980 chunk 123 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3454 r_free = 0.3454 target = 0.128934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.096388 restraints weight = 25159.646| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.88 r_work: 0.2926 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1954 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= 0.086 Angle : 0.399 5.136 28428 Z= 0.202 Chirality : 0.034 0.125 3172 Planarity : 0.003 0.039 3536 Dihedral : 7.138 133.051 2856 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.27 % Allowed : 7.79 % Favored : 90.94 % 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 aren not related in a simple way. whole: 1.81 (0.17), residues: 2464 helix: 2.22 (0.14), residues: 1496 sheet: 0.64 (0.61), residues: 84 loop : -0.53 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 687 TYR 0.008 0.001 TYR B 271 PHE 0.006 0.001 PHE B 705 TRP 0.007 0.001 TRP A 677 HIS 0.003 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00199 (20984) covalent geometry : angle 0.39902 (28428) hydrogen bonds : bond 0.03038 ( 1116) hydrogen bonds : angle 3.53428 ( 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 200 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.854 Fit side-chains REVERT: A 37 SER cc_start: 0.8036 (t) cc_final: 0.7733 (p) REVERT: A 159 ASP cc_start: 0.7416 (t0) cc_final: 0.7195 (t70) REVERT: B 37 SER cc_start: 0.8048 (t) cc_final: 0.7743 (p) REVERT: B 159 ASP cc_start: 0.7404 (t0) cc_final: 0.7179 (t70) REVERT: C 37 SER cc_start: 0.8047 (t) cc_final: 0.7745 (p) REVERT: C 159 ASP cc_start: 0.7395 (t0) cc_final: 0.7170 (t70) REVERT: D 37 SER cc_start: 0.8042 (t) cc_final: 0.7743 (p) REVERT: D 159 ASP cc_start: 0.7409 (t0) cc_final: 0.7186 (t70) outliers start: 28 outliers final: 16 residues processed: 192 average time/residue: 0.1574 time to fit residues: 47.7650 Evaluate side-chains 184 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.996 ------------------------------------------------------------------------------- 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 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 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 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 678 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 211 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 200 optimal weight: 0.5980 chunk 147 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3650 r_free = 0.3650 target = 0.141711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.116125 restraints weight = 23695.700| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.34 r_work: 0.2973 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20984 Z= 0.106 Angle : 0.420 6.363 28428 Z= 0.211 Chirality : 0.035 0.116 3172 Planarity : 0.003 0.038 3536 Dihedral : 6.976 130.160 2856 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.27 % Allowed : 7.97 % 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 aren not related in a simple way. whole: 1.95 (0.17), residues: 2464 helix: 2.33 (0.14), residues: 1500 sheet: 0.63 (0.61), residues: 84 loop : -0.47 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 687 TYR 0.008 0.001 TYR C 271 PHE 0.007 0.001 PHE C 319 TRP 0.008 0.001 TRP B 677 HIS 0.004 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00255 (20984) covalent geometry : angle 0.42042 (28428) hydrogen bonds : bond 0.03136 ( 1116) hydrogen bonds : angle 3.52085 ( 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 216 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.860 Fit side-chains REVERT: A 37 SER cc_start: 0.8229 (t) cc_final: 0.7912 (p) REVERT: A 159 ASP cc_start: 0.7620 (t0) cc_final: 0.7416 (t70) REVERT: B 37 SER cc_start: 0.8235 (t) cc_final: 0.7919 (p) REVERT: B 159 ASP cc_start: 0.7609 (t0) cc_final: 0.7405 (t70) REVERT: C 37 SER cc_start: 0.8229 (t) cc_final: 0.7913 (p) REVERT: C 159 ASP cc_start: 0.7611 (t0) cc_final: 0.7405 (t70) REVERT: D 37 SER cc_start: 0.8236 (t) cc_final: 0.7921 (p) REVERT: D 159 ASP cc_start: 0.7615 (t0) cc_final: 0.7412 (t70) outliers start: 28 outliers final: 16 residues processed: 212 average time/residue: 0.1508 time to fit residues: 50.8202 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 : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 641 LEU 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: 5.9990 chunk 210 optimal weight: 0.5980 chunk 214 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 217 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3393 r_free = 0.3393 target = 0.123737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.091014 restraints weight = 25811.621| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.87 r_work: 0.2825 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20984 Z= 0.218 Angle : 0.532 7.099 28428 Z= 0.264 Chirality : 0.039 0.120 3172 Planarity : 0.004 0.039 3536 Dihedral : 7.249 130.289 2856 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.27 % Allowed : 8.61 % Favored : 90.13 % 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 aren not related in a simple way. whole: 1.56 (0.17), residues: 2464 helix: 2.00 (0.13), residues: 1500 sheet: 0.30 (0.60), residues: 84 loop : -0.59 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 687 TYR 0.013 0.002 TYR B 271 PHE 0.013 0.002 PHE D 319 TRP 0.014 0.001 TRP B 677 HIS 0.008 0.002 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00540 (20984) covalent geometry : angle 0.53234 (28428) hydrogen bonds : bond 0.03939 ( 1116) hydrogen bonds : angle 3.79016 ( 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 204 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.839 Fit side-chains REVERT: A 159 ASP cc_start: 0.7695 (t0) cc_final: 0.7421 (t70) REVERT: B 159 ASP cc_start: 0.7688 (t0) cc_final: 0.7413 (t70) REVERT: C 159 ASP cc_start: 0.7696 (t0) cc_final: 0.7419 (t70) REVERT: D 159 ASP cc_start: 0.7694 (t0) cc_final: 0.7420 (t70) outliers start: 28 outliers final: 20 residues processed: 200 average time/residue: 0.1614 time to fit residues: 50.5030 Evaluate side-chains 192 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 641 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 641 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 641 LEU 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 641 LEU 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: 0.7980 chunk 69 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 219 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 238 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 124 optimal weight: 0.0870 chunk 68 optimal weight: 3.9990 chunk 194 optimal weight: 0.1980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.127638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.095089 restraints weight = 25356.821| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.89 r_work: 0.2931 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20984 Z= 0.088 Angle : 0.418 7.567 28428 Z= 0.209 Chirality : 0.034 0.115 3172 Planarity : 0.003 0.039 3536 Dihedral : 7.009 131.788 2856 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.09 % Allowed : 9.24 % 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 aren not related in a simple way. whole: 1.96 (0.17), residues: 2464 helix: 2.35 (0.14), residues: 1496 sheet: 0.57 (0.61), residues: 84 loop : -0.49 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 687 TYR 0.007 0.001 TYR A 544 PHE 0.006 0.001 PHE B 705 TRP 0.007 0.001 TRP C 509 HIS 0.003 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00206 (20984) covalent geometry : angle 0.41782 (28428) hydrogen bonds : bond 0.02998 ( 1116) hydrogen bonds : angle 3.51647 ( 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 216 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.903 Fit side-chains REVERT: A 159 ASP cc_start: 0.7630 (t0) cc_final: 0.7380 (t70) REVERT: B 159 ASP cc_start: 0.7623 (t0) cc_final: 0.7367 (t70) REVERT: C 159 ASP cc_start: 0.7611 (t0) cc_final: 0.7355 (t70) REVERT: D 159 ASP cc_start: 0.7637 (t0) cc_final: 0.7386 (t70) outliers start: 24 outliers final: 20 residues processed: 212 average time/residue: 0.1575 time to fit residues: 52.2582 Evaluate side-chains 208 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 641 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 641 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 641 LEU 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 641 LEU 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: 0.8980 chunk 91 optimal weight: 0.8980 chunk 125 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 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 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 = 0.126581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.096555 restraints weight = 25215.430| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.64 r_work: 0.2906 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 0.028 20984 Z= 0.120 Angle : 0.454 8.203 28428 Z= 0.225 Chirality : 0.036 0.159 3172 Planarity : 0.003 0.038 3536 Dihedral : 6.961 129.445 2856 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.27 % Allowed : 9.24 % Favored : 89.49 % 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 aren not related in a simple way. whole: 1.97 (0.17), residues: 2464 helix: 2.35 (0.14), residues: 1496 sheet: 0.45 (0.61), residues: 84 loop : -0.46 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 687 TYR 0.009 0.001 TYR D 271 PHE 0.007 0.001 PHE C 319 TRP 0.008 0.001 TRP B 677 HIS 0.005 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00294 (20984) covalent geometry : angle 0.45443 (28428) hydrogen bonds : bond 0.03232 ( 1116) hydrogen bonds : angle 3.55034 ( 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 212 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.543 Fit side-chains REVERT: A 159 ASP cc_start: 0.7691 (t0) cc_final: 0.7476 (t70) REVERT: A 651 HIS cc_start: 0.6533 (m90) cc_final: 0.6163 (m90) REVERT: B 159 ASP cc_start: 0.7677 (t0) cc_final: 0.7461 (t70) REVERT: B 651 HIS cc_start: 0.6532 (m90) cc_final: 0.6165 (m90) REVERT: C 159 ASP cc_start: 0.7677 (t0) cc_final: 0.7460 (t70) REVERT: C 651 HIS cc_start: 0.6536 (m90) cc_final: 0.6171 (m90) REVERT: D 159 ASP cc_start: 0.7689 (t0) cc_final: 0.7474 (t70) REVERT: D 651 HIS cc_start: 0.6539 (m90) cc_final: 0.6174 (m90) outliers start: 28 outliers final: 20 residues processed: 208 average time/residue: 0.1363 time to fit residues: 44.2730 Evaluate side-chains 204 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 641 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 641 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 641 LEU 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 641 LEU 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: 0.7980 chunk 199 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 165 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 201 optimal weight: 0.6980 chunk 246 optimal weight: 1.9990 chunk 62 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3441 r_free = 0.3441 target = 0.127767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.095307 restraints weight = 25292.258| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.88 r_work: 0.2895 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20984 Z= 0.095 Angle : 0.434 8.651 28428 Z= 0.215 Chirality : 0.035 0.146 3172 Planarity : 0.003 0.037 3536 Dihedral : 6.845 128.157 2856 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.77 % Allowed : 9.92 % 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 aren not related in a simple way. whole: 2.10 (0.17), residues: 2464 helix: 2.46 (0.14), residues: 1496 sheet: 0.52 (0.63), residues: 84 loop : -0.40 (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 0.006 0.001 PHE C 705 TRP 0.006 0.001 TRP C 677 HIS 0.003 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00226 (20984) covalent geometry : angle 0.43364 (28428) hydrogen bonds : bond 0.02996 ( 1116) hydrogen bonds : angle 3.46521 ( 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 205 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.814 Fit side-chains REVERT: A 37 SER cc_start: 0.8145 (t) cc_final: 0.7899 (p) REVERT: A 159 ASP cc_start: 0.7543 (t0) cc_final: 0.7310 (t70) REVERT: A 651 HIS cc_start: 0.6522 (m90) cc_final: 0.6206 (m90) REVERT: B 37 SER cc_start: 0.8147 (t) cc_final: 0.7903 (p) REVERT: B 159 ASP cc_start: 0.7532 (t0) cc_final: 0.7300 (t70) REVERT: B 651 HIS cc_start: 0.6524 (m90) cc_final: 0.6210 (m90) REVERT: C 37 SER cc_start: 0.8144 (t) cc_final: 0.7902 (p) REVERT: C 159 ASP cc_start: 0.7519 (t0) cc_final: 0.7285 (t70) REVERT: C 651 HIS cc_start: 0.6518 (m90) cc_final: 0.6205 (m90) REVERT: D 37 SER cc_start: 0.8143 (t) cc_final: 0.7892 (p) REVERT: D 159 ASP cc_start: 0.7533 (t0) cc_final: 0.7303 (t70) REVERT: D 651 HIS cc_start: 0.6524 (m90) cc_final: 0.6214 (m90) outliers start: 17 outliers final: 17 residues processed: 205 average time/residue: 0.1517 time to fit residues: 48.9208 Evaluate side-chains 201 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 641 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 641 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 641 LEU 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 641 LEU 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: 0.0270 chunk 47 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 186 optimal weight: 0.0040 chunk 79 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 214 optimal weight: 0.2980 chunk 217 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 overall best weight: 0.3850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.143954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.118632 restraints weight = 23673.229| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.35 r_work: 0.3008 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 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 : 0.002 0.032 20984 Z= 0.081 Angle : 0.400 5.143 28428 Z= 0.201 Chirality : 0.034 0.141 3172 Planarity : 0.003 0.036 3536 Dihedral : 6.602 124.215 2856 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.91 % Allowed : 9.78 % 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 aren not related in a simple way. whole: 2.28 (0.17), residues: 2464 helix: 2.59 (0.14), residues: 1496 sheet: 0.68 (0.64), residues: 84 loop : -0.31 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 687 TYR 0.006 0.001 TYR D 544 PHE 0.004 0.001 PHE C 393 TRP 0.005 0.001 TRP C 677 HIS 0.002 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00183 (20984) covalent geometry : angle 0.39975 (28428) hydrogen bonds : bond 0.02733 ( 1116) hydrogen bonds : angle 3.32395 ( 3264) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4881.78 seconds wall clock time: 84 minutes 31.91 seconds (5071.91 seconds total)