Starting phenix.real_space_refine on Wed Jun 18 00:20:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jee_61414/06_2025/9jee_61414.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jee_61414/06_2025/9jee_61414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jee_61414/06_2025/9jee_61414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jee_61414/06_2025/9jee_61414.map" model { file = "/net/cci-nas-00/data/ceres_data/9jee_61414/06_2025/9jee_61414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jee_61414/06_2025/9jee_61414.cif" } resolution = 3.51 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= 0.000 sd= 0.019 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 20 5.49 5 S 124 5.16 5 C 13524 2.51 5 N 3296 2.21 5 O 3696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20660 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4974 Classifications: {'peptide': 612} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 14, 'TRANS': 597} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4974 Classifications: {'peptide': 612} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 14, 'TRANS': 597} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4974 Classifications: {'peptide': 612} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 14, 'TRANS': 597} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 191 Unusual residues: {'GRQ': 1, 'POV': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 191 Unusual residues: {'GRQ': 1, 'POV': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 191 Unusual residues: {'GRQ': 1, 'POV': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 80 Planarities with less than four sites: {'POV:plan-1': 3} Unresolved non-hydrogen planarities: 7 Restraints were copied for chains: C Time building chain proxies: 17.75, per 1000 atoms: 0.86 Number of scatterers: 20660 At special positions: 0 Unit cell: (119.48, 119.48, 122.776, 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 124 16.00 P 20 15.00 O 3696 8.00 N 3296 7.00 C 13524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 131 " distance=0.00 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 146 " distance=0.00 Simple disulfide: pdb=" SG CYS C 171 " - pdb=" SG CYS C 171 " distance=0.00 Simple disulfide: pdb=" SG CYS C 271 " - pdb=" SG CYS C 271 " distance=0.00 Simple disulfide: pdb=" SG CYS C 446 " - pdb=" SG CYS C 446 " distance=0.00 Simple disulfide: pdb=" SG CYS C 496 " - pdb=" SG CYS C 496 " distance=0.00 Simple disulfide: pdb=" SG CYS C 550 " - pdb=" SG CYS C 550 " distance=0.00 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 612 " distance=0.00 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 612 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 619 " distance=0.00 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 721 " distance=0.00 Simple disulfide: pdb=" SG CYS C 731 " - pdb=" SG CYS C 731 " distance=0.00 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 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: 5.40 Conformation dependent library (CDL) restraints added in 2.7 seconds 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4680 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 59.8% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 120 through 130 removed outlier: 4.267A pdb=" N PHE A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 146 removed outlier: 3.710A pdb=" N LEU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU A 141 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 removed outlier: 3.601A pdb=" N LEU A 162 " --> pdb=" O MET A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.691A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 177 " --> pdb=" O MET A 173 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 228 through 237 Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.868A pdb=" N VAL A 278 " --> pdb=" O GLN A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 315 through 329 Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 402 through 409 Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.700A pdb=" N LEU A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 436 removed outlier: 4.058A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 457 removed outlier: 3.617A pdb=" N SER A 444 " --> pdb=" O MET A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 490 removed outlier: 3.555A pdb=" N PHE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 485 through 490' Processing helix chain 'A' and resid 490 through 505 Processing helix chain 'A' and resid 510 through 515 removed outlier: 3.528A pdb=" N GLN A 514 " --> pdb=" O PRO A 510 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 510 through 515' Processing helix chain 'A' and resid 520 through 542 Processing helix chain 'A' and resid 551 through 559 removed outlier: 3.639A pdb=" N MET A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 568 removed outlier: 3.620A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 576 Processing helix chain 'A' and resid 577 through 586 removed outlier: 3.640A pdb=" N ILE A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 609 removed outlier: 3.542A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'A' and resid 624 through 637 Processing helix chain 'A' and resid 650 through 681 removed outlier: 3.836A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 681 " --> pdb=" O MET A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 706 removed outlier: 3.590A pdb=" N TRP A 692 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 712 Processing helix chain 'B' and resid 120 through 130 removed outlier: 4.267A pdb=" N PHE B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 146 removed outlier: 3.710A pdb=" N LEU B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU B 144 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 removed outlier: 3.601A pdb=" N LEU B 162 " --> pdb=" O MET B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.691A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU B 177 " --> pdb=" O MET B 173 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 197 Processing helix chain 'B' and resid 218 through 223 Processing helix chain 'B' and resid 228 through 237 Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 274 through 283 removed outlier: 3.868A pdb=" N VAL B 278 " --> pdb=" O GLN B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 315 through 329 Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'B' and resid 353 through 362 Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 402 through 409 Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.700A pdb=" N LEU B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 4.058A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 457 removed outlier: 3.617A pdb=" N SER B 444 " --> pdb=" O MET B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 490 removed outlier: 3.555A pdb=" N PHE B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 485 through 490' Processing helix chain 'B' and resid 490 through 505 Processing helix chain 'B' and resid 510 through 515 removed outlier: 3.528A pdb=" N GLN B 514 " --> pdb=" O PRO B 510 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 510 through 515' Processing helix chain 'B' and resid 520 through 542 Processing helix chain 'B' and resid 551 through 559 removed outlier: 3.639A pdb=" N MET B 555 " --> pdb=" O LEU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 568 removed outlier: 3.620A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 576 Processing helix chain 'B' and resid 577 through 586 removed outlier: 3.640A pdb=" N ILE B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 609 removed outlier: 3.542A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'B' and resid 624 through 637 Processing helix chain 'B' and resid 650 through 681 removed outlier: 3.836A pdb=" N LEU B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL B 681 " --> pdb=" O MET B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 706 removed outlier: 3.590A pdb=" N TRP B 692 " --> pdb=" O SER B 688 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS B 705 " --> pdb=" O LEU B 701 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 712 Processing helix chain 'C' and resid 120 through 130 removed outlier: 4.267A pdb=" N PHE C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 146 removed outlier: 3.710A pdb=" N LEU C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL C 140 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU C 141 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU C 144 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.601A pdb=" N LEU C 162 " --> pdb=" O MET C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.691A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU C 177 " --> pdb=" O MET C 173 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 197 Processing helix chain 'C' and resid 218 through 223 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 266 through 272 Processing helix chain 'C' and resid 274 through 283 removed outlier: 3.868A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 Processing helix chain 'C' and resid 315 through 329 Processing helix chain 'C' and resid 343 through 351 Processing helix chain 'C' and resid 353 through 362 Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 402 through 409 Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.699A pdb=" N LEU C 420 " --> pdb=" O ARG C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 436 removed outlier: 4.058A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 457 removed outlier: 3.618A pdb=" N SER C 444 " --> pdb=" O MET C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 490 removed outlier: 3.555A pdb=" N PHE C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 485 through 490' Processing helix chain 'C' and resid 490 through 505 Processing helix chain 'C' and resid 510 through 515 removed outlier: 3.529A pdb=" N GLN C 514 " --> pdb=" O PRO C 510 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER C 515 " --> pdb=" O SER C 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 510 through 515' Processing helix chain 'C' and resid 520 through 542 Processing helix chain 'C' and resid 551 through 559 removed outlier: 3.639A pdb=" N MET C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 568 removed outlier: 3.620A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 576 Processing helix chain 'C' and resid 577 through 586 removed outlier: 3.640A pdb=" N ILE C 583 " --> pdb=" O ILE C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 609 removed outlier: 3.541A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'C' and resid 624 through 637 Processing helix chain 'C' and resid 650 through 681 removed outlier: 3.836A pdb=" N LEU C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL C 681 " --> pdb=" O MET C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 706 removed outlier: 3.590A pdb=" N TRP C 692 " --> pdb=" O SER C 688 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS C 705 " --> pdb=" O LEU C 701 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 712 Processing helix chain 'D' and resid 120 through 130 removed outlier: 4.267A pdb=" N PHE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 146 removed outlier: 3.710A pdb=" N LEU D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL D 140 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU D 144 " --> pdb=" O VAL D 140 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N CYS D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 removed outlier: 3.601A pdb=" N LEU D 162 " --> pdb=" O MET D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.691A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU D 177 " --> pdb=" O MET D 173 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 197 Processing helix chain 'D' and resid 218 through 223 Processing helix chain 'D' and resid 228 through 237 Processing helix chain 'D' and resid 266 through 272 Processing helix chain 'D' and resid 274 through 283 removed outlier: 3.868A pdb=" N VAL D 278 " --> pdb=" O GLN D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'D' and resid 315 through 329 Processing helix chain 'D' and resid 343 through 351 Processing helix chain 'D' and resid 353 through 362 Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 402 through 409 Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.700A pdb=" N LEU D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 436 removed outlier: 4.058A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 457 removed outlier: 3.617A pdb=" N SER D 444 " --> pdb=" O MET D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 490 removed outlier: 3.554A pdb=" N PHE D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 485 through 490' Processing helix chain 'D' and resid 490 through 505 Processing helix chain 'D' and resid 510 through 515 removed outlier: 3.528A pdb=" N GLN D 514 " --> pdb=" O PRO D 510 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER D 515 " --> pdb=" O SER D 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 510 through 515' Processing helix chain 'D' and resid 520 through 542 Processing helix chain 'D' and resid 551 through 559 removed outlier: 3.639A pdb=" N MET D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 568 removed outlier: 3.620A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 576 Processing helix chain 'D' and resid 577 through 586 removed outlier: 3.640A pdb=" N ILE D 583 " --> pdb=" O ILE D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 609 removed outlier: 3.542A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) WARNING: missing atoms! Processing helix chain 'D' and resid 624 through 637 Processing helix chain 'D' and resid 650 through 681 removed outlier: 3.836A pdb=" N LEU D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL D 681 " --> pdb=" O MET D 677 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 706 removed outlier: 3.590A pdb=" N TRP D 692 " --> pdb=" O SER D 688 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS D 705 " --> pdb=" O LEU D 701 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 712 Processing sheet with id=AA1, first strand: chain 'A' and resid 377 through 382 removed outlier: 6.595A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 377 through 382 removed outlier: 6.595A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 377 through 382 removed outlier: 6.596A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 377 through 382 removed outlier: 6.595A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) 896 hydrogen bonds defined for protein. 2592 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: 7.35 Time building geometry restraints manager: 6.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3224 1.32 - 1.44: 5636 1.44 - 1.57: 11956 1.57 - 1.69: 40 1.69 - 1.82: 204 Bond restraints: 21060 Sorted by residual: bond pdb=" C6 GRQ D 806 " pdb=" C7 GRQ D 806 " ideal model delta sigma weight residual 1.453 1.541 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C6 GRQ C 805 " pdb=" C7 GRQ C 805 " ideal model delta sigma weight residual 1.453 1.541 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C6 GRQ A 804 " pdb=" C7 GRQ A 804 " ideal model delta sigma weight residual 1.453 1.541 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C6 GRQ B 805 " pdb=" C7 GRQ B 805 " ideal model delta sigma weight residual 1.453 1.541 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C4 GRQ B 805 " pdb=" C5 GRQ B 805 " ideal model delta sigma weight residual 1.499 1.555 -0.056 2.00e-02 2.50e+03 7.74e+00 ... (remaining 21055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 28235 3.92 - 7.84: 117 7.84 - 11.76: 12 11.76 - 15.69: 8 15.69 - 19.61: 4 Bond angle restraints: 28376 Sorted by residual: angle pdb=" C4 GRQ D 806 " pdb=" C5 GRQ D 806 " pdb=" C8 GRQ D 806 " ideal model delta sigma weight residual 115.45 95.84 19.61 3.00e+00 1.11e-01 4.27e+01 angle pdb=" C4 GRQ B 805 " pdb=" C5 GRQ B 805 " pdb=" C8 GRQ B 805 " ideal model delta sigma weight residual 115.45 95.84 19.61 3.00e+00 1.11e-01 4.27e+01 angle pdb=" C4 GRQ A 804 " pdb=" C5 GRQ A 804 " pdb=" C8 GRQ A 804 " ideal model delta sigma weight residual 115.45 95.84 19.61 3.00e+00 1.11e-01 4.27e+01 angle pdb=" C4 GRQ C 805 " pdb=" C5 GRQ C 805 " pdb=" C8 GRQ C 805 " ideal model delta sigma weight residual 115.45 95.88 19.57 3.00e+00 1.11e-01 4.26e+01 angle pdb=" C5 GRQ D 806 " pdb=" C6 GRQ D 806 " pdb=" C7 GRQ D 806 " ideal model delta sigma weight residual 125.02 111.04 13.98 3.00e+00 1.11e-01 2.17e+01 ... (remaining 28371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 10665 18.00 - 35.99: 1504 35.99 - 53.99: 454 53.99 - 71.98: 60 71.98 - 89.98: 36 Dihedral angle restraints: 12719 sinusoidal: 5511 harmonic: 7208 Sorted by residual: dihedral pdb=" CB CYS C 612 " pdb=" SG CYS C 612 " pdb=" SG CYS C 619 " pdb=" CB CYS C 619 " ideal model delta sinusoidal sigma weight residual -86.00 -39.07 -46.93 1 1.00e+01 1.00e-02 3.04e+01 dihedral pdb=" CB CYS A 612 " pdb=" SG CYS A 612 " pdb=" SG CYS A 619 " pdb=" CB CYS A 619 " ideal model delta sinusoidal sigma weight residual -86.00 -39.09 -46.91 1 1.00e+01 1.00e-02 3.04e+01 dihedral pdb=" CB CYS B 612 " pdb=" SG CYS B 612 " pdb=" SG CYS B 619 " pdb=" CB CYS B 619 " ideal model delta sinusoidal sigma weight residual -86.00 -39.11 -46.89 1 1.00e+01 1.00e-02 3.04e+01 ... (remaining 12716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2195 0.036 - 0.072: 790 0.072 - 0.108: 135 0.108 - 0.144: 32 0.144 - 0.180: 12 Chirality restraints: 3164 Sorted by residual: chirality pdb=" CG LEU A 642 " pdb=" CB LEU A 642 " pdb=" CD1 LEU A 642 " pdb=" CD2 LEU A 642 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CG LEU B 642 " pdb=" CB LEU B 642 " pdb=" CD1 LEU B 642 " pdb=" CD2 LEU B 642 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CG LEU D 642 " pdb=" CB LEU D 642 " pdb=" CD1 LEU D 642 " pdb=" CD2 LEU D 642 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.10e-01 ... (remaining 3161 not shown) Planarity restraints: 3468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 612 " 0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO B 613 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 613 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 613 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 612 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO A 613 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 613 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 613 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 612 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO D 613 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 613 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 613 " -0.019 5.00e-02 4.00e+02 ... (remaining 3465 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 229 2.61 - 3.18: 17025 3.18 - 3.75: 31993 3.75 - 4.33: 43428 4.33 - 4.90: 71494 Nonbonded interactions: 164169 Sorted by model distance: nonbonded pdb=" SG CYS D 612 " pdb=" SG CYS D 619 " model vdw 2.032 3.760 nonbonded pdb=" OD2 ASP A 752 " pdb=" NZ LYS D 169 " model vdw 2.210 3.120 nonbonded pdb=" NZ LYS C 169 " pdb=" OD2 ASP D 752 " model vdw 2.211 3.120 nonbonded pdb=" NZ LYS A 169 " pdb=" OD2 ASP B 752 " model vdw 2.217 3.120 nonbonded pdb=" NZ LYS B 169 " pdb=" OD2 ASP C 752 " model vdw 2.217 3.120 ... (remaining 164164 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 119 through 755 or resid 801 or (resid 802 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 o \ r name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C \ 27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or nam \ e O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or \ name O32 or name P )) or (resid 803 and (name N or name C1 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or na \ me C23 or name C24 or name C25 or name C26 or name C27 or name C3 or name C31 or \ name C32 or name C33 or name O11 or name O12 or name O13 or name O14 or name O2 \ 1 or name O22 or name O31 or name O32 or name P )))) selection = (chain 'B' and (resid 119 through 755 or resid 801 or (resid 802 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 o \ r name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C \ 27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or nam \ e O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or \ name O32 or name P )) or (resid 803 and (name N or name C1 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or na \ me C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 o \ r name C3 or name C31 or name C38 or name O11 or name O12 or name O13 or name O1 \ 4 or name O21 or name O22 or name O31 or name O32)))) selection = (chain 'C' and (resid 119 through 755 or resid 801 or (resid 802 and (name N or \ name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 o \ r name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C \ 27 or name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or nam \ e O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or \ name O32 or name P )) or (resid 803 and (name N or name C1 or name C11 or name \ C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or na \ me C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 o \ r name C3 or name C31 or name C38 or name O11 or name O12 or name O13 or name O1 \ 4 or name O21 or name O22 or name O31 or name O32)))) selection = (chain 'D' and (resid 119 through 755 or (resid 801 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name O11 or name \ O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or \ name P or name C210 or name C211)) or (resid 802 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or na \ me C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C3 or name C31 or name C32 or name C33 or name O11 or name O1 \ 2 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or nam \ e P )) or (resid 803 and (name N or name C1 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C \ 24 or name C25 or name C26 or name C27 or name C3 or name C31 or name C32 or nam \ e C33 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or \ name O31 or name O32 or name P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.180 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: 0.050 Extract box with map and model: 0.890 Check model and map are aligned: 0.140 Set scattering table: 0.230 Process input model: 54.440 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 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 0.088 21063 Z= 0.162 Angle : 0.743 19.607 28393 Z= 0.362 Chirality : 0.039 0.180 3164 Planarity : 0.004 0.039 3468 Dihedral : 18.110 89.977 8008 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 28.51 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.15), residues: 2424 helix: -0.92 (0.13), residues: 1416 sheet: -1.36 (0.45), residues: 76 loop : -2.48 (0.18), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 380 HIS 0.003 0.001 HIS C 301 PHE 0.022 0.001 PHE A 656 TYR 0.013 0.001 TYR C 213 ARG 0.009 0.000 ARG C 188 Details of bonding type rmsd hydrogen bonds : bond 0.19678 ( 896) hydrogen bonds : angle 7.05651 ( 2592) SS BOND : bond 0.00040 ( 3) SS BOND : angle 0.20885 ( 17) covalent geometry : bond 0.00324 (21060) covalent geometry : angle 0.74311 (28376) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.2882 time to fit residues: 148.3387 Evaluate side-chains 297 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.9990 chunk 184 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 142 optimal weight: 0.0370 chunk 221 optimal weight: 0.8980 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN A 417 HIS ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN B 417 HIS ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 ASN C 417 HIS ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN D 417 HIS ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.191895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.184608 restraints weight = 24279.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.168115 restraints weight = 32081.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.167473 restraints weight = 34951.696| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21063 Z= 0.117 Angle : 0.545 6.662 28393 Z= 0.278 Chirality : 0.038 0.147 3164 Planarity : 0.004 0.038 3468 Dihedral : 11.024 83.703 3220 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.18 % Allowed : 28.00 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.17), residues: 2424 helix: -0.37 (0.13), residues: 1512 sheet: -0.30 (0.57), residues: 56 loop : -2.38 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 559 HIS 0.004 0.001 HIS B 301 PHE 0.021 0.001 PHE A 310 TYR 0.013 0.001 TYR A 213 ARG 0.004 0.000 ARG C 188 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 896) hydrogen bonds : angle 4.34123 ( 2592) SS BOND : bond 0.00083 ( 3) SS BOND : angle 0.05942 ( 17) covalent geometry : bond 0.00273 (21060) covalent geometry : angle 0.54468 (28376) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 340 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7177 (tp40) REVERT: A 642 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8404 (tt) REVERT: B 570 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7151 (tp40) REVERT: B 642 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8412 (tt) REVERT: C 570 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7135 (tp40) REVERT: C 642 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8396 (tt) REVERT: D 570 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7193 (tp40) REVERT: D 642 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8418 (tt) outliers start: 69 outliers final: 20 residues processed: 405 average time/residue: 0.3128 time to fit residues: 194.8238 Evaluate side-chains 316 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 288 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 745 HIS Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 745 HIS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 570 GLN Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 745 HIS Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 745 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 57 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 15 optimal weight: 0.0570 chunk 30 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 231 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 671 ASN B 220 ASN B 671 ASN C 220 ASN C 671 ASN D 220 ASN D 671 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.192703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.185325 restraints weight = 24022.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.169725 restraints weight = 33172.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.169469 restraints weight = 36124.664| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 21063 Z= 0.108 Angle : 0.517 5.762 28393 Z= 0.267 Chirality : 0.038 0.160 3164 Planarity : 0.003 0.041 3468 Dihedral : 10.785 84.280 3220 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.64 % Allowed : 27.03 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.17), residues: 2424 helix: -0.04 (0.14), residues: 1488 sheet: -0.53 (0.52), residues: 56 loop : -2.17 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 493 HIS 0.004 0.001 HIS B 301 PHE 0.013 0.001 PHE B 193 TYR 0.010 0.001 TYR D 547 ARG 0.005 0.000 ARG B 716 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 896) hydrogen bonds : angle 3.99307 ( 2592) SS BOND : bond 0.00119 ( 3) SS BOND : angle 0.11313 ( 17) covalent geometry : bond 0.00248 (21060) covalent geometry : angle 0.51753 (28376) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 326 time to evaluate : 2.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7655 (tp40) REVERT: B 570 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7651 (tp40) REVERT: C 570 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7648 (tp40) REVERT: D 570 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7653 (tp40) outliers start: 79 outliers final: 25 residues processed: 388 average time/residue: 0.3001 time to fit residues: 183.0933 Evaluate side-chains 337 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 308 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 745 HIS Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 570 GLN Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 745 HIS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 570 GLN Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 745 HIS Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 570 GLN Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 745 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 90 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 173 optimal weight: 4.9990 chunk 220 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 190 optimal weight: 9.9990 chunk 84 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.191327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.183862 restraints weight = 24215.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.168889 restraints weight = 35091.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.168542 restraints weight = 43281.335| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21063 Z= 0.114 Angle : 0.536 7.853 28393 Z= 0.271 Chirality : 0.039 0.201 3164 Planarity : 0.003 0.043 3468 Dihedral : 10.690 84.882 3220 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.38 % Allowed : 26.61 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.17), residues: 2424 helix: 0.17 (0.14), residues: 1460 sheet: -0.74 (0.49), residues: 56 loop : -2.05 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 493 HIS 0.004 0.001 HIS B 301 PHE 0.011 0.001 PHE A 569 TYR 0.009 0.001 TYR D 213 ARG 0.010 0.000 ARG C 698 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 896) hydrogen bonds : angle 3.87058 ( 2592) SS BOND : bond 0.00144 ( 3) SS BOND : angle 0.12307 ( 17) covalent geometry : bond 0.00269 (21060) covalent geometry : angle 0.53621 (28376) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 311 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 47 residues processed: 395 average time/residue: 0.3169 time to fit residues: 198.7217 Evaluate side-chains 346 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 299 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 745 HIS Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 745 HIS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 745 HIS Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 745 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 232 optimal weight: 0.0000 chunk 190 optimal weight: 9.9990 chunk 223 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 75 optimal weight: 0.4980 chunk 202 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 209 optimal weight: 0.4980 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 220 ASN A 570 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN B 570 GLN B 671 ASN C 220 ASN C 570 GLN C 671 ASN D 178 ASN D 220 ASN D 570 GLN D 671 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.188880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.181447 restraints weight = 24244.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.167014 restraints weight = 31916.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.166138 restraints weight = 31983.536| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21063 Z= 0.131 Angle : 0.565 8.449 28393 Z= 0.283 Chirality : 0.039 0.190 3164 Planarity : 0.004 0.047 3468 Dihedral : 10.801 85.315 3220 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.47 % Allowed : 26.48 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.17), residues: 2424 helix: 0.03 (0.14), residues: 1488 sheet: -0.88 (0.49), residues: 56 loop : -2.08 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 493 HIS 0.006 0.001 HIS B 301 PHE 0.012 0.001 PHE A 569 TYR 0.011 0.002 TYR D 213 ARG 0.011 0.000 ARG D 698 Details of bonding type rmsd hydrogen bonds : bond 0.03301 ( 896) hydrogen bonds : angle 3.84969 ( 2592) SS BOND : bond 0.00141 ( 3) SS BOND : angle 0.09407 ( 17) covalent geometry : bond 0.00311 (21060) covalent geometry : angle 0.56537 (28376) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 326 time to evaluate : 2.326 Fit side-chains revert: symmetry clash REVERT: A 574 MET cc_start: 0.5320 (mmm) cc_final: 0.4935 (mmm) REVERT: B 574 MET cc_start: 0.5524 (mmm) cc_final: 0.5098 (mmm) REVERT: B 672 MET cc_start: 0.7655 (mmm) cc_final: 0.7348 (tpt) REVERT: C 574 MET cc_start: 0.5230 (mmm) cc_final: 0.4846 (mmm) REVERT: C 672 MET cc_start: 0.7641 (mmm) cc_final: 0.7369 (tpt) REVERT: D 574 MET cc_start: 0.5483 (mmm) cc_final: 0.5052 (mmm) REVERT: D 672 MET cc_start: 0.7626 (mmm) cc_final: 0.7322 (tpt) outliers start: 97 outliers final: 67 residues processed: 404 average time/residue: 0.2938 time to fit residues: 189.1422 Evaluate side-chains 380 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 313 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 745 HIS Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 745 HIS Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 745 HIS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 745 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 18 optimal weight: 0.8980 chunk 204 optimal weight: 0.7980 chunk 205 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 217 optimal weight: 8.9990 chunk 150 optimal weight: 0.9980 chunk 220 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 671 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.189883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.182455 restraints weight = 24203.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.166572 restraints weight = 34144.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.165994 restraints weight = 35976.361| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21063 Z= 0.124 Angle : 0.553 7.790 28393 Z= 0.278 Chirality : 0.039 0.195 3164 Planarity : 0.004 0.048 3468 Dihedral : 10.699 85.940 3220 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 6.00 % Allowed : 26.01 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.17), residues: 2424 helix: 0.07 (0.14), residues: 1488 sheet: -0.93 (0.48), residues: 56 loop : -2.07 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 493 HIS 0.005 0.001 HIS A 301 PHE 0.014 0.001 PHE D 569 TYR 0.010 0.001 TYR D 213 ARG 0.008 0.000 ARG D 698 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 896) hydrogen bonds : angle 3.77541 ( 2592) SS BOND : bond 0.00135 ( 3) SS BOND : angle 0.09690 ( 17) covalent geometry : bond 0.00295 (21060) covalent geometry : angle 0.55364 (28376) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 324 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8782 (pp) REVERT: A 574 MET cc_start: 0.5365 (mmm) cc_final: 0.5013 (mmm) REVERT: A 672 MET cc_start: 0.7645 (mmm) cc_final: 0.7388 (tpt) REVERT: B 392 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8791 (pp) REVERT: B 574 MET cc_start: 0.5239 (mmm) cc_final: 0.4963 (mmm) REVERT: C 392 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8794 (pp) REVERT: C 574 MET cc_start: 0.5272 (mmm) cc_final: 0.4950 (mmm) REVERT: C 672 MET cc_start: 0.7674 (mmm) cc_final: 0.7441 (tpt) REVERT: D 392 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8787 (pp) REVERT: D 574 MET cc_start: 0.5219 (mmm) cc_final: 0.4956 (mmm) outliers start: 130 outliers final: 88 residues processed: 429 average time/residue: 0.3135 time to fit residues: 214.0248 Evaluate side-chains 405 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 313 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 745 HIS Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 745 HIS Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 745 HIS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 716 ARG Chi-restraints excluded: chain D residue 731 CYS Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 745 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 237 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 91 optimal weight: 0.3980 chunk 231 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.184709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.177890 restraints weight = 24122.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.176414 restraints weight = 41828.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.175878 restraints weight = 51168.298| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21063 Z= 0.209 Angle : 0.643 7.937 28393 Z= 0.327 Chirality : 0.042 0.228 3164 Planarity : 0.004 0.051 3468 Dihedral : 11.174 86.607 3220 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 5.30 % Allowed : 27.68 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.17), residues: 2424 helix: -0.14 (0.13), residues: 1480 sheet: -1.42 (0.52), residues: 56 loop : -2.24 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 331 HIS 0.007 0.001 HIS C 301 PHE 0.022 0.002 PHE C 310 TYR 0.017 0.002 TYR D 213 ARG 0.004 0.001 ARG D 698 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 896) hydrogen bonds : angle 4.07373 ( 2592) SS BOND : bond 0.00145 ( 3) SS BOND : angle 0.06279 ( 17) covalent geometry : bond 0.00506 (21060) covalent geometry : angle 0.64326 (28376) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 324 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 598 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8441 (tt) REVERT: D 598 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8443 (tt) outliers start: 115 outliers final: 85 residues processed: 418 average time/residue: 0.3597 time to fit residues: 237.5253 Evaluate side-chains 401 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 314 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 745 HIS Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 745 HIS Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 745 HIS Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 716 ARG Chi-restraints excluded: chain D residue 731 CYS Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 745 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 65 optimal weight: 2.9990 chunk 168 optimal weight: 0.2980 chunk 149 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 220 ASN A 570 GLN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN B 220 ASN B 570 GLN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN C 570 GLN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 182 ASN D 220 ASN D 570 GLN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.189471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.181739 restraints weight = 24124.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.166462 restraints weight = 37625.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.166286 restraints weight = 36318.112| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21063 Z= 0.116 Angle : 0.602 10.002 28393 Z= 0.295 Chirality : 0.040 0.242 3164 Planarity : 0.004 0.049 3468 Dihedral : 10.730 87.447 3220 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.43 % Allowed : 28.78 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.17), residues: 2424 helix: 0.13 (0.14), residues: 1456 sheet: -1.39 (0.51), residues: 56 loop : -2.13 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 493 HIS 0.004 0.001 HIS B 301 PHE 0.025 0.001 PHE B 310 TYR 0.011 0.001 TYR D 213 ARG 0.005 0.000 ARG D 698 Details of bonding type rmsd hydrogen bonds : bond 0.03153 ( 896) hydrogen bonds : angle 3.77955 ( 2592) SS BOND : bond 0.00188 ( 3) SS BOND : angle 0.17351 ( 17) covalent geometry : bond 0.00270 (21060) covalent geometry : angle 0.60183 (28376) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 324 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8178 (tt) REVERT: A 672 MET cc_start: 0.7689 (mmm) cc_final: 0.7441 (tpt) REVERT: A 677 MET cc_start: 0.5778 (mtt) cc_final: 0.5530 (mtt) REVERT: B 293 ASP cc_start: 0.8001 (t0) cc_final: 0.7149 (t0) REVERT: B 598 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8230 (tt) REVERT: B 677 MET cc_start: 0.6405 (mmm) cc_final: 0.5813 (mmt) REVERT: C 598 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8346 (tt) REVERT: D 598 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8348 (tt) REVERT: D 672 MET cc_start: 0.7701 (mmm) cc_final: 0.7405 (tpt) outliers start: 96 outliers final: 81 residues processed: 387 average time/residue: 0.3393 time to fit residues: 207.6298 Evaluate side-chains 399 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 314 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 745 HIS Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 745 HIS Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 745 HIS Chi-restraints excluded: chain D residue 182 ASN Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 649 LYS Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 716 ARG Chi-restraints excluded: chain D residue 731 CYS Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 745 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 143 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.188801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.180809 restraints weight = 24084.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.180575 restraints weight = 37601.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.165088 restraints weight = 39177.194| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21063 Z= 0.127 Angle : 0.602 8.718 28393 Z= 0.298 Chirality : 0.040 0.200 3164 Planarity : 0.004 0.048 3468 Dihedral : 10.680 87.566 3220 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 4.38 % Allowed : 28.64 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.17), residues: 2424 helix: 0.25 (0.14), residues: 1452 sheet: -1.42 (0.55), residues: 56 loop : -2.03 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 493 HIS 0.005 0.001 HIS B 301 PHE 0.018 0.001 PHE B 538 TYR 0.017 0.001 TYR C 213 ARG 0.005 0.000 ARG D 698 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 896) hydrogen bonds : angle 3.78070 ( 2592) SS BOND : bond 0.00151 ( 3) SS BOND : angle 0.10148 ( 17) covalent geometry : bond 0.00305 (21060) covalent geometry : angle 0.60221 (28376) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 311 time to evaluate : 4.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8160 (tt) REVERT: A 672 MET cc_start: 0.7625 (mmm) cc_final: 0.7395 (tpt) REVERT: B 677 MET cc_start: 0.6383 (mmm) cc_final: 0.5408 (mmt) REVERT: C 598 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8325 (tt) REVERT: D 672 MET cc_start: 0.7640 (mmm) cc_final: 0.7407 (tpt) REVERT: D 677 MET cc_start: 0.6404 (mmm) cc_final: 0.5973 (mmt) outliers start: 95 outliers final: 85 residues processed: 382 average time/residue: 0.3872 time to fit residues: 236.2913 Evaluate side-chains 393 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 306 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 716 ARG Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 745 HIS Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 599 LEU Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 716 ARG Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 745 HIS Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 182 ASN Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 598 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 716 ARG Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 745 HIS Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 716 ARG Chi-restraints excluded: chain D residue 731 CYS Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 737 VAL Chi-restraints excluded: chain D residue 745 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 217 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 212 optimal weight: 0.4980 chunk 219 optimal weight: 0.0770 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 63 optimal weight: 0.0980 chunk 237 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN C 570 GLN C 671 ASN D 570 GLN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.193011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.185609 restraints weight = 24064.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.172154 restraints weight = 33935.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.171313 restraints weight = 42961.076| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 21063 Z= 0.104 Angle : 0.592 8.637 28393 Z= 0.289 Chirality : 0.039 0.180 3164 Planarity : 0.003 0.046 3468 Dihedral : 10.425 87.453 3220 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.95 % Allowed : 30.21 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.17), residues: 2424 helix: 0.45 (0.14), residues: 1440 sheet: -1.22 (0.55), residues: 56 loop : -2.09 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 493 HIS 0.003 0.001 HIS D 523 PHE 0.030 0.001 PHE C 310 TYR 0.011 0.001 TYR A 213 ARG 0.006 0.000 ARG D 188 Details of bonding type rmsd hydrogen bonds : bond 0.02907 ( 896) hydrogen bonds : angle 3.56905 ( 2592) SS BOND : bond 0.00161 ( 3) SS BOND : angle 0.14356 ( 17) covalent geometry : bond 0.00238 (21060) covalent geometry : angle 0.59195 (28376) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 313 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 598 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8225 (tt) REVERT: A 672 MET cc_start: 0.7599 (mmm) cc_final: 0.7336 (tpt) REVERT: B 293 ASP cc_start: 0.7873 (t0) cc_final: 0.6332 (m-30) REVERT: B 598 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8219 (tt) REVERT: D 672 MET cc_start: 0.7563 (mmm) cc_final: 0.7313 (tpt) outliers start: 64 outliers final: 48 residues processed: 368 average time/residue: 0.3597 time to fit residues: 217.0979 Evaluate side-chains 356 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 306 time to evaluate : 3.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 ASN Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 745 HIS Chi-restraints excluded: chain B residue 178 ASN Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 731 CYS Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 745 HIS Chi-restraints excluded: chain C residue 178 ASN Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 745 HIS Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 731 CYS Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 745 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 34 optimal weight: 0.0870 chunk 229 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 205 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.188072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.181354 restraints weight = 24129.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.169875 restraints weight = 40950.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.167564 restraints weight = 38350.987| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21063 Z= 0.147 Angle : 0.620 9.724 28393 Z= 0.305 Chirality : 0.040 0.199 3164 Planarity : 0.004 0.048 3468 Dihedral : 10.600 87.487 3220 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.18 % Allowed : 29.84 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.17), residues: 2424 helix: 0.31 (0.14), residues: 1444 sheet: -1.16 (0.60), residues: 56 loop : -2.01 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 493 HIS 0.006 0.001 HIS C 301 PHE 0.026 0.001 PHE B 569 TYR 0.018 0.002 TYR A 213 ARG 0.007 0.000 ARG B 188 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 896) hydrogen bonds : angle 3.76693 ( 2592) SS BOND : bond 0.00132 ( 3) SS BOND : angle 0.06726 ( 17) covalent geometry : bond 0.00353 (21060) covalent geometry : angle 0.62008 (28376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9174.45 seconds wall clock time: 168 minutes 59.08 seconds (10139.08 seconds total)