Starting phenix.real_space_refine on Tue May 20 23:10:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eks_28212/05_2025/8eks_28212.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eks_28212/05_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_28212/05_2025/8eks_28212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eks_28212/05_2025/8eks_28212.map" model { file = "/net/cci-nas-00/data/ceres_data/8eks_28212/05_2025/8eks_28212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eks_28212/05_2025/8eks_28212.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLU:plan': 2, 'TRP:plan': 1, 'ASP: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: C, B, D Time building chain proxies: 11.67, per 1000 atoms: 0.57 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: 4.79 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.12 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: 6.06 Time building geometry restraints manager: 5.62 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 1.530 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: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 43.330 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.970 ------------------------------------------------------------------------------- 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 : 3.64 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (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 TRP 0.011 0.001 TRP D 101 HIS 0.004 0.001 HIS A 251 PHE 0.010 0.001 PHE D 405 TYR 0.005 0.001 TYR C 514 ARG 0.009 0.000 ARG B 687 Details of bonding type rmsd hydrogen bonds : bond 0.26234 ( 1116) hydrogen bonds : angle 7.21755 ( 3264) covalent geometry : bond 0.00274 (20984) covalent geometry : angle 0.61745 (28428) *********************** 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 : 2.168 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.3135 time to fit residues: 94.2001 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 : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 0.0040 chunk 187 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 194 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 225 optimal weight: 0.7980 overall best weight: 1.9596 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.135592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.104902 restraints weight = 24653.015| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.70 r_work: 0.2897 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20984 Z= 0.194 Angle : 0.535 6.174 28428 Z= 0.271 Chirality : 0.038 0.157 3172 Planarity : 0.004 0.036 3536 Dihedral : 7.635 136.576 2856 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.91 % Allowed : 5.98 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.16), residues: 2464 helix: 0.73 (0.13), residues: 1512 sheet: 0.08 (0.58), residues: 84 loop : -0.85 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 509 HIS 0.007 0.001 HIS A 251 PHE 0.013 0.002 PHE A 472 TYR 0.013 0.002 TYR A 271 ARG 0.003 0.001 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.05272 ( 1116) hydrogen bonds : angle 4.25554 ( 3264) covalent geometry : bond 0.00470 (20984) covalent geometry : angle 0.53495 (28428) *********************** 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 : 2.164 Fit side-chains REVERT: A 595 ASP cc_start: 0.7937 (m-30) cc_final: 0.7737 (m-30) REVERT: C 595 ASP cc_start: 0.7921 (m-30) cc_final: 0.7720 (m-30) REVERT: D 595 ASP cc_start: 0.7922 (m-30) cc_final: 0.7721 (m-30) outliers start: 20 outliers final: 12 residues processed: 188 average time/residue: 0.3082 time to fit residues: 91.3288 Evaluate side-chains 171 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 2.616 ------------------------------------------------------------------------------- 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 111 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 213 optimal weight: 0.0970 chunk 80 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.138886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.114126 restraints weight = 24138.746| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.27 r_work: 0.2978 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20984 Z= 0.126 Angle : 0.449 5.175 28428 Z= 0.226 Chirality : 0.036 0.130 3172 Planarity : 0.004 0.037 3536 Dihedral : 7.498 135.424 2856 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.91 % Allowed : 7.43 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.17), residues: 2464 helix: 1.67 (0.13), residues: 1492 sheet: 0.38 (0.60), residues: 84 loop : -0.72 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 509 HIS 0.005 0.001 HIS B 251 PHE 0.010 0.001 PHE B 319 TYR 0.011 0.001 TYR B 271 ARG 0.003 0.000 ARG C 687 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 1116) hydrogen bonds : angle 3.81764 ( 3264) covalent geometry : bond 0.00305 (20984) covalent geometry : angle 0.44948 (28428) *********************** 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: 20 poor density : 184 time to evaluate : 2.563 Fit side-chains REVERT: A 433 MET cc_start: 0.7611 (tpt) cc_final: 0.7391 (tpt) REVERT: B 433 MET cc_start: 0.7611 (tpt) cc_final: 0.7389 (tpt) REVERT: C 433 MET cc_start: 0.7616 (tpt) cc_final: 0.7398 (tpt) REVERT: D 433 MET cc_start: 0.7609 (tpt) cc_final: 0.7388 (tpt) outliers start: 20 outliers final: 16 residues processed: 200 average time/residue: 0.3369 time to fit residues: 102.0032 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 : 2.116 ------------------------------------------------------------------------------- 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 151 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3381 r_free = 0.3381 target = 0.123064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.090914 restraints weight = 25932.210| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.82 r_work: 0.2827 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 20984 Z= 0.226 Angle : 0.542 5.422 28428 Z= 0.271 Chirality : 0.039 0.117 3172 Planarity : 0.004 0.039 3536 Dihedral : 7.748 134.655 2856 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.81 % Allowed : 6.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.17), residues: 2464 helix: 1.61 (0.13), residues: 1496 sheet: 0.09 (0.60), residues: 84 loop : -0.71 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 677 HIS 0.008 0.002 HIS B 251 PHE 0.015 0.002 PHE A 319 TYR 0.014 0.002 TYR C 271 ARG 0.004 0.001 ARG C 684 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 1116) hydrogen bonds : angle 3.96057 ( 3264) covalent geometry : bond 0.00565 (20984) covalent geometry : angle 0.54248 (28428) *********************** 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: 40 poor density : 164 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.7669 (t0) cc_final: 0.7405 (t70) REVERT: B 159 ASP cc_start: 0.7657 (t0) cc_final: 0.7391 (t70) REVERT: C 159 ASP cc_start: 0.7671 (t0) cc_final: 0.7407 (t70) REVERT: D 159 ASP cc_start: 0.7678 (t0) cc_final: 0.7414 (t70) outliers start: 40 outliers final: 24 residues processed: 200 average time/residue: 0.2951 time to fit residues: 93.1973 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 : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU 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 439 ILE Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 91 GLU 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 439 ILE Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain C residue 91 GLU 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 439 ILE Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 91 GLU 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 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 33 optimal weight: 0.0970 chunk 182 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 174 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3433 r_free = 0.3433 target = 0.127335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.095274 restraints weight = 25374.802| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.82 r_work: 0.2931 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2068 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 : 0.422 5.173 28428 Z= 0.215 Chirality : 0.035 0.120 3172 Planarity : 0.004 0.038 3536 Dihedral : 7.280 134.989 2856 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.91 % Allowed : 8.02 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.17), residues: 2464 helix: 2.07 (0.14), residues: 1500 sheet: 0.52 (0.61), residues: 84 loop : -0.66 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 509 HIS 0.003 0.001 HIS D 251 PHE 0.007 0.001 PHE A 705 TYR 0.008 0.001 TYR C 271 ARG 0.004 0.000 ARG C 687 Details of bonding type rmsd hydrogen bonds : bond 0.03198 ( 1116) hydrogen bonds : angle 3.62670 ( 3264) covalent geometry : bond 0.00213 (20984) covalent geometry : angle 0.42213 (28428) *********************** 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 192 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 2.308 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 188 average time/residue: 0.3076 time to fit residues: 91.4217 Evaluate side-chains 180 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 2.384 ------------------------------------------------------------------------------- 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 196 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 169 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 236 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3425 r_free = 0.3425 target = 0.126662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.094114 restraints weight = 25416.361| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.87 r_work: 0.2874 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2144 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= 0.113 Angle : 0.432 5.236 28428 Z= 0.217 Chirality : 0.035 0.119 3172 Planarity : 0.004 0.039 3536 Dihedral : 7.107 131.885 2856 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.91 % Allowed : 8.51 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.17), residues: 2464 helix: 2.21 (0.13), residues: 1496 sheet: 0.57 (0.62), residues: 84 loop : -0.60 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 677 HIS 0.004 0.001 HIS A 251 PHE 0.007 0.001 PHE D 319 TYR 0.012 0.001 TYR B 98 ARG 0.004 0.000 ARG A 687 Details of bonding type rmsd hydrogen bonds : bond 0.03223 ( 1116) hydrogen bonds : angle 3.57016 ( 3264) covalent geometry : bond 0.00274 (20984) covalent geometry : angle 0.43219 (28428) *********************** 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 191 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 2.197 Fit side-chains REVERT: A 159 ASP cc_start: 0.7512 (t0) cc_final: 0.7287 (t70) REVERT: B 159 ASP cc_start: 0.7492 (t0) cc_final: 0.7264 (t70) REVERT: C 159 ASP cc_start: 0.7497 (t0) cc_final: 0.7268 (t70) REVERT: D 159 ASP cc_start: 0.7507 (t0) cc_final: 0.7281 (t70) outliers start: 20 outliers final: 16 residues processed: 187 average time/residue: 0.3086 time to fit residues: 91.3717 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 : 2.212 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 11 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 217 optimal weight: 6.9990 chunk 228 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 127 optimal weight: 0.0980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.126650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.094120 restraints weight = 25213.507| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.87 r_work: 0.2895 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2194 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= 0.111 Angle : 0.433 5.239 28428 Z= 0.216 Chirality : 0.035 0.118 3172 Planarity : 0.004 0.039 3536 Dihedral : 7.031 130.746 2856 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.27 % Allowed : 8.65 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.17), residues: 2464 helix: 2.27 (0.14), residues: 1496 sheet: 0.52 (0.62), residues: 84 loop : -0.56 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 677 HIS 0.004 0.001 HIS A 251 PHE 0.007 0.001 PHE C 705 TYR 0.011 0.001 TYR B 98 ARG 0.004 0.000 ARG B 687 Details of bonding type rmsd hydrogen bonds : bond 0.03165 ( 1116) hydrogen bonds : angle 3.54423 ( 3264) covalent geometry : bond 0.00268 (20984) covalent geometry : angle 0.43298 (28428) *********************** 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 205 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 2.459 Fit side-chains REVERT: A 159 ASP cc_start: 0.7537 (t0) cc_final: 0.7310 (t70) REVERT: A 490 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6950 (ttt-90) REVERT: A 645 MET cc_start: 0.7595 (mtp) cc_final: 0.7309 (mtm) REVERT: B 159 ASP cc_start: 0.7523 (t0) cc_final: 0.7295 (t70) REVERT: B 490 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6949 (ttt-90) REVERT: B 645 MET cc_start: 0.7589 (mtp) cc_final: 0.7302 (mtm) REVERT: C 159 ASP cc_start: 0.7520 (t0) cc_final: 0.7292 (t70) REVERT: C 490 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6957 (ttt-90) REVERT: C 645 MET cc_start: 0.7574 (mtp) cc_final: 0.7285 (mtm) REVERT: D 159 ASP cc_start: 0.7531 (t0) cc_final: 0.7306 (t70) REVERT: D 490 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6947 (ttt-90) REVERT: D 645 MET cc_start: 0.7578 (mtp) cc_final: 0.7292 (mtm) outliers start: 28 outliers final: 20 residues processed: 201 average time/residue: 0.3339 time to fit residues: 103.4315 Evaluate side-chains 196 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 2.296 ------------------------------------------------------------------------------- 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 490 ARG 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 490 ARG 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 490 ARG 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 490 ARG 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 210 optimal weight: 0.6980 chunk 208 optimal weight: 0.8980 chunk 193 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 206 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3428 r_free = 0.3428 target = 0.126828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.094203 restraints weight = 25358.771| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.88 r_work: 0.2935 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2255 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= 0.109 Angle : 0.446 7.752 28428 Z= 0.220 Chirality : 0.035 0.120 3172 Planarity : 0.004 0.056 3536 Dihedral : 6.976 129.773 2856 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.27 % Allowed : 9.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.17), residues: 2464 helix: 2.33 (0.13), residues: 1496 sheet: 0.50 (0.63), residues: 84 loop : -0.54 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 677 HIS 0.004 0.001 HIS A 251 PHE 0.007 0.001 PHE A 612 TYR 0.011 0.001 TYR C 98 ARG 0.013 0.000 ARG D 687 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 1116) hydrogen bonds : angle 3.51274 ( 3264) covalent geometry : bond 0.00265 (20984) covalent geometry : angle 0.44554 (28428) *********************** 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 212 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 2.163 Fit side-chains REVERT: A 159 ASP cc_start: 0.7612 (t0) cc_final: 0.7390 (t70) REVERT: A 490 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7022 (ttt-90) REVERT: A 645 MET cc_start: 0.7667 (mtp) cc_final: 0.7378 (mtm) REVERT: A 651 HIS cc_start: 0.6496 (m90) cc_final: 0.6181 (m90) REVERT: B 159 ASP cc_start: 0.7598 (t0) cc_final: 0.7374 (t70) REVERT: B 490 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7019 (ttt-90) REVERT: B 645 MET cc_start: 0.7658 (mtp) cc_final: 0.7368 (mtm) REVERT: B 651 HIS cc_start: 0.6497 (m90) cc_final: 0.6182 (m90) REVERT: C 159 ASP cc_start: 0.7594 (t0) cc_final: 0.7371 (t70) REVERT: C 490 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.7028 (ttt-90) REVERT: C 645 MET cc_start: 0.7643 (mtp) cc_final: 0.7353 (mtm) REVERT: C 651 HIS cc_start: 0.6495 (m90) cc_final: 0.6182 (m90) REVERT: D 159 ASP cc_start: 0.7605 (t0) cc_final: 0.7382 (t70) REVERT: D 490 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.7021 (ttt-90) REVERT: D 645 MET cc_start: 0.7656 (mtp) cc_final: 0.7367 (mtm) REVERT: D 651 HIS cc_start: 0.6505 (m90) cc_final: 0.6189 (m90) outliers start: 28 outliers final: 16 residues processed: 208 average time/residue: 0.3284 time to fit residues: 105.1097 Evaluate side-chains 200 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 2.304 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 203 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 chunk 247 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 chunk 9 optimal weight: 0.0770 chunk 61 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 244 optimal weight: 0.0070 chunk 156 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.128677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.096190 restraints weight = 25344.084| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.88 r_work: 0.2912 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20984 Z= 0.087 Angle : 0.429 7.970 28428 Z= 0.212 Chirality : 0.034 0.116 3172 Planarity : 0.004 0.058 3536 Dihedral : 6.832 128.090 2856 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.91 % Allowed : 9.65 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.17), residues: 2464 helix: 2.45 (0.13), residues: 1496 sheet: 0.62 (0.63), residues: 84 loop : -0.51 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 677 HIS 0.003 0.001 HIS D 251 PHE 0.005 0.001 PHE B 705 TYR 0.011 0.001 TYR C 98 ARG 0.013 0.000 ARG B 687 Details of bonding type rmsd hydrogen bonds : bond 0.02888 ( 1116) hydrogen bonds : angle 3.41588 ( 3264) covalent geometry : bond 0.00203 (20984) covalent geometry : angle 0.42934 (28428) *********************** 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 228 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 2.131 Fit side-chains REVERT: A 37 SER cc_start: 0.8029 (t) cc_final: 0.7799 (p) REVERT: A 159 ASP cc_start: 0.7453 (t0) cc_final: 0.7242 (t70) REVERT: A 490 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6917 (ttt-90) REVERT: A 645 MET cc_start: 0.7526 (mtp) cc_final: 0.7268 (mtm) REVERT: A 651 HIS cc_start: 0.6451 (m90) cc_final: 0.6193 (m90) REVERT: B 37 SER cc_start: 0.8040 (t) cc_final: 0.7810 (p) REVERT: B 159 ASP cc_start: 0.7434 (t0) cc_final: 0.7222 (t70) REVERT: B 490 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6912 (ttt-90) REVERT: B 645 MET cc_start: 0.7524 (mtp) cc_final: 0.7267 (mtm) REVERT: B 651 HIS cc_start: 0.6456 (m90) cc_final: 0.6199 (m90) REVERT: C 37 SER cc_start: 0.8034 (t) cc_final: 0.7806 (p) REVERT: C 159 ASP cc_start: 0.7436 (t0) cc_final: 0.7224 (t70) REVERT: C 490 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6917 (ttt-90) REVERT: C 645 MET cc_start: 0.7517 (mtp) cc_final: 0.7257 (mtm) REVERT: C 651 HIS cc_start: 0.6453 (m90) cc_final: 0.6198 (m90) REVERT: D 37 SER cc_start: 0.8036 (t) cc_final: 0.7808 (p) REVERT: D 159 ASP cc_start: 0.7441 (t0) cc_final: 0.7231 (t70) REVERT: D 490 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6906 (ttt-90) REVERT: D 645 MET cc_start: 0.7508 (mtp) cc_final: 0.7249 (mtm) REVERT: D 651 HIS cc_start: 0.6453 (m90) cc_final: 0.6198 (m90) outliers start: 20 outliers final: 12 residues processed: 224 average time/residue: 0.3241 time to fit residues: 110.7688 Evaluate side-chains 216 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 678 CYS 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 678 CYS 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 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 87 optimal weight: 2.9990 chunk 189 optimal weight: 0.0050 chunk 203 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 146 optimal weight: 0.0030 chunk 88 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 52 optimal weight: 0.2980 chunk 199 optimal weight: 6.9990 overall best weight: 0.8406 ------------------------------------------------------------------------------- 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 = 0.3438 r_free = 0.3438 target = 0.127679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.095177 restraints weight = 25212.865| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.87 r_work: 0.2948 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20984 Z= 0.107 Angle : 0.452 8.679 28428 Z= 0.224 Chirality : 0.035 0.163 3172 Planarity : 0.004 0.061 3536 Dihedral : 6.789 126.063 2856 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.91 % Allowed : 10.19 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.17), residues: 2464 helix: 2.45 (0.13), residues: 1496 sheet: 0.62 (0.63), residues: 84 loop : -0.47 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 677 HIS 0.004 0.001 HIS B 251 PHE 0.006 0.001 PHE A 705 TYR 0.010 0.001 TYR D 98 ARG 0.014 0.000 ARG C 687 Details of bonding type rmsd hydrogen bonds : bond 0.03057 ( 1116) hydrogen bonds : angle 3.44914 ( 3264) covalent geometry : bond 0.00258 (20984) covalent geometry : angle 0.45223 (28428) ********************** 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 212 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 2.415 Fit side-chains REVERT: A 37 SER cc_start: 0.8108 (t) cc_final: 0.7864 (p) REVERT: A 159 ASP cc_start: 0.7581 (t0) cc_final: 0.7367 (t70) REVERT: A 490 ARG cc_start: 0.7484 (OUTLIER) cc_final: 0.7017 (ttt-90) REVERT: A 645 MET cc_start: 0.7686 (mtp) cc_final: 0.7397 (mtm) REVERT: A 651 HIS cc_start: 0.6470 (m90) cc_final: 0.6218 (m90) REVERT: B 37 SER cc_start: 0.8111 (t) cc_final: 0.7869 (p) REVERT: B 159 ASP cc_start: 0.7566 (t0) cc_final: 0.7348 (t70) REVERT: B 490 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7016 (ttt-90) REVERT: B 645 MET cc_start: 0.7690 (mtp) cc_final: 0.7402 (mtm) REVERT: B 651 HIS cc_start: 0.6471 (m90) cc_final: 0.6220 (m90) REVERT: C 37 SER cc_start: 0.8103 (t) cc_final: 0.7861 (p) REVERT: C 159 ASP cc_start: 0.7569 (t0) cc_final: 0.7352 (t70) REVERT: C 490 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7022 (ttt-90) REVERT: C 645 MET cc_start: 0.7682 (mtp) cc_final: 0.7393 (mtm) REVERT: C 651 HIS cc_start: 0.6478 (m90) cc_final: 0.6228 (m90) REVERT: D 37 SER cc_start: 0.8103 (t) cc_final: 0.7861 (p) REVERT: D 159 ASP cc_start: 0.7584 (t0) cc_final: 0.7367 (t70) REVERT: D 490 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7019 (ttt-90) REVERT: D 645 MET cc_start: 0.7670 (mtp) cc_final: 0.7381 (mtm) REVERT: D 651 HIS cc_start: 0.6475 (m90) cc_final: 0.6226 (m90) outliers start: 20 outliers final: 16 residues processed: 212 average time/residue: 0.3215 time to fit residues: 105.9106 Evaluate side-chains 215 residues out of total 2228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 490 ARG Chi-restraints excluded: chain A residue 678 CYS 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 490 ARG Chi-restraints excluded: chain B residue 678 CYS 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 490 ARG Chi-restraints excluded: chain C residue 678 CYS 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 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 19 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 243 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 49 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.128178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.095806 restraints weight = 25403.911| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.87 r_work: 0.2957 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20984 Z= 0.096 Angle : 0.428 5.217 28428 Z= 0.214 Chirality : 0.035 0.153 3172 Planarity : 0.004 0.059 3536 Dihedral : 6.705 124.605 2856 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.45 % Allowed : 9.65 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.17), residues: 2464 helix: 2.49 (0.14), residues: 1496 sheet: 0.68 (0.64), residues: 84 loop : -0.44 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 677 HIS 0.003 0.001 HIS C 251 PHE 0.006 0.001 PHE A 705 TYR 0.010 0.001 TYR D 98 ARG 0.014 0.000 ARG C 687 Details of bonding type rmsd hydrogen bonds : bond 0.02947 ( 1116) hydrogen bonds : angle 3.40677 ( 3264) covalent geometry : bond 0.00228 (20984) covalent geometry : angle 0.42823 (28428) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9753.87 seconds wall clock time: 169 minutes 38.04 seconds (10178.04 seconds total)