Starting phenix.real_space_refine on Thu Sep 18 22:02:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jee_61414/09_2025/9jee_61414.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jee_61414/09_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_61414/09_2025/9jee_61414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jee_61414/09_2025/9jee_61414.map" model { file = "/net/cci-nas-00/data/ceres_data/9jee_61414/09_2025/9jee_61414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jee_61414/09_2025/9jee_61414.cif" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 6.27, per 1000 atoms: 0.30 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: 1.48 Conformation dependent library (CDL) restraints added in 701.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.47 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: 2.76 Time building geometry restraints manager: 1.89 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 119 through 801 or (resid 802 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 (resid 803 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e 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 O21 or name O22 \ or name O31 or name O32 or name P )))) selection = (chain 'B' and (resid 119 through 801 or (resid 802 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 (resid 803 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or \ name C31 or name C38 or name O11 or name O12 or name O13 or name O14 or name O21 \ or name O22 or name O31 or name O32)))) selection = (chain 'C' and (resid 119 through 801 or (resid 802 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 (resid 803 and (name N or name C1 or name C11 or name C12 or name C \ 13 or name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or \ name C31 or name C38 or name O11 or name O12 or name O13 or name O14 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: 3.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.420 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.000 ------------------------------------------------------------------------------- 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 : 10.34 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (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 ARG 0.009 0.000 ARG C 188 TYR 0.013 0.001 TYR C 213 PHE 0.022 0.001 PHE A 656 TRP 0.008 0.001 TRP C 380 HIS 0.003 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00324 (21060) covalent geometry : angle 0.74311 (28376) SS BOND : bond 0.00040 ( 3) SS BOND : angle 0.20885 ( 17) hydrogen bonds : bond 0.19678 ( 896) hydrogen bonds : angle 7.05651 ( 2592) *********************** 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 : 0.681 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: 0.1223 time to fit residues: 63.8293 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 : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.4128 r_free = 0.4128 target = 0.190310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.182922 restraints weight = 24277.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.167232 restraints weight = 36883.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.165859 restraints weight = 39771.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.166329 restraints weight = 41722.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.166471 restraints weight = 44952.485| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21063 Z= 0.135 Angle : 0.559 6.639 28393 Z= 0.287 Chirality : 0.038 0.151 3164 Planarity : 0.004 0.039 3468 Dihedral : 11.109 83.812 3220 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.55 % Allowed : 27.54 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.17), residues: 2424 helix: -0.43 (0.13), residues: 1512 sheet: -0.33 (0.57), residues: 56 loop : -2.38 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 716 TYR 0.013 0.001 TYR D 213 PHE 0.019 0.001 PHE D 310 TRP 0.009 0.001 TRP B 559 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00319 (21060) covalent geometry : angle 0.55889 (28376) SS BOND : bond 0.00075 ( 3) SS BOND : angle 0.05984 ( 17) hydrogen bonds : bond 0.04039 ( 896) hydrogen bonds : angle 4.40830 ( 2592) *********************** 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 408 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 331 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 567 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7402 (mtt180) REVERT: A 570 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7154 (tp40) REVERT: A 642 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8352 (tt) REVERT: B 567 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7388 (mtt180) REVERT: B 570 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7123 (tp40) REVERT: B 642 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8370 (tt) REVERT: C 567 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7383 (mtt180) REVERT: C 570 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7095 (tp40) REVERT: C 642 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8392 (tt) REVERT: D 567 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7397 (mtt180) REVERT: D 570 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7102 (tp40) REVERT: D 642 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8375 (tt) outliers start: 77 outliers final: 20 residues processed: 400 average time/residue: 0.1386 time to fit residues: 85.5831 Evaluate side-chains 318 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 286 time to evaluate : 0.719 ------------------------------------------------------------------------------- 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 567 ARG 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 567 ARG 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 567 ARG 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 567 ARG 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 23 optimal weight: 0.2980 chunk 203 optimal weight: 2.9990 chunk 137 optimal weight: 0.4980 chunk 159 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 209 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.188843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.181346 restraints weight = 24350.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.165356 restraints weight = 36366.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.164508 restraints weight = 41522.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.164657 restraints weight = 39548.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.164728 restraints weight = 44221.085| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21063 Z= 0.141 Angle : 0.548 6.048 28393 Z= 0.285 Chirality : 0.039 0.165 3164 Planarity : 0.004 0.045 3468 Dihedral : 11.029 84.673 3220 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.70 % Allowed : 25.78 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.17), residues: 2424 helix: -0.06 (0.14), residues: 1436 sheet: -0.73 (0.50), residues: 56 loop : -2.08 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 188 TYR 0.011 0.002 TYR B 213 PHE 0.016 0.001 PHE C 193 TRP 0.012 0.001 TRP A 493 HIS 0.006 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00334 (21060) covalent geometry : angle 0.54833 (28376) SS BOND : bond 0.00135 ( 3) SS BOND : angle 0.10996 ( 17) hydrogen bonds : bond 0.03712 ( 896) hydrogen bonds : angle 4.17649 ( 2592) *********************** 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 419 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 317 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7684 (tp40) REVERT: B 570 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7679 (tp40) REVERT: C 570 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7706 (tp40) REVERT: D 570 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7692 (tp40) outliers start: 102 outliers final: 53 residues processed: 400 average time/residue: 0.1303 time to fit residues: 82.8131 Evaluate side-chains 349 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 292 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 356 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 570 GLN 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 281 LEU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 570 GLN 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 281 LEU Chi-restraints excluded: chain C residue 285 GLU Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 570 GLN 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 281 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 570 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 117 optimal weight: 0.3980 chunk 84 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 188 optimal weight: 0.2980 chunk 82 optimal weight: 0.9990 chunk 183 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 220 ASN A 242 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 ASN C 220 ASN C 242 ASN C 671 ASN D 182 ASN D 220 ASN D 242 ASN D 671 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.190654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.183265 restraints weight = 24200.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.167107 restraints weight = 33823.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.166262 restraints weight = 34511.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.166047 restraints weight = 41430.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.166117 restraints weight = 36332.336| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21063 Z= 0.111 Angle : 0.524 6.665 28393 Z= 0.268 Chirality : 0.038 0.180 3164 Planarity : 0.003 0.045 3468 Dihedral : 10.750 85.426 3220 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 5.49 % Allowed : 26.06 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.17), residues: 2424 helix: 0.16 (0.14), residues: 1440 sheet: -0.97 (0.47), residues: 56 loop : -2.05 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 188 TYR 0.009 0.001 TYR C 213 PHE 0.016 0.001 PHE C 538 TRP 0.014 0.001 TRP A 493 HIS 0.004 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00260 (21060) covalent geometry : angle 0.52414 (28376) SS BOND : bond 0.00131 ( 3) SS BOND : angle 0.13504 ( 17) hydrogen bonds : bond 0.03233 ( 896) hydrogen bonds : angle 3.89423 ( 2592) *********************** 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 434 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 315 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 672 MET cc_start: 0.7598 (mmm) cc_final: 0.7390 (tpt) outliers start: 119 outliers final: 53 residues processed: 412 average time/residue: 0.1287 time to fit residues: 84.2883 Evaluate side-chains 354 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 301 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASN 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 356 ILE Chi-restraints excluded: chain A residue 420 LEU 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 711 LEU Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 745 HIS 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 420 LEU 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 711 LEU Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 745 HIS 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 420 LEU 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 711 LEU Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 745 HIS Chi-restraints excluded: chain D residue 182 ASN 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 420 LEU 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 711 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 109 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 203 optimal weight: 0.8980 chunk 187 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 220 ASN A 671 ASN B 178 ASN B 182 ASN B 220 ASN B 570 GLN B 671 ASN C 178 ASN C 220 ASN C 570 GLN ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.188282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.180891 restraints weight = 24107.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.165558 restraints weight = 32618.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.164911 restraints weight = 40204.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.165137 restraints weight = 39394.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.165059 restraints weight = 39310.449| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21063 Z= 0.143 Angle : 0.573 8.991 28393 Z= 0.287 Chirality : 0.039 0.191 3164 Planarity : 0.004 0.048 3468 Dihedral : 10.789 85.851 3220 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 4.70 % Allowed : 26.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.17), residues: 2424 helix: 0.05 (0.14), residues: 1460 sheet: -1.18 (0.47), residues: 56 loop : -2.07 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 698 TYR 0.011 0.002 TYR D 213 PHE 0.017 0.001 PHE B 538 TRP 0.017 0.001 TRP B 493 HIS 0.006 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00342 (21060) covalent geometry : angle 0.57280 (28376) SS BOND : bond 0.00144 ( 3) SS BOND : angle 0.09688 ( 17) hydrogen bonds : bond 0.03441 ( 896) hydrogen bonds : angle 3.94709 ( 2592) *********************** 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 441 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 339 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 672 MET cc_start: 0.7531 (mmm) cc_final: 0.7313 (tpt) REVERT: B 574 MET cc_start: 0.5502 (mmm) cc_final: 0.5004 (mmm) REVERT: B 672 MET cc_start: 0.7691 (mmm) cc_final: 0.7399 (tpt) REVERT: C 574 MET cc_start: 0.5419 (mmm) cc_final: 0.4967 (mmm) outliers start: 102 outliers final: 74 residues processed: 421 average time/residue: 0.1174 time to fit residues: 79.6417 Evaluate side-chains 391 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 317 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 356 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 458 VAL 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 B residue 182 ASN 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 356 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 420 LEU 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 356 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 420 LEU 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 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 356 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 458 VAL 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 676 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 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 232 optimal weight: 1.9990 chunk 211 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 114 optimal weight: 0.3980 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 GLN ** 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 570 GLN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.189836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.182588 restraints weight = 24101.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.167578 restraints weight = 34428.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.166885 restraints weight = 38868.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.166875 restraints weight = 38516.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.166834 restraints weight = 36271.126| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2644 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= 0.116 Angle : 0.552 8.436 28393 Z= 0.276 Chirality : 0.039 0.190 3164 Planarity : 0.004 0.048 3468 Dihedral : 10.595 86.266 3220 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 5.40 % Allowed : 26.80 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.17), residues: 2424 helix: 0.01 (0.14), residues: 1492 sheet: -1.23 (0.48), residues: 56 loop : -2.04 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 698 TYR 0.010 0.001 TYR C 213 PHE 0.015 0.001 PHE B 538 TRP 0.018 0.001 TRP D 493 HIS 0.004 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00274 (21060) covalent geometry : angle 0.55217 (28376) SS BOND : bond 0.00147 ( 3) SS BOND : angle 0.12254 ( 17) hydrogen bonds : bond 0.03213 ( 896) hydrogen bonds : angle 3.81707 ( 2592) *********************** 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 450 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 333 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.5450 (mmm) cc_final: 0.4900 (mmm) REVERT: A 672 MET cc_start: 0.7591 (mmm) cc_final: 0.7287 (tpt) REVERT: B 574 MET cc_start: 0.5148 (mmm) cc_final: 0.4899 (mmm) REVERT: B 672 MET cc_start: 0.7599 (mmm) cc_final: 0.7307 (tpt) REVERT: C 574 MET cc_start: 0.5102 (mmm) cc_final: 0.4865 (mmm) REVERT: D 574 MET cc_start: 0.5442 (mmm) cc_final: 0.4884 (mmm) REVERT: D 672 MET cc_start: 0.7632 (mmm) cc_final: 0.7298 (tpt) outliers start: 117 outliers final: 79 residues processed: 424 average time/residue: 0.1213 time to fit residues: 83.6593 Evaluate side-chains 398 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 319 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 356 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 458 VAL 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 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 731 CYS Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 745 HIS 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 356 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 420 LEU 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 669 LEU 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 731 CYS 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 356 ILE Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 420 LEU 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 669 LEU Chi-restraints excluded: chain C residue 670 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 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 356 ILE Chi-restraints excluded: chain D residue 362 SER 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 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 669 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 731 CYS Chi-restraints excluded: chain D residue 732 LEU 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 143 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 36 optimal weight: 0.0000 chunk 115 optimal weight: 0.7980 chunk 159 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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 182 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN D 671 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.191049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.183634 restraints weight = 24031.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.168036 restraints weight = 35355.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.166618 restraints weight = 40678.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.166623 restraints weight = 44664.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.166908 restraints weight = 45401.769| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21063 Z= 0.106 Angle : 0.577 10.006 28393 Z= 0.283 Chirality : 0.039 0.184 3164 Planarity : 0.003 0.046 3468 Dihedral : 10.435 86.616 3220 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 4.20 % Allowed : 28.46 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.17), residues: 2424 helix: 0.21 (0.14), residues: 1468 sheet: -0.92 (0.50), residues: 56 loop : -2.01 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 698 TYR 0.023 0.001 TYR C 540 PHE 0.028 0.001 PHE B 310 TRP 0.016 0.001 TRP D 493 HIS 0.003 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00245 (21060) covalent geometry : angle 0.57709 (28376) SS BOND : bond 0.00146 ( 3) SS BOND : angle 0.12841 ( 17) hydrogen bonds : bond 0.03053 ( 896) hydrogen bonds : angle 3.68315 ( 2592) *********************** 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 437 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 346 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.5336 (mmm) cc_final: 0.4853 (mmm) REVERT: A 672 MET cc_start: 0.7564 (mmm) cc_final: 0.7342 (tpt) REVERT: B 672 MET cc_start: 0.7643 (mmm) cc_final: 0.7389 (tpt) REVERT: D 574 MET cc_start: 0.5187 (mmm) cc_final: 0.4752 (mmm) REVERT: D 672 MET cc_start: 0.7602 (mmm) cc_final: 0.7354 (tpt) outliers start: 91 outliers final: 72 residues processed: 416 average time/residue: 0.1297 time to fit residues: 85.3880 Evaluate side-chains 387 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 315 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 356 ILE Chi-restraints excluded: chain A residue 388 SER 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 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 731 CYS Chi-restraints excluded: chain A residue 745 HIS Chi-restraints excluded: chain B residue 182 ASN 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 356 ILE Chi-restraints excluded: chain B residue 388 SER 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 669 LEU 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 731 CYS 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 356 ILE 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 599 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain C residue 669 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 264 THR Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 458 VAL 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 669 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 731 CYS 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 69 optimal weight: 0.3980 chunk 233 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 570 GLN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.189136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.181271 restraints weight = 24062.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.165491 restraints weight = 37276.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.165627 restraints weight = 44336.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.165580 restraints weight = 42632.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.165776 restraints weight = 40984.483| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21063 Z= 0.129 Angle : 0.616 12.305 28393 Z= 0.300 Chirality : 0.040 0.199 3164 Planarity : 0.004 0.047 3468 Dihedral : 10.515 86.841 3220 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 5.07 % Allowed : 27.58 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.17), residues: 2424 helix: 0.22 (0.14), residues: 1464 sheet: -1.22 (0.50), residues: 56 loop : -2.10 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 188 TYR 0.024 0.001 TYR C 540 PHE 0.027 0.001 PHE C 310 TRP 0.016 0.001 TRP D 493 HIS 0.005 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00307 (21060) covalent geometry : angle 0.61604 (28376) SS BOND : bond 0.00142 ( 3) SS BOND : angle 0.04881 ( 17) hydrogen bonds : bond 0.03218 ( 896) hydrogen bonds : angle 3.75020 ( 2592) *********************** 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 437 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 327 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.5283 (mmm) cc_final: 0.4801 (mmm) REVERT: A 598 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8110 (tt) REVERT: C 598 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8095 (tt) REVERT: C 677 MET cc_start: 0.6258 (mmm) cc_final: 0.5899 (mmt) REVERT: D 574 MET cc_start: 0.5284 (mmm) cc_final: 0.4817 (mmm) outliers start: 110 outliers final: 91 residues processed: 412 average time/residue: 0.1181 time to fit residues: 79.5891 Evaluate side-chains 412 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 319 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 356 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 420 LEU 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 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 731 CYS Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 745 HIS Chi-restraints excluded: chain B residue 182 ASN 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 356 ILE Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 420 LEU 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 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 669 LEU 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 731 CYS Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 740 THR 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 356 ILE 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 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 599 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 649 LYS 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 740 THR 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 356 ILE Chi-restraints excluded: chain D residue 362 SER Chi-restraints excluded: chain D residue 388 SER 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 528 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 599 LEU Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 669 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 731 CYS Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 740 THR 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 142 optimal weight: 0.0980 chunk 57 optimal weight: 0.0470 chunk 211 optimal weight: 3.9990 chunk 237 optimal weight: 7.9990 chunk 205 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 225 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 238 optimal weight: 0.6980 chunk 147 optimal weight: 0.7980 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.191941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.184327 restraints weight = 23920.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.169796 restraints weight = 37031.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.169316 restraints weight = 45614.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.169266 restraints weight = 46885.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.169463 restraints weight = 38456.089| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21063 Z= 0.105 Angle : 0.587 11.543 28393 Z= 0.285 Chirality : 0.039 0.185 3164 Planarity : 0.003 0.046 3468 Dihedral : 10.323 86.674 3220 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.06 % Allowed : 28.64 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.17), residues: 2424 helix: 0.37 (0.14), residues: 1468 sheet: -1.04 (0.51), residues: 56 loop : -2.00 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 188 TYR 0.024 0.001 TYR C 540 PHE 0.021 0.001 PHE D 569 TRP 0.015 0.001 TRP D 493 HIS 0.003 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00240 (21060) covalent geometry : angle 0.58742 (28376) SS BOND : bond 0.00160 ( 3) SS BOND : angle 0.10544 ( 17) hydrogen bonds : bond 0.02914 ( 896) hydrogen bonds : angle 3.57362 ( 2592) *********************** 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 416 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 328 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.5030 (mmm) cc_final: 0.4661 (mmm) REVERT: A 677 MET cc_start: 0.5987 (mmm) cc_final: 0.5689 (mmt) REVERT: B 672 MET cc_start: 0.7442 (mmm) cc_final: 0.7241 (tpt) REVERT: C 598 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8098 (tt) REVERT: C 677 MET cc_start: 0.6264 (mmm) cc_final: 0.5903 (mmt) REVERT: D 574 MET cc_start: 0.5060 (mmm) cc_final: 0.4683 (mmm) REVERT: D 598 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8298 (tt) outliers start: 88 outliers final: 73 residues processed: 398 average time/residue: 0.1220 time to fit residues: 78.8216 Evaluate side-chains 388 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 313 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 278 VAL 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 356 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 599 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 731 CYS Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 745 HIS Chi-restraints excluded: chain B residue 264 THR 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 362 SER Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 598 LEU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 669 LEU 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 731 CYS 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 278 VAL 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 420 LEU 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 599 LEU Chi-restraints excluded: chain C residue 649 LYS 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 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 456 THR Chi-restraints excluded: chain D residue 458 VAL 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 599 LEU Chi-restraints excluded: chain D residue 669 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 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 155 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 75 optimal weight: 0.4980 overall best weight: 1.6988 ------------------------------------------------------------------------------- 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 242 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 = 0.4085 r_free = 0.4085 target = 0.185654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.179000 restraints weight = 24200.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.178346 restraints weight = 38454.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.177536 restraints weight = 46827.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.165811 restraints weight = 43240.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.162351 restraints weight = 47728.356| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 21063 Z= 0.196 Angle : 0.684 11.700 28393 Z= 0.337 Chirality : 0.042 0.221 3164 Planarity : 0.004 0.049 3468 Dihedral : 10.831 87.267 3220 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 4.24 % Allowed : 28.51 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.17), residues: 2424 helix: 0.09 (0.13), residues: 1468 sheet: -1.55 (0.54), residues: 56 loop : -2.12 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 188 TYR 0.025 0.002 TYR C 540 PHE 0.031 0.002 PHE D 569 TRP 0.013 0.001 TRP A 493 HIS 0.008 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00473 (21060) covalent geometry : angle 0.68373 (28376) SS BOND : bond 0.00132 ( 3) SS BOND : angle 0.07051 ( 17) hydrogen bonds : bond 0.03588 ( 896) hydrogen bonds : angle 3.95509 ( 2592) ********************** 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 409 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 317 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 MET cc_start: 0.5434 (mmm) cc_final: 0.4848 (mmm) REVERT: A 598 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8224 (tt) REVERT: A 677 MET cc_start: 0.6331 (mmm) cc_final: 0.5728 (mmt) REVERT: B 672 MET cc_start: 0.7553 (mmm) cc_final: 0.7261 (tpt) REVERT: C 598 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8231 (tt) REVERT: C 677 MET cc_start: 0.6244 (mmm) cc_final: 0.5869 (mmt) REVERT: D 574 MET cc_start: 0.5434 (mmm) cc_final: 0.4890 (mmm) REVERT: D 598 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8244 (tt) outliers start: 92 outliers final: 80 residues processed: 384 average time/residue: 0.1210 time to fit residues: 75.4489 Evaluate side-chains 388 residues out of total 2168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 305 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 VAL 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 356 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 456 THR 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 598 LEU Chi-restraints excluded: chain A residue 599 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 731 CYS Chi-restraints excluded: chain A residue 732 LEU Chi-restraints excluded: chain A residue 745 HIS 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 356 ILE 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 420 LEU Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 528 ILE 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 711 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 278 VAL 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 356 ILE 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 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 599 LEU Chi-restraints excluded: chain C residue 649 LYS 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 278 VAL 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 356 ILE 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 456 THR 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 599 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 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 26 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 84 optimal weight: 0.5980 chunk 186 optimal weight: 7.9990 chunk 138 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 160 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN ** 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 182 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.188773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.181079 restraints weight = 24204.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 79)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.166109 restraints weight = 36482.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.164847 restraints weight = 45446.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.164700 restraints weight = 47996.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.164755 restraints weight = 44659.755| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21063 Z= 0.128 Angle : 0.627 11.472 28393 Z= 0.306 Chirality : 0.040 0.199 3164 Planarity : 0.004 0.048 3468 Dihedral : 10.597 87.664 3220 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 4.15 % Allowed : 28.97 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.17), residues: 2424 helix: 0.24 (0.14), residues: 1444 sheet: -1.64 (0.51), residues: 56 loop : -2.03 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 188 TYR 0.023 0.002 TYR C 540 PHE 0.028 0.001 PHE A 569 TRP 0.017 0.001 TRP A 493 HIS 0.005 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00302 (21060) covalent geometry : angle 0.62692 (28376) SS BOND : bond 0.00173 ( 3) SS BOND : angle 0.09294 ( 17) hydrogen bonds : bond 0.03130 ( 896) hydrogen bonds : angle 3.73549 ( 2592) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3028.44 seconds wall clock time: 53 minutes 24.32 seconds (3204.32 seconds total)