Starting phenix.real_space_refine on Sat Sep 28 22:47:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eks_28212/09_2024/8eks_28212.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eks_28212/09_2024/8eks_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eks_28212/09_2024/8eks_28212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eks_28212/09_2024/8eks_28212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eks_28212/09_2024/8eks_28212.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eks_28212/09_2024/8eks_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-5461/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: 11.76, 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: 4.94 Conformation dependent library (CDL) restraints added in 2.5 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: 2.28 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: 6.13 Time building geometry restraints manager: 5.75 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 44.130 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.050 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.730 ------------------------------------------------------------------------------- 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= 0.173 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 2.417 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2967 time to fit residues: 88.9933 Evaluate side-chains 156 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 2.369 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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= 0.303 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 *********************** 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 fitting. rotamer outliers: 20 poor density : 176 time to evaluate : 3.014 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 188 average time/residue: 0.3343 time to fit residues: 100.4060 Evaluate side-chains 168 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 2.327 ------------------------------------------------------------------------------- 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 125 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 187 optimal weight: 0.0170 chunk 153 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 20984 Z= 0.395 Angle : 0.578 5.859 28428 Z= 0.287 Chirality : 0.040 0.117 3172 Planarity : 0.005 0.041 3536 Dihedral : 8.098 136.866 2856 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.09 % Allowed : 7.25 % 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: 0.71 (0.16), residues: 2464 helix: 1.28 (0.13), residues: 1488 sheet: -0.09 (0.59), residues: 84 loop : -0.82 (0.19), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 509 HIS 0.009 0.002 HIS D 251 PHE 0.018 0.002 PHE B 319 TYR 0.015 0.002 TYR A 471 ARG 0.004 0.001 ARG B 684 *********************** 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 200 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 176 time to evaluate : 2.517 Fit side-chains REVERT: A 433 MET cc_start: 0.7725 (tpt) cc_final: 0.7438 (tpt) REVERT: B 433 MET cc_start: 0.7727 (tpt) cc_final: 0.7440 (tpt) REVERT: C 433 MET cc_start: 0.7725 (tpt) cc_final: 0.7441 (tpt) REVERT: D 433 MET cc_start: 0.7721 (tpt) cc_final: 0.7438 (tpt) outliers start: 24 outliers final: 20 residues processed: 196 average time/residue: 0.3475 time to fit residues: 103.7134 Evaluate side-chains 172 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 2.401 ------------------------------------------------------------------------------- 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 439 ILE Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 439 ILE 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 222 optimal weight: 9.9990 chunk 169 optimal weight: 6.9990 chunk 117 optimal weight: 0.0040 chunk 24 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 151 optimal weight: 0.6980 chunk 226 optimal weight: 3.9990 chunk 239 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 214 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2008 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= 0.145 Angle : 0.429 5.112 28428 Z= 0.217 Chirality : 0.035 0.120 3172 Planarity : 0.004 0.038 3536 Dihedral : 7.565 137.251 2856 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.45 % Allowed : 7.43 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.17), residues: 2464 helix: 1.84 (0.14), residues: 1492 sheet: 0.43 (0.62), residues: 84 loop : -0.71 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 509 HIS 0.003 0.001 HIS D 251 PHE 0.007 0.001 PHE A 705 TYR 0.009 0.001 TYR C 544 ARG 0.003 0.000 ARG B 687 *********************** 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 196 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 MET cc_start: 0.7683 (tpt) cc_final: 0.7449 (tpt) REVERT: B 433 MET cc_start: 0.7684 (tpt) cc_final: 0.7450 (tpt) REVERT: C 433 MET cc_start: 0.7682 (tpt) cc_final: 0.7449 (tpt) REVERT: D 433 MET cc_start: 0.7682 (tpt) cc_final: 0.7447 (tpt) outliers start: 32 outliers final: 20 residues processed: 192 average time/residue: 0.3104 time to fit residues: 94.4152 Evaluate side-chains 180 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 160 time to evaluate : 2.359 ------------------------------------------------------------------------------- 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 224 ASP Chi-restraints excluded: chain A residue 254 VAL 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 224 ASP Chi-restraints excluded: chain B residue 254 VAL 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 224 ASP Chi-restraints excluded: chain C residue 254 VAL 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 224 ASP Chi-restraints excluded: chain D residue 254 VAL 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 199 optimal weight: 10.0000 chunk 136 optimal weight: 0.0980 chunk 3 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 98 optimal weight: 0.0970 chunk 204 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 215 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20984 Z= 0.155 Angle : 0.423 5.168 28428 Z= 0.214 Chirality : 0.035 0.118 3172 Planarity : 0.003 0.038 3536 Dihedral : 7.155 133.000 2856 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.45 % Allowed : 7.79 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.68 (0.17), residues: 2464 helix: 2.13 (0.14), residues: 1496 sheet: 0.55 (0.61), residues: 84 loop : -0.62 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 509 HIS 0.004 0.001 HIS D 251 PHE 0.006 0.001 PHE D 319 TYR 0.008 0.001 TYR C 271 ARG 0.004 0.000 ARG B 687 *********************** 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 208 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 176 time to evaluate : 2.403 Fit side-chains outliers start: 32 outliers final: 12 residues processed: 200 average time/residue: 0.3145 time to fit residues: 98.9083 Evaluate side-chains 172 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 160 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 140 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 199 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 125 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2167 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= 0.217 Angle : 0.456 5.251 28428 Z= 0.229 Chirality : 0.036 0.112 3172 Planarity : 0.004 0.039 3536 Dihedral : 7.139 131.443 2856 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.45 % Allowed : 8.33 % Favored : 90.22 % 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: 1.70 (0.17), residues: 2464 helix: 2.15 (0.14), residues: 1496 sheet: 0.47 (0.61), residues: 84 loop : -0.59 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 677 HIS 0.005 0.001 HIS B 251 PHE 0.008 0.001 PHE A 319 TYR 0.010 0.001 TYR C 271 ARG 0.003 0.000 ARG D 687 *********************** 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 196 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 2.306 Fit side-chains outliers start: 32 outliers final: 16 residues processed: 192 average time/residue: 0.3132 time to fit residues: 94.7512 Evaluate side-chains 180 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 439 ILE 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 231 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 136 optimal weight: 0.0980 chunk 175 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 201 optimal weight: 0.9980 chunk 133 optimal weight: 8.9990 chunk 239 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 20984 Z= 0.150 Angle : 0.427 5.173 28428 Z= 0.213 Chirality : 0.035 0.113 3172 Planarity : 0.003 0.039 3536 Dihedral : 7.002 130.865 2856 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.09 % Allowed : 9.24 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.87 (0.17), residues: 2464 helix: 2.30 (0.14), residues: 1496 sheet: 0.54 (0.62), residues: 84 loop : -0.57 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 677 HIS 0.004 0.001 HIS D 251 PHE 0.006 0.001 PHE C 705 TYR 0.008 0.001 TYR D 544 ARG 0.006 0.000 ARG A 687 *********************** 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 196 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 172 time to evaluate : 2.209 Fit side-chains outliers start: 24 outliers final: 20 residues processed: 192 average time/residue: 0.3116 time to fit residues: 95.2611 Evaluate side-chains 192 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 172 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 334 CYS Chi-restraints excluded: chain A residue 678 CYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 334 CYS Chi-restraints excluded: chain B residue 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 151 optimal weight: 0.7980 chunk 162 optimal weight: 0.6980 chunk 118 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 187 optimal weight: 0.0770 chunk 217 optimal weight: 6.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20984 Z= 0.161 Angle : 0.438 7.765 28428 Z= 0.216 Chirality : 0.035 0.116 3172 Planarity : 0.004 0.038 3536 Dihedral : 6.941 129.345 2856 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.09 % Allowed : 9.24 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.95 (0.17), residues: 2464 helix: 2.37 (0.14), residues: 1496 sheet: 0.55 (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 A 677 HIS 0.004 0.001 HIS C 251 PHE 0.006 0.001 PHE C 705 TYR 0.008 0.001 TYR A 544 ARG 0.006 0.000 ARG B 687 *********************** 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 208 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 184 time to evaluate : 2.451 Fit side-chains REVERT: A 37 SER cc_start: 0.8300 (t) cc_final: 0.7991 (p) REVERT: B 37 SER cc_start: 0.8303 (t) cc_final: 0.7996 (p) REVERT: C 37 SER cc_start: 0.8297 (t) cc_final: 0.7992 (p) REVERT: D 37 SER cc_start: 0.8300 (t) cc_final: 0.7993 (p) outliers start: 24 outliers final: 16 residues processed: 204 average time/residue: 0.3061 time to fit residues: 99.4866 Evaluate side-chains 196 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 180 time to evaluate : 2.323 ------------------------------------------------------------------------------- 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 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 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 222 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 210 optimal weight: 0.1980 chunk 221 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2345 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= 0.206 Angle : 0.464 8.234 28428 Z= 0.229 Chirality : 0.036 0.117 3172 Planarity : 0.004 0.039 3536 Dihedral : 6.970 128.807 2856 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.09 % Allowed : 9.60 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.90 (0.17), residues: 2464 helix: 2.32 (0.14), residues: 1496 sheet: 0.44 (0.63), residues: 84 loop : -0.53 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 677 HIS 0.005 0.001 HIS A 251 PHE 0.008 0.001 PHE A 705 TYR 0.009 0.001 TYR C 271 ARG 0.006 0.000 ARG C 687 *********************** 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 208 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 184 time to evaluate : 2.211 Fit side-chains REVERT: A 651 HIS cc_start: 0.6352 (m90) cc_final: 0.6134 (m90) REVERT: B 651 HIS cc_start: 0.6353 (m90) cc_final: 0.6135 (m90) REVERT: C 651 HIS cc_start: 0.6353 (m90) cc_final: 0.6136 (m90) REVERT: D 651 HIS cc_start: 0.6352 (m90) cc_final: 0.6133 (m90) outliers start: 24 outliers final: 16 residues processed: 204 average time/residue: 0.2942 time to fit residues: 95.0725 Evaluate side-chains 196 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 180 time to evaluate : 2.378 ------------------------------------------------------------------------------- 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 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 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 chunk 247 optimal weight: 0.0770 chunk 227 optimal weight: 0.9980 chunk 196 optimal weight: 0.9990 chunk 20 optimal weight: 0.0980 chunk 151 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20984 Z= 0.137 Angle : 0.434 8.590 28428 Z= 0.215 Chirality : 0.034 0.113 3172 Planarity : 0.004 0.038 3536 Dihedral : 6.840 127.892 2856 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.72 % Allowed : 10.19 % Favored : 89.09 % 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: 2.07 (0.17), residues: 2464 helix: 2.46 (0.14), residues: 1496 sheet: 0.55 (0.63), residues: 84 loop : -0.48 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 677 HIS 0.003 0.001 HIS D 251 PHE 0.006 0.001 PHE C 705 TYR 0.007 0.001 TYR A 544 ARG 0.007 0.000 ARG C 687 ********************** 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 204 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 2.318 Fit side-chains REVERT: A 37 SER cc_start: 0.8307 (t) cc_final: 0.8009 (p) REVERT: A 651 HIS cc_start: 0.6352 (m90) cc_final: 0.6105 (m90) REVERT: B 37 SER cc_start: 0.8308 (t) cc_final: 0.8010 (p) REVERT: B 651 HIS cc_start: 0.6348 (m90) cc_final: 0.6101 (m90) REVERT: C 37 SER cc_start: 0.8302 (t) cc_final: 0.8008 (p) REVERT: C 651 HIS cc_start: 0.6346 (m90) cc_final: 0.6099 (m90) REVERT: D 37 SER cc_start: 0.8305 (t) cc_final: 0.8008 (p) REVERT: D 651 HIS cc_start: 0.6351 (m90) cc_final: 0.6102 (m90) outliers start: 16 outliers final: 16 residues processed: 204 average time/residue: 0.3089 time to fit residues: 99.5111 Evaluate side-chains 204 residues out of total 2228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 2.283 ------------------------------------------------------------------------------- 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 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 678 CYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 334 CYS Chi-restraints excluded: chain D residue 678 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 82 optimal weight: 0.1980 chunk 202 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.0370 chunk 173 optimal weight: 6.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.129396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.097038 restraints weight = 25133.240| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.87 r_work: 0.2992 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2386 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= 0.127 Angle : 0.415 5.558 28428 Z= 0.208 Chirality : 0.034 0.117 3172 Planarity : 0.004 0.057 3536 Dihedral : 6.667 124.473 2856 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.72 % Allowed : 10.14 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.23 (0.17), residues: 2464 helix: 2.58 (0.14), residues: 1496 sheet: 0.68 (0.64), residues: 84 loop : -0.41 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 677 HIS 0.003 0.001 HIS A 251 PHE 0.005 0.001 PHE B 705 TYR 0.006 0.001 TYR C 544 ARG 0.013 0.000 ARG B 687 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3804.48 seconds wall clock time: 69 minutes 2.60 seconds (4142.60 seconds total)