Starting phenix.real_space_refine on Sat Jul 4 20:45:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dxc_30904/07_2026/7dxc_30904.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dxc_30904/07_2026/7dxc_30904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7dxc_30904/07_2026/7dxc_30904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dxc_30904/07_2026/7dxc_30904.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dxc_30904/07_2026/7dxc_30904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dxc_30904/07_2026/7dxc_30904.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7dxc_30904/07_2026/7dxc_30904.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dxc_30904/07_2026/7dxc_30904.cif" } resolution = 3.06 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= 0.012 sd= 0.113 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 4 5.49 5 S 112 5.16 5 C 15080 2.51 5 N 3628 2.21 5 O 4068 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 116 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22896 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5579 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 26, 'TRANS': 675} Chain breaks: 4 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 6, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 5579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5579 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 26, 'TRANS': 675} Chain breaks: 4 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 6, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 5579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5579 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 26, 'TRANS': 675} Chain breaks: 4 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 6, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 5579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5579 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 26, 'TRANS': 675} Chain breaks: 4 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 6, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 145 Unusual residues: {' ZN': 1, '98R': 1, 'POV': 1, 'Y01': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'98R:plan-4': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 145 Unusual residues: {' ZN': 1, '98R': 1, 'POV': 1, 'Y01': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'98R:plan-4': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 145 Unusual residues: {' ZN': 1, '98R': 1, 'POV': 1, 'Y01': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'98R:plan-4': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 145 Unusual residues: {' ZN': 1, '98R': 1, 'POV': 1, 'Y01': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'98R:plan-4': 1} Unresolved non-hydrogen planarities: 4 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1221 SG CYS A 182 99.875 85.306 59.851 1.00242.97 S ATOM 1236 SG CYS A 184 100.674 87.694 57.034 1.00253.14 S ATOM 1254 SG CYS A 187 97.162 86.326 57.318 1.00238.49 S ATOM 6800 SG CYS B 182 85.321 23.431 59.858 1.00242.97 S ATOM 6815 SG CYS B 184 87.710 22.632 57.041 1.00253.14 S ATOM 6833 SG CYS B 187 86.342 26.143 57.325 1.00238.49 S ATOM 12379 SG CYS C 182 37.999 99.860 59.845 1.00242.97 S ATOM 12394 SG CYS C 184 35.611 100.658 57.027 1.00253.14 S ATOM 12412 SG CYS C 187 36.979 97.147 57.312 1.00238.49 S ATOM 17958 SG CYS D 182 23.446 37.984 59.851 1.00242.97 S ATOM 17973 SG CYS D 184 22.647 35.596 57.034 1.00253.14 S ATOM 17991 SG CYS D 187 26.159 36.964 57.319 1.00238.49 S Time building chain proxies: 6.04, per 1000 atoms: 0.26 Number of scatterers: 22896 At special positions: 0 Unit cell: (124.355, 124.355, 148.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 112 16.00 P 4 15.00 O 4068 8.00 N 3628 7.00 C 15080 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 823.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 902 " pdb="ZN ZN A 902 " - pdb=" ND1 HIS A 178 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 184 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 187 " pdb="ZN ZN A 902 " - pdb=" SG CYS A 182 " pdb=" ZN B 903 " pdb="ZN ZN B 903 " - pdb=" ND1 HIS B 178 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 184 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 187 " pdb="ZN ZN B 903 " - pdb=" SG CYS B 182 " pdb=" ZN C 902 " pdb="ZN ZN C 902 " - pdb=" ND1 HIS C 178 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 184 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 187 " pdb="ZN ZN C 902 " - pdb=" SG CYS C 182 " pdb=" ZN D 903 " pdb="ZN ZN D 903 " - pdb=" ND1 HIS D 178 " pdb="ZN ZN D 903 " - pdb=" SG CYS D 184 " pdb="ZN ZN D 903 " - pdb=" SG CYS D 187 " pdb="ZN ZN D 903 " - pdb=" SG CYS D 182 " Number of angles added : 12 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5376 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 0 sheets defined 75.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 25 through 37 Processing helix chain 'A' and resid 39 through 48 Processing helix chain 'A' and resid 64 through 72 Processing helix chain 'A' and resid 74 through 84 removed outlier: 3.888A pdb=" N LYS A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 100 Processing helix chain 'A' and resid 102 through 111 Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 150 through 159 Processing helix chain 'A' and resid 160 through 170 Processing helix chain 'A' and resid 184 through 193 removed outlier: 3.984A pdb=" N HIS A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 210 Processing helix chain 'A' and resid 211 through 219 removed outlier: 4.466A pdb=" N SER A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 241 removed outlier: 3.604A pdb=" N LYS A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 264 Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 311 through 323 removed outlier: 3.528A pdb=" N GLN A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN A 317 " --> pdb=" O ASN A 313 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 318 " --> pdb=" O CYS A 314 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 320 " --> pdb=" O GLN A 316 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 321 " --> pdb=" O GLN A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 347 Processing helix chain 'A' and resid 347 through 354 removed outlier: 3.735A pdb=" N GLY A 354 " --> pdb=" O PHE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 368 removed outlier: 3.815A pdb=" N ILE A 366 " --> pdb=" O ARG A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 392 Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.818A pdb=" N LYS A 418 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 448 Processing helix chain 'A' and resid 448 through 455 removed outlier: 3.616A pdb=" N LEU A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 492 removed outlier: 3.542A pdb=" N ALA A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP A 490 " --> pdb=" O GLN A 486 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 491 " --> pdb=" O GLN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 510 removed outlier: 4.210A pdb=" N PHE A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 538 removed outlier: 3.562A pdb=" N PHE A 538 " --> pdb=" O VAL A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 544 Processing helix chain 'A' and resid 551 through 588 removed outlier: 3.556A pdb=" N ILE A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 558 " --> pdb=" O LEU A 554 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 564 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS A 567 " --> pdb=" O LYS A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 614 removed outlier: 3.752A pdb=" N ILE A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE A 614 " --> pdb=" O PHE A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 623 removed outlier: 4.096A pdb=" N VAL A 622 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 623 " --> pdb=" O THR A 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 619 through 623' Processing helix chain 'A' and resid 628 through 662 removed outlier: 4.105A pdb=" N TYR A 662 " --> pdb=" O ILE A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 686 removed outlier: 3.570A pdb=" N TRP A 673 " --> pdb=" O SER A 669 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR A 684 " --> pdb=" O LEU A 680 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 685 " --> pdb=" O TRP A 681 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP A 686 " --> pdb=" O LEU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 696 Processing helix chain 'A' and resid 761 through 785 removed outlier: 3.677A pdb=" N GLN A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 766 " --> pdb=" O ARG A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 802 Processing helix chain 'B' and resid 25 through 37 Processing helix chain 'B' and resid 39 through 48 Processing helix chain 'B' and resid 64 through 72 Processing helix chain 'B' and resid 74 through 84 removed outlier: 3.888A pdb=" N LYS B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 100 Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 112 through 117 Processing helix chain 'B' and resid 150 through 159 Processing helix chain 'B' and resid 160 through 170 Processing helix chain 'B' and resid 184 through 193 removed outlier: 3.983A pdb=" N HIS B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 210 Processing helix chain 'B' and resid 211 through 219 removed outlier: 4.466A pdb=" N SER B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 241 removed outlier: 3.604A pdb=" N LYS B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 264 Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 311 through 323 removed outlier: 3.528A pdb=" N GLN B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLN B 317 " --> pdb=" O ASN B 313 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 318 " --> pdb=" O CYS B 314 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR B 320 " --> pdb=" O GLN B 316 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 321 " --> pdb=" O GLN B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 347 Processing helix chain 'B' and resid 347 through 354 removed outlier: 3.734A pdb=" N GLY B 354 " --> pdb=" O PHE B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 368 removed outlier: 3.815A pdb=" N ILE B 366 " --> pdb=" O ARG B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 392 Processing helix chain 'B' and resid 414 through 421 removed outlier: 3.819A pdb=" N LYS B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 448 Processing helix chain 'B' and resid 448 through 455 removed outlier: 3.615A pdb=" N LEU B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 492 removed outlier: 3.541A pdb=" N ALA B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP B 490 " --> pdb=" O GLN B 486 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 491 " --> pdb=" O GLN B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 510 removed outlier: 4.210A pdb=" N PHE B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 538 removed outlier: 3.562A pdb=" N PHE B 538 " --> pdb=" O VAL B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 551 through 588 removed outlier: 3.556A pdb=" N ILE B 556 " --> pdb=" O GLY B 552 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 558 " --> pdb=" O LEU B 554 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP B 564 " --> pdb=" O ARG B 560 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS B 567 " --> pdb=" O LYS B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.751A pdb=" N ILE B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE B 614 " --> pdb=" O PHE B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 623 removed outlier: 4.096A pdb=" N VAL B 622 " --> pdb=" O VAL B 619 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL B 623 " --> pdb=" O THR B 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 619 through 623' Processing helix chain 'B' and resid 628 through 662 removed outlier: 4.105A pdb=" N TYR B 662 " --> pdb=" O ILE B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 686 removed outlier: 3.571A pdb=" N TRP B 673 " --> pdb=" O SER B 669 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR B 684 " --> pdb=" O LEU B 680 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE B 685 " --> pdb=" O TRP B 681 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP B 686 " --> pdb=" O LEU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 696 Processing helix chain 'B' and resid 761 through 785 removed outlier: 3.677A pdb=" N GLN B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 766 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 802 Processing helix chain 'C' and resid 25 through 37 Processing helix chain 'C' and resid 39 through 48 Processing helix chain 'C' and resid 64 through 72 Processing helix chain 'C' and resid 74 through 84 removed outlier: 3.888A pdb=" N LYS C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 100 Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 150 through 159 Processing helix chain 'C' and resid 160 through 170 Processing helix chain 'C' and resid 184 through 193 removed outlier: 3.983A pdb=" N HIS C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 210 Processing helix chain 'C' and resid 211 through 219 removed outlier: 4.466A pdb=" N SER C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 241 removed outlier: 3.604A pdb=" N LYS C 241 " --> pdb=" O ALA C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 264 Processing helix chain 'C' and resid 267 through 276 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 305 through 310 Processing helix chain 'C' and resid 311 through 323 removed outlier: 3.528A pdb=" N GLN C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN C 317 " --> pdb=" O ASN C 313 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 318 " --> pdb=" O CYS C 314 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR C 320 " --> pdb=" O GLN C 316 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE C 321 " --> pdb=" O GLN C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 347 Processing helix chain 'C' and resid 347 through 354 removed outlier: 3.735A pdb=" N GLY C 354 " --> pdb=" O PHE C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 368 removed outlier: 3.816A pdb=" N ILE C 366 " --> pdb=" O ARG C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 392 Processing helix chain 'C' and resid 414 through 421 removed outlier: 3.819A pdb=" N LYS C 418 " --> pdb=" O ILE C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 448 Processing helix chain 'C' and resid 448 through 455 removed outlier: 3.616A pdb=" N LEU C 454 " --> pdb=" O ARG C 450 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 492 removed outlier: 3.542A pdb=" N ALA C 474 " --> pdb=" O ALA C 470 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 490 " --> pdb=" O GLN C 486 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 491 " --> pdb=" O GLN C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 510 removed outlier: 4.210A pdb=" N PHE C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 538 removed outlier: 3.562A pdb=" N PHE C 538 " --> pdb=" O VAL C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 544 Processing helix chain 'C' and resid 551 through 588 removed outlier: 3.557A pdb=" N ILE C 556 " --> pdb=" O GLY C 552 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 558 " --> pdb=" O LEU C 554 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP C 564 " --> pdb=" O ARG C 560 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS C 567 " --> pdb=" O LYS C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 614 removed outlier: 3.752A pdb=" N ILE C 613 " --> pdb=" O LEU C 609 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE C 614 " --> pdb=" O PHE C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 623 removed outlier: 4.097A pdb=" N VAL C 622 " --> pdb=" O VAL C 619 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 623 " --> pdb=" O THR C 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 619 through 623' Processing helix chain 'C' and resid 628 through 662 removed outlier: 4.105A pdb=" N TYR C 662 " --> pdb=" O ILE C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 668 through 686 removed outlier: 3.570A pdb=" N TRP C 673 " --> pdb=" O SER C 669 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR C 684 " --> pdb=" O LEU C 680 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 685 " --> pdb=" O TRP C 681 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP C 686 " --> pdb=" O LEU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 696 Processing helix chain 'C' and resid 761 through 785 removed outlier: 3.678A pdb=" N GLN C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C 766 " --> pdb=" O ARG C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 786 through 802 Processing helix chain 'D' and resid 25 through 37 Processing helix chain 'D' and resid 39 through 48 Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 74 through 84 removed outlier: 3.888A pdb=" N LYS D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 100 Processing helix chain 'D' and resid 102 through 111 Processing helix chain 'D' and resid 112 through 117 Processing helix chain 'D' and resid 150 through 159 Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 184 through 193 removed outlier: 3.984A pdb=" N HIS D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 210 Processing helix chain 'D' and resid 211 through 219 removed outlier: 4.467A pdb=" N SER D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 241 removed outlier: 3.604A pdb=" N LYS D 241 " --> pdb=" O ALA D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 264 Processing helix chain 'D' and resid 267 through 276 Processing helix chain 'D' and resid 294 through 303 Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 311 through 323 removed outlier: 3.528A pdb=" N GLN D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN D 317 " --> pdb=" O ASN D 313 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 318 " --> pdb=" O CYS D 314 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR D 320 " --> pdb=" O GLN D 316 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 321 " --> pdb=" O GLN D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 347 Processing helix chain 'D' and resid 347 through 354 removed outlier: 3.735A pdb=" N GLY D 354 " --> pdb=" O PHE D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 368 removed outlier: 3.815A pdb=" N ILE D 366 " --> pdb=" O ARG D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 392 Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.818A pdb=" N LYS D 418 " --> pdb=" O ILE D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 448 Processing helix chain 'D' and resid 448 through 455 removed outlier: 3.616A pdb=" N LEU D 454 " --> pdb=" O ARG D 450 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN D 455 " --> pdb=" O GLU D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 492 removed outlier: 3.543A pdb=" N ALA D 474 " --> pdb=" O ALA D 470 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP D 490 " --> pdb=" O GLN D 486 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER D 491 " --> pdb=" O GLN D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 510 removed outlier: 4.210A pdb=" N PHE D 510 " --> pdb=" O GLU D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 538 removed outlier: 3.562A pdb=" N PHE D 538 " --> pdb=" O VAL D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 544 Processing helix chain 'D' and resid 551 through 588 removed outlier: 3.557A pdb=" N ILE D 556 " --> pdb=" O GLY D 552 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 558 " --> pdb=" O LEU D 554 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP D 564 " --> pdb=" O ARG D 560 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS D 567 " --> pdb=" O LYS D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 removed outlier: 3.752A pdb=" N ILE D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE D 614 " --> pdb=" O PHE D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 623 removed outlier: 4.096A pdb=" N VAL D 622 " --> pdb=" O VAL D 619 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL D 623 " --> pdb=" O THR D 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 619 through 623' Processing helix chain 'D' and resid 628 through 662 removed outlier: 4.104A pdb=" N TYR D 662 " --> pdb=" O ILE D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 686 removed outlier: 3.571A pdb=" N TRP D 673 " --> pdb=" O SER D 669 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR D 684 " --> pdb=" O LEU D 680 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE D 685 " --> pdb=" O TRP D 681 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP D 686 " --> pdb=" O LEU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 696 Processing helix chain 'D' and resid 761 through 785 removed outlier: 3.678A pdb=" N GLN D 765 " --> pdb=" O THR D 761 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE D 766 " --> pdb=" O ARG D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 802 1416 hydrogen bonds defined for protein. 4188 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: 2.91 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4958 1.33 - 1.45: 4996 1.45 - 1.57: 13266 1.57 - 1.69: 8 1.69 - 1.81: 184 Bond restraints: 23412 Sorted by residual: bond pdb=" CAY Y01 B 904 " pdb=" OAW Y01 B 904 " ideal model delta sigma weight residual 1.332 1.459 -0.127 2.00e-02 2.50e+03 4.00e+01 bond pdb=" CAY Y01 D 904 " pdb=" OAW Y01 D 904 " ideal model delta sigma weight residual 1.332 1.458 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" CAY Y01 A 903 " pdb=" OAW Y01 A 903 " ideal model delta sigma weight residual 1.332 1.458 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" CAY Y01 C 903 " pdb=" OAW Y01 C 903 " ideal model delta sigma weight residual 1.332 1.458 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C21 POV A 905 " pdb=" O21 POV A 905 " ideal model delta sigma weight residual 1.330 1.455 -0.125 2.00e-02 2.50e+03 3.92e+01 ... (remaining 23407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 31058 1.99 - 3.98: 442 3.98 - 5.96: 145 5.96 - 7.95: 38 7.95 - 9.94: 29 Bond angle restraints: 31712 Sorted by residual: angle pdb=" C32 98R D 905 " pdb=" C31 98R D 905 " pdb=" O2 98R D 905 " ideal model delta sigma weight residual 110.89 120.83 -9.94 3.00e+00 1.11e-01 1.10e+01 angle pdb=" C32 98R C 904 " pdb=" C31 98R C 904 " pdb=" O2 98R C 904 " ideal model delta sigma weight residual 110.89 120.80 -9.91 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C32 98R A 904 " pdb=" C31 98R A 904 " pdb=" O2 98R A 904 " ideal model delta sigma weight residual 110.89 120.79 -9.90 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C32 98R B 905 " pdb=" C31 98R B 905 " pdb=" O2 98R B 905 " ideal model delta sigma weight residual 110.89 120.79 -9.90 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C12 98R D 905 " pdb=" C11 98R D 905 " pdb=" O3 98R D 905 " ideal model delta sigma weight residual 111.15 120.45 -9.30 3.00e+00 1.11e-01 9.61e+00 ... (remaining 31707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.56: 13520 28.56 - 57.12: 352 57.12 - 85.67: 60 85.67 - 114.23: 24 114.23 - 142.79: 16 Dihedral angle restraints: 13972 sinusoidal: 5680 harmonic: 8292 Sorted by residual: dihedral pdb=" CA THR B 761 " pdb=" C THR B 761 " pdb=" N ARG B 762 " pdb=" CA ARG B 762 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA THR D 761 " pdb=" C THR D 761 " pdb=" N ARG D 762 " pdb=" CA ARG D 762 " ideal model delta harmonic sigma weight residual 180.00 154.62 25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA THR A 761 " pdb=" C THR A 761 " pdb=" N ARG A 762 " pdb=" CA ARG A 762 " ideal model delta harmonic sigma weight residual 180.00 154.64 25.36 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 13969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3076 0.054 - 0.109: 492 0.109 - 0.163: 26 0.163 - 0.218: 6 0.218 - 0.272: 12 Chirality restraints: 3612 Sorted by residual: chirality pdb=" C2 98R A 904 " pdb=" C1 98R A 904 " pdb=" C3 98R A 904 " pdb=" O2 98R A 904 " both_signs ideal model delta sigma weight residual False -2.31 -2.59 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C2 98R B 905 " pdb=" C1 98R B 905 " pdb=" C3 98R B 905 " pdb=" O2 98R B 905 " both_signs ideal model delta sigma weight residual False -2.31 -2.59 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C2 98R D 905 " pdb=" C1 98R D 905 " pdb=" C3 98R D 905 " pdb=" O2 98R D 905 " both_signs ideal model delta sigma weight residual False -2.31 -2.59 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 3609 not shown) Planarity restraints: 3900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 545 " 0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO D 546 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 546 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 546 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 545 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO B 546 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 546 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 546 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 545 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.82e+00 pdb=" N PRO C 546 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 546 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 546 " -0.028 5.00e-02 4.00e+02 ... (remaining 3897 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 168 2.67 - 3.23: 22678 3.23 - 3.78: 34945 3.78 - 4.34: 47733 4.34 - 4.90: 77814 Nonbonded interactions: 183338 Sorted by model distance: nonbonded pdb=" O PRO B 760 " pdb=" OG1 THR B 761 " model vdw 2.110 3.040 nonbonded pdb=" O PRO C 760 " pdb=" OG1 THR C 761 " model vdw 2.110 3.040 nonbonded pdb=" O PRO A 760 " pdb=" OG1 THR A 761 " model vdw 2.110 3.040 nonbonded pdb=" O PRO D 760 " pdb=" OG1 THR D 761 " model vdw 2.110 3.040 nonbonded pdb=" O TYR B 639 " pdb=" ND2 ASN B 643 " model vdw 2.352 3.120 ... (remaining 183333 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 22 through 802) selection = (chain 'B' and resid 22 through 802) selection = (chain 'C' and resid 22 through 802) selection = (chain 'D' and resid 22 through 802) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.910 Find NCS groups from input model: 0.590 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5981 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 : 0.005 0.127 23428 Z= 0.253 Angle : 0.706 9.940 31724 Z= 0.310 Chirality : 0.040 0.272 3612 Planarity : 0.004 0.049 3900 Dihedral : 15.368 142.787 8596 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.53 % Favored : 97.33 % Rotamer: Outliers : 4.88 % Allowed : 6.73 % Favored : 88.38 % 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 are not related in a simple way. whole: 0.98 (0.15), residues: 2768 helix: 1.23 (0.11), residues: 1940 sheet: None (None), residues: 0 loop : -0.64 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 248 TYR 0.010 0.001 TYR B 410 PHE 0.007 0.001 PHE B 614 TRP 0.011 0.001 TRP D 432 HIS 0.003 0.001 HIS D 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.25 (23412) covalent geometry : angle 0.70442 / 0.31 (31712) hydrogen bonds : bond 0.22805 / 15.73 ( 1416) hydrogen bonds : angle 5.83172 / 4.20 ( 4188) metal coordination : bond 0.01190 / 0.82 ( 16) metal coordination : angle 2.51662 / 1.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 472 time to evaluate : 0.599 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: A 24 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6966 (mt) REVERT: A 37 TYR cc_start: 0.6741 (m-80) cc_final: 0.6504 (m-10) REVERT: A 194 ASP cc_start: 0.6827 (OUTLIER) cc_final: 0.5877 (t70) REVERT: A 232 GLU cc_start: 0.6937 (tt0) cc_final: 0.6405 (tt0) REVERT: A 252 MET cc_start: 0.6502 (mmm) cc_final: 0.6097 (mmt) REVERT: A 304 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7308 (mt-10) REVERT: A 515 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6570 (m-30) REVERT: A 627 ASP cc_start: 0.6488 (t0) cc_final: 0.5875 (t0) REVERT: A 672 GLU cc_start: 0.7710 (tt0) cc_final: 0.7434 (tp30) REVERT: B 24 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7006 (mt) REVERT: B 37 TYR cc_start: 0.6736 (m-80) cc_final: 0.6483 (m-80) REVERT: B 194 ASP cc_start: 0.6843 (OUTLIER) cc_final: 0.5906 (t70) REVERT: B 252 MET cc_start: 0.6538 (mmm) cc_final: 0.6131 (mmt) REVERT: B 304 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7313 (mt-10) REVERT: B 515 ASP cc_start: 0.7036 (OUTLIER) cc_final: 0.6646 (m-30) REVERT: B 626 TYR cc_start: 0.6698 (m-10) cc_final: 0.6414 (m-10) REVERT: B 627 ASP cc_start: 0.6487 (t0) cc_final: 0.5888 (t0) REVERT: B 672 GLU cc_start: 0.7708 (tt0) cc_final: 0.7429 (tp30) REVERT: C 24 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7041 (mt) REVERT: C 37 TYR cc_start: 0.6846 (m-80) cc_final: 0.6598 (m-10) REVERT: C 194 ASP cc_start: 0.6835 (OUTLIER) cc_final: 0.5872 (t70) REVERT: C 252 MET cc_start: 0.6509 (mmm) cc_final: 0.6125 (mmt) REVERT: C 304 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7297 (mt-10) REVERT: C 515 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6726 (m-30) REVERT: C 627 ASP cc_start: 0.6574 (t0) cc_final: 0.5966 (t0) REVERT: C 672 GLU cc_start: 0.7742 (tt0) cc_final: 0.7460 (tp30) REVERT: D 24 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7022 (mt) REVERT: D 37 TYR cc_start: 0.6611 (m-80) cc_final: 0.6362 (m-80) REVERT: D 194 ASP cc_start: 0.6850 (OUTLIER) cc_final: 0.5899 (t70) REVERT: D 252 MET cc_start: 0.6566 (mmm) cc_final: 0.6168 (mmt) REVERT: D 304 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7310 (mt-10) REVERT: D 515 ASP cc_start: 0.7044 (OUTLIER) cc_final: 0.6641 (m-30) REVERT: D 626 TYR cc_start: 0.6702 (m-10) cc_final: 0.6428 (m-10) REVERT: D 627 ASP cc_start: 0.6487 (t0) cc_final: 0.5888 (t0) REVERT: D 672 GLU cc_start: 0.7749 (tt0) cc_final: 0.7473 (tp30) outliers start: 116 outliers final: 28 residues processed: 568 average time/residue: 0.1456 time to fit residues: 128.2404 Evaluate side-chains 312 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 272 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 59 ASP Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 515 ASP Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 59 ASP Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 59 ASP Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 468 PHE Chi-restraints excluded: chain D residue 489 VAL Chi-restraints excluded: chain D residue 515 ASP Chi-restraints excluded: chain D residue 558 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 HIS A 487 GLN A 633 ASN B 157 HIS B 487 GLN B 633 ASN C 157 HIS C 198 HIS C 487 GLN C 633 ASN D 157 HIS D 198 HIS D 487 GLN D 633 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.139957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.100844 restraints weight = 32236.210| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.79 r_work: 0.3191 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23428 Z= 0.152 Angle : 0.618 7.621 31724 Z= 0.313 Chirality : 0.040 0.217 3612 Planarity : 0.004 0.043 3900 Dihedral : 13.699 118.562 3452 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.60 % Favored : 97.25 % Rotamer: Outliers : 3.20 % Allowed : 12.37 % Favored : 84.43 % 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 are not related in a simple way. whole: 1.70 (0.15), residues: 2768 helix: 1.93 (0.11), residues: 1948 sheet: None (None), residues: 0 loop : -0.84 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 395 TYR 0.013 0.001 TYR A 636 PHE 0.013 0.002 PHE D 551 TRP 0.014 0.002 TRP D 432 HIS 0.002 0.001 HIS D 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (23412) covalent geometry : angle 0.61721 / 0.31 (31712) hydrogen bonds : bond 0.06014 / 4.07 ( 1416) hydrogen bonds : angle 3.94529 / 2.84 ( 4188) metal coordination : bond 0.00546 / 0.37 ( 16) metal coordination : angle 1.93254 / 1.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 294 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7327 (mt) REVERT: A 37 TYR cc_start: 0.7255 (m-80) cc_final: 0.6995 (m-80) REVERT: A 79 GLU cc_start: 0.8770 (tt0) cc_final: 0.8556 (tm-30) REVERT: A 169 MET cc_start: 0.8712 (mmt) cc_final: 0.8494 (mmm) REVERT: A 194 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.6979 (t0) REVERT: A 232 GLU cc_start: 0.8037 (tt0) cc_final: 0.7449 (tt0) REVERT: A 252 MET cc_start: 0.7704 (mmm) cc_final: 0.7203 (mmt) REVERT: A 304 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7929 (mt-10) REVERT: A 372 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8312 (mmm) REVERT: A 459 VAL cc_start: 0.7997 (t) cc_final: 0.7736 (m) REVERT: A 548 ASN cc_start: 0.8791 (t0) cc_final: 0.8344 (t0) REVERT: A 672 GLU cc_start: 0.7930 (tt0) cc_final: 0.7688 (tp30) REVERT: A 768 LYS cc_start: 0.8197 (ttmt) cc_final: 0.7337 (tptt) REVERT: B 24 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7376 (mt) REVERT: B 37 TYR cc_start: 0.7157 (m-80) cc_final: 0.6867 (m-80) REVERT: B 194 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7034 (t0) REVERT: B 232 GLU cc_start: 0.8047 (tt0) cc_final: 0.7463 (tt0) REVERT: B 252 MET cc_start: 0.7708 (mmm) cc_final: 0.7195 (mmt) REVERT: B 304 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7940 (mt-10) REVERT: B 372 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8389 (mmm) REVERT: B 459 VAL cc_start: 0.7993 (t) cc_final: 0.7735 (m) REVERT: B 548 ASN cc_start: 0.8795 (t0) cc_final: 0.8364 (t0) REVERT: B 627 ASP cc_start: 0.7791 (t0) cc_final: 0.7279 (t0) REVERT: B 672 GLU cc_start: 0.7928 (tt0) cc_final: 0.7681 (tp30) REVERT: B 768 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7323 (tptt) REVERT: C 24 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7374 (mt) REVERT: C 37 TYR cc_start: 0.7255 (m-80) cc_final: 0.6999 (m-80) REVERT: C 79 GLU cc_start: 0.8778 (tt0) cc_final: 0.8574 (tm-30) REVERT: C 120 ARG cc_start: 0.7247 (tpp-160) cc_final: 0.6952 (mtt180) REVERT: C 169 MET cc_start: 0.8680 (mmt) cc_final: 0.8439 (mmm) REVERT: C 232 GLU cc_start: 0.8031 (tt0) cc_final: 0.7448 (tt0) REVERT: C 252 MET cc_start: 0.7679 (mmm) cc_final: 0.7174 (mmt) REVERT: C 304 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7946 (mt-10) REVERT: C 459 VAL cc_start: 0.7988 (t) cc_final: 0.7720 (m) REVERT: C 515 ASP cc_start: 0.7293 (m-30) cc_final: 0.7092 (m-30) REVERT: C 548 ASN cc_start: 0.8795 (t0) cc_final: 0.8366 (t0) REVERT: C 672 GLU cc_start: 0.7931 (tt0) cc_final: 0.7700 (tp30) REVERT: C 768 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7352 (tptt) REVERT: D 24 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7390 (mt) REVERT: D 37 TYR cc_start: 0.7257 (m-80) cc_final: 0.6946 (m-80) REVERT: D 120 ARG cc_start: 0.7155 (tpp-160) cc_final: 0.6836 (mtt180) REVERT: D 194 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.6949 (t0) REVERT: D 232 GLU cc_start: 0.8037 (tt0) cc_final: 0.7458 (tt0) REVERT: D 252 MET cc_start: 0.7681 (mmm) cc_final: 0.7162 (mmt) REVERT: D 304 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7922 (mt-10) REVERT: D 459 VAL cc_start: 0.7979 (t) cc_final: 0.7715 (m) REVERT: D 548 ASN cc_start: 0.8807 (t0) cc_final: 0.8372 (t0) REVERT: D 627 ASP cc_start: 0.7789 (t0) cc_final: 0.7274 (t0) REVERT: D 672 GLU cc_start: 0.7936 (tt0) cc_final: 0.7692 (tp30) REVERT: D 768 LYS cc_start: 0.8217 (ttmt) cc_final: 0.7338 (tptt) outliers start: 76 outliers final: 36 residues processed: 352 average time/residue: 0.1362 time to fit residues: 76.9366 Evaluate side-chains 273 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 228 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 468 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 761 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 119 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 140 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 246 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 HIS B 165 HIS B 198 HIS C 779 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.137744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.097739 restraints weight = 32124.065| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.80 r_work: 0.3139 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23428 Z= 0.136 Angle : 0.559 8.479 31724 Z= 0.282 Chirality : 0.038 0.216 3612 Planarity : 0.004 0.036 3900 Dihedral : 11.723 112.454 3430 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.71 % Favored : 97.15 % Rotamer: Outliers : 3.41 % Allowed : 12.63 % Favored : 83.96 % 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 are not related in a simple way. whole: 2.00 (0.16), residues: 2768 helix: 2.08 (0.11), residues: 1964 sheet: None (None), residues: 0 loop : -0.57 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 330 TYR 0.010 0.001 TYR A 410 PHE 0.014 0.001 PHE D 579 TRP 0.012 0.001 TRP A 432 HIS 0.002 0.000 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (23412) covalent geometry : angle 0.55839 / 0.28 (31712) hydrogen bonds : bond 0.05148 / 3.48 ( 1416) hydrogen bonds : angle 3.60450 / 2.61 ( 4188) metal coordination : bond 0.00317 / 0.21 ( 16) metal coordination : angle 1.39320 / 0.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 250 time to evaluate : 0.856 Fit side-chains REVERT: A 24 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7420 (mp) REVERT: A 37 TYR cc_start: 0.7212 (m-80) cc_final: 0.6926 (m-80) REVERT: A 120 ARG cc_start: 0.7137 (tpp-160) cc_final: 0.6662 (mtt180) REVERT: A 188 MET cc_start: 0.8078 (tpt) cc_final: 0.7874 (tpt) REVERT: A 232 GLU cc_start: 0.8020 (tt0) cc_final: 0.7493 (tt0) REVERT: A 252 MET cc_start: 0.7670 (mmm) cc_final: 0.7153 (mmt) REVERT: A 304 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8006 (mt-10) REVERT: A 372 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8423 (mmm) REVERT: A 459 VAL cc_start: 0.8006 (t) cc_final: 0.7786 (m) REVERT: A 465 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6900 (mm) REVERT: A 583 MET cc_start: 0.8822 (tpp) cc_final: 0.8548 (mmt) REVERT: A 672 GLU cc_start: 0.7976 (tt0) cc_final: 0.7697 (tp30) REVERT: B 24 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7428 (mp) REVERT: B 37 TYR cc_start: 0.7194 (m-80) cc_final: 0.6903 (m-80) REVERT: B 120 ARG cc_start: 0.7093 (tpp-160) cc_final: 0.6748 (mtt-85) REVERT: B 194 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.6941 (t0) REVERT: B 232 GLU cc_start: 0.8031 (tt0) cc_final: 0.7512 (tt0) REVERT: B 252 MET cc_start: 0.7674 (mmm) cc_final: 0.7142 (mmt) REVERT: B 304 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8012 (mt-10) REVERT: B 459 VAL cc_start: 0.7945 (t) cc_final: 0.7711 (m) REVERT: B 465 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6895 (mm) REVERT: B 583 MET cc_start: 0.8816 (tpp) cc_final: 0.8543 (mmt) REVERT: B 672 GLU cc_start: 0.7992 (tt0) cc_final: 0.7705 (tp30) REVERT: B 768 LYS cc_start: 0.8181 (ttmt) cc_final: 0.7342 (tptt) REVERT: C 24 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7416 (mp) REVERT: C 37 TYR cc_start: 0.7204 (m-80) cc_final: 0.6921 (m-80) REVERT: C 120 ARG cc_start: 0.7126 (tpp-160) cc_final: 0.6644 (mtt180) REVERT: C 232 GLU cc_start: 0.8055 (tt0) cc_final: 0.7524 (tt0) REVERT: C 252 MET cc_start: 0.7708 (mmm) cc_final: 0.7182 (mmt) REVERT: C 304 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8020 (mt-10) REVERT: C 459 VAL cc_start: 0.7947 (t) cc_final: 0.7708 (m) REVERT: C 465 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6885 (mm) REVERT: C 583 MET cc_start: 0.8822 (tpp) cc_final: 0.8545 (mmt) REVERT: C 672 GLU cc_start: 0.7968 (tt0) cc_final: 0.7728 (tp30) REVERT: C 768 LYS cc_start: 0.8266 (ttmt) cc_final: 0.7393 (tptt) REVERT: C 784 ASN cc_start: 0.7181 (t0) cc_final: 0.6745 (m-40) REVERT: D 24 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7428 (mp) REVERT: D 37 TYR cc_start: 0.7187 (m-80) cc_final: 0.6899 (m-80) REVERT: D 92 ASP cc_start: 0.7389 (t0) cc_final: 0.7162 (t0) REVERT: D 120 ARG cc_start: 0.7094 (tpp-160) cc_final: 0.6617 (mtt180) REVERT: D 232 GLU cc_start: 0.8026 (tt0) cc_final: 0.7496 (tt0) REVERT: D 252 MET cc_start: 0.7709 (mmm) cc_final: 0.7181 (mmt) REVERT: D 304 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8003 (mt-10) REVERT: D 459 VAL cc_start: 0.7943 (t) cc_final: 0.7706 (m) REVERT: D 465 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6878 (mm) REVERT: D 583 MET cc_start: 0.8818 (tpp) cc_final: 0.8547 (mmt) REVERT: D 672 GLU cc_start: 0.7949 (tt0) cc_final: 0.7692 (tp30) REVERT: D 784 ASN cc_start: 0.7194 (t0) cc_final: 0.6741 (m-40) outliers start: 81 outliers final: 42 residues processed: 318 average time/residue: 0.1267 time to fit residues: 65.6051 Evaluate side-chains 282 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 230 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 468 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 792 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 170 optimal weight: 0.8980 chunk 236 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 251 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 258 optimal weight: 0.6980 chunk 262 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 779 GLN B 779 GLN C 494 GLN D 494 GLN D 779 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.134539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.095485 restraints weight = 31687.111| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.76 r_work: 0.3112 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 23428 Z= 0.126 Angle : 0.529 9.053 31724 Z= 0.267 Chirality : 0.037 0.238 3612 Planarity : 0.003 0.027 3900 Dihedral : 10.802 113.776 3426 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.75 % Favored : 97.11 % Rotamer: Outliers : 3.75 % Allowed : 12.42 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.16), residues: 2768 helix: 2.20 (0.11), residues: 1980 sheet: None (None), residues: 0 loop : -0.69 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 330 TYR 0.010 0.001 TYR B 636 PHE 0.017 0.001 PHE B 568 TRP 0.012 0.001 TRP B 432 HIS 0.003 0.000 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (23412) covalent geometry : angle 0.52817 / 0.27 (31712) hydrogen bonds : bond 0.04645 / 3.13 ( 1416) hydrogen bonds : angle 3.40729 / 2.46 ( 4188) metal coordination : bond 0.00280 / 0.18 ( 16) metal coordination : angle 1.22416 / 0.70 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 259 time to evaluate : 0.728 Fit side-chains REVERT: A 24 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7487 (mp) REVERT: A 37 TYR cc_start: 0.7185 (m-80) cc_final: 0.6896 (m-80) REVERT: A 92 ASP cc_start: 0.7416 (t0) cc_final: 0.7188 (t0) REVERT: A 120 ARG cc_start: 0.7240 (tpp-160) cc_final: 0.6897 (mtt-85) REVERT: A 232 GLU cc_start: 0.8048 (tt0) cc_final: 0.7535 (tt0) REVERT: A 252 MET cc_start: 0.7762 (mmm) cc_final: 0.7216 (mmt) REVERT: A 304 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8027 (mt-10) REVERT: A 394 ASP cc_start: 0.8132 (t0) cc_final: 0.7867 (m-30) REVERT: A 459 VAL cc_start: 0.8202 (t) cc_final: 0.7969 (m) REVERT: A 506 GLU cc_start: 0.7546 (tp30) cc_final: 0.6655 (pm20) REVERT: A 569 MET cc_start: 0.6707 (tpp) cc_final: 0.6051 (mtm) REVERT: A 583 MET cc_start: 0.8879 (tpp) cc_final: 0.8581 (mmt) REVERT: A 768 LYS cc_start: 0.8283 (ttmt) cc_final: 0.7442 (tptt) REVERT: A 784 ASN cc_start: 0.7312 (t0) cc_final: 0.6970 (m-40) REVERT: B 24 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7486 (mp) REVERT: B 37 TYR cc_start: 0.7178 (m-80) cc_final: 0.6897 (m-80) REVERT: B 92 ASP cc_start: 0.7427 (t0) cc_final: 0.7200 (t0) REVERT: B 120 ARG cc_start: 0.7205 (tpp-160) cc_final: 0.6875 (mtt-85) REVERT: B 194 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.6999 (t0) REVERT: B 232 GLU cc_start: 0.8053 (tt0) cc_final: 0.7543 (tt0) REVERT: B 252 MET cc_start: 0.7754 (mmm) cc_final: 0.7202 (mmt) REVERT: B 304 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8036 (mt-10) REVERT: B 394 ASP cc_start: 0.8128 (t0) cc_final: 0.7877 (m-30) REVERT: B 459 VAL cc_start: 0.8203 (t) cc_final: 0.7973 (m) REVERT: B 506 GLU cc_start: 0.7546 (tp30) cc_final: 0.6658 (pm20) REVERT: B 569 MET cc_start: 0.6735 (tpp) cc_final: 0.6091 (mtm) REVERT: B 583 MET cc_start: 0.8877 (tpp) cc_final: 0.8582 (mmt) REVERT: B 768 LYS cc_start: 0.8280 (ttmt) cc_final: 0.7439 (tptt) REVERT: B 782 LYS cc_start: 0.8455 (tptp) cc_final: 0.8223 (tmtt) REVERT: B 784 ASN cc_start: 0.7287 (t0) cc_final: 0.6936 (m-40) REVERT: C 24 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7485 (mp) REVERT: C 37 TYR cc_start: 0.7239 (m-80) cc_final: 0.7012 (m-80) REVERT: C 92 ASP cc_start: 0.7422 (t0) cc_final: 0.7187 (t0) REVERT: C 120 ARG cc_start: 0.7219 (tpp-160) cc_final: 0.6889 (mtt-85) REVERT: C 232 GLU cc_start: 0.8041 (tt0) cc_final: 0.7522 (tt0) REVERT: C 252 MET cc_start: 0.7759 (mmm) cc_final: 0.7211 (mmt) REVERT: C 304 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8026 (mt-10) REVERT: C 394 ASP cc_start: 0.8140 (t0) cc_final: 0.7870 (m-30) REVERT: C 459 VAL cc_start: 0.8149 (t) cc_final: 0.7922 (m) REVERT: C 506 GLU cc_start: 0.7543 (tp30) cc_final: 0.6658 (pm20) REVERT: C 569 MET cc_start: 0.6757 (tpp) cc_final: 0.6122 (mtm) REVERT: C 583 MET cc_start: 0.8879 (tpp) cc_final: 0.8580 (mmt) REVERT: C 768 LYS cc_start: 0.8291 (ttmt) cc_final: 0.7440 (tptt) REVERT: C 783 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7659 (tm-30) REVERT: C 784 ASN cc_start: 0.7365 (t0) cc_final: 0.7006 (m-40) REVERT: D 24 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7486 (mp) REVERT: D 37 TYR cc_start: 0.7244 (m-80) cc_final: 0.6969 (m-80) REVERT: D 120 ARG cc_start: 0.7195 (tpp-160) cc_final: 0.6868 (mtt-85) REVERT: D 169 MET cc_start: 0.8697 (mmt) cc_final: 0.8481 (mtm) REVERT: D 232 GLU cc_start: 0.8049 (tt0) cc_final: 0.7531 (tt0) REVERT: D 252 MET cc_start: 0.7751 (mmm) cc_final: 0.7198 (mmt) REVERT: D 304 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8032 (mt-10) REVERT: D 394 ASP cc_start: 0.8128 (t0) cc_final: 0.7880 (m-30) REVERT: D 459 VAL cc_start: 0.8130 (t) cc_final: 0.7905 (m) REVERT: D 506 GLU cc_start: 0.7546 (tp30) cc_final: 0.6659 (pm20) REVERT: D 569 MET cc_start: 0.6788 (tpp) cc_final: 0.6169 (mtm) REVERT: D 583 MET cc_start: 0.8875 (tpp) cc_final: 0.8580 (mmt) REVERT: D 768 LYS cc_start: 0.8284 (ttmt) cc_final: 0.7434 (tptt) REVERT: D 783 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7654 (tm-30) REVERT: D 784 ASN cc_start: 0.7366 (t0) cc_final: 0.7002 (m-40) outliers start: 89 outliers final: 49 residues processed: 337 average time/residue: 0.1347 time to fit residues: 72.6374 Evaluate side-chains 295 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 241 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 468 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 780 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 160 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 271 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 494 GLN B 494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.134965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.095261 restraints weight = 31322.933| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.77 r_work: 0.3115 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23428 Z= 0.114 Angle : 0.504 9.302 31724 Z= 0.252 Chirality : 0.037 0.212 3612 Planarity : 0.003 0.025 3900 Dihedral : 10.418 114.695 3426 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.32 % Allowed : 13.05 % Favored : 83.63 % 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 are not related in a simple way. whole: 2.25 (0.16), residues: 2768 helix: 2.27 (0.11), residues: 1980 sheet: None (None), residues: 0 loop : -0.58 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 202 TYR 0.009 0.001 TYR D 206 PHE 0.013 0.001 PHE C 568 TRP 0.011 0.001 TRP C 432 HIS 0.001 0.000 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (23412) covalent geometry : angle 0.50392 / 0.25 (31712) hydrogen bonds : bond 0.04387 / 2.96 ( 1416) hydrogen bonds : angle 3.30115 / 2.39 ( 4188) metal coordination : bond 0.00269 / 0.18 ( 16) metal coordination : angle 1.06248 / 0.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 260 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: A 24 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7420 (mp) REVERT: A 37 TYR cc_start: 0.7182 (m-80) cc_final: 0.6961 (m-80) REVERT: A 120 ARG cc_start: 0.7231 (tpp-160) cc_final: 0.6312 (mtp85) REVERT: A 232 GLU cc_start: 0.8040 (tt0) cc_final: 0.7535 (tt0) REVERT: A 252 MET cc_start: 0.7768 (mmm) cc_final: 0.7233 (mmt) REVERT: A 459 VAL cc_start: 0.8168 (t) cc_final: 0.7923 (m) REVERT: A 465 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7162 (mm) REVERT: A 506 GLU cc_start: 0.7449 (tp30) cc_final: 0.6653 (pm20) REVERT: A 569 MET cc_start: 0.6694 (tpp) cc_final: 0.6075 (mtm) REVERT: A 583 MET cc_start: 0.8815 (tpp) cc_final: 0.8507 (mmt) REVERT: A 768 LYS cc_start: 0.8262 (ttmt) cc_final: 0.7430 (tptt) REVERT: A 784 ASN cc_start: 0.7384 (t0) cc_final: 0.6987 (m-40) REVERT: B 24 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7445 (mp) REVERT: B 37 TYR cc_start: 0.7170 (m-80) cc_final: 0.6879 (m-80) REVERT: B 194 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.6924 (t0) REVERT: B 232 GLU cc_start: 0.8045 (tt0) cc_final: 0.7545 (tt0) REVERT: B 252 MET cc_start: 0.7766 (mmm) cc_final: 0.7225 (mmt) REVERT: B 304 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8070 (mt-10) REVERT: B 459 VAL cc_start: 0.8161 (t) cc_final: 0.7919 (m) REVERT: B 465 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7146 (mm) REVERT: B 506 GLU cc_start: 0.7450 (tp30) cc_final: 0.6651 (pm20) REVERT: B 569 MET cc_start: 0.6688 (tpp) cc_final: 0.6076 (mtm) REVERT: B 583 MET cc_start: 0.8821 (tpp) cc_final: 0.8513 (mmt) REVERT: B 768 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7426 (tptt) REVERT: B 782 LYS cc_start: 0.8443 (tptp) cc_final: 0.8236 (tmtt) REVERT: B 784 ASN cc_start: 0.7433 (t0) cc_final: 0.6990 (m-40) REVERT: C 24 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7452 (mp) REVERT: C 37 TYR cc_start: 0.7235 (m-80) cc_final: 0.6944 (m-80) REVERT: C 232 GLU cc_start: 0.8033 (tt0) cc_final: 0.7523 (tt0) REVERT: C 252 MET cc_start: 0.7764 (mmm) cc_final: 0.7228 (mmt) REVERT: C 459 VAL cc_start: 0.8131 (t) cc_final: 0.7884 (m) REVERT: C 465 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7135 (mm) REVERT: C 506 GLU cc_start: 0.7447 (tp30) cc_final: 0.6662 (pm20) REVERT: C 569 MET cc_start: 0.6704 (tpp) cc_final: 0.6083 (mtm) REVERT: C 583 MET cc_start: 0.8810 (tpp) cc_final: 0.8499 (mmt) REVERT: C 768 LYS cc_start: 0.8261 (ttmt) cc_final: 0.7428 (tptt) REVERT: C 783 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7553 (tm-30) REVERT: C 784 ASN cc_start: 0.7451 (t0) cc_final: 0.7022 (m-40) REVERT: D 24 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7472 (mp) REVERT: D 37 TYR cc_start: 0.7165 (m-80) cc_final: 0.6876 (m-80) REVERT: D 232 GLU cc_start: 0.8045 (tt0) cc_final: 0.7539 (tt0) REVERT: D 252 MET cc_start: 0.7767 (mmm) cc_final: 0.7225 (mmt) REVERT: D 459 VAL cc_start: 0.8123 (t) cc_final: 0.7877 (m) REVERT: D 506 GLU cc_start: 0.7454 (tp30) cc_final: 0.6663 (pm20) REVERT: D 569 MET cc_start: 0.6727 (tpp) cc_final: 0.6116 (mtm) REVERT: D 583 MET cc_start: 0.8820 (tpp) cc_final: 0.8518 (mmt) REVERT: D 768 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7424 (tptt) REVERT: D 783 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7586 (tm-30) REVERT: D 784 ASN cc_start: 0.7497 (t0) cc_final: 0.7071 (m-40) outliers start: 79 outliers final: 58 residues processed: 325 average time/residue: 0.1308 time to fit residues: 69.1234 Evaluate side-chains 309 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 243 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 468 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 780 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 44 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 206 optimal weight: 0.2980 chunk 189 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 236 optimal weight: 0.8980 chunk 144 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 652 ASN B 652 ASN C 652 ASN D 652 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.132369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.092909 restraints weight = 31656.454| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.81 r_work: 0.3020 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23428 Z= 0.165 Angle : 0.545 6.962 31724 Z= 0.276 Chirality : 0.039 0.235 3612 Planarity : 0.004 0.029 3900 Dihedral : 10.376 114.821 3426 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.89 % Favored : 96.97 % Rotamer: Outliers : 3.45 % Allowed : 13.93 % Favored : 82.62 % 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 are not related in a simple way. whole: 1.97 (0.16), residues: 2768 helix: 2.05 (0.11), residues: 1984 sheet: None (None), residues: 0 loop : -0.62 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 202 TYR 0.015 0.001 TYR D 636 PHE 0.016 0.002 PHE D 572 TRP 0.011 0.002 TRP B 432 HIS 0.013 0.001 HIS A 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (23412) covalent geometry : angle 0.54481 / 0.28 (31712) hydrogen bonds : bond 0.04875 / 3.29 ( 1416) hydrogen bonds : angle 3.42774 / 2.47 ( 4188) metal coordination : bond 0.00284 / 0.18 ( 16) metal coordination : angle 1.44959 / 0.89 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 235 time to evaluate : 0.682 Fit side-chains REVERT: A 24 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7484 (mp) REVERT: A 37 TYR cc_start: 0.7253 (m-80) cc_final: 0.6935 (m-80) REVERT: A 232 GLU cc_start: 0.8146 (tt0) cc_final: 0.7915 (tt0) REVERT: A 252 MET cc_start: 0.7918 (mmm) cc_final: 0.7333 (mmt) REVERT: A 432 TRP cc_start: 0.8517 (OUTLIER) cc_final: 0.6719 (m-90) REVERT: A 459 VAL cc_start: 0.8219 (t) cc_final: 0.7886 (m) REVERT: A 465 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7491 (mm) REVERT: A 506 GLU cc_start: 0.7523 (tp30) cc_final: 0.6875 (pm20) REVERT: A 569 MET cc_start: 0.6915 (tpp) cc_final: 0.6386 (mtm) REVERT: A 583 MET cc_start: 0.8987 (tpp) cc_final: 0.8664 (mmt) REVERT: A 768 LYS cc_start: 0.8347 (ttmt) cc_final: 0.7583 (tptt) REVERT: A 784 ASN cc_start: 0.7374 (t0) cc_final: 0.6963 (m-40) REVERT: B 24 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7465 (mp) REVERT: B 37 TYR cc_start: 0.7180 (m-80) cc_final: 0.6865 (m-80) REVERT: B 232 GLU cc_start: 0.8123 (tt0) cc_final: 0.7891 (tt0) REVERT: B 252 MET cc_start: 0.7929 (mmm) cc_final: 0.7344 (mmt) REVERT: B 459 VAL cc_start: 0.8221 (t) cc_final: 0.7888 (m) REVERT: B 465 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7475 (mm) REVERT: B 506 GLU cc_start: 0.7523 (tp30) cc_final: 0.6877 (pm20) REVERT: B 569 MET cc_start: 0.6910 (tpp) cc_final: 0.6383 (mtm) REVERT: B 583 MET cc_start: 0.8978 (tpp) cc_final: 0.8658 (mmt) REVERT: B 768 LYS cc_start: 0.8349 (ttmt) cc_final: 0.7584 (tptt) REVERT: B 784 ASN cc_start: 0.7506 (t0) cc_final: 0.7109 (m-40) REVERT: C 24 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7486 (mp) REVERT: C 37 TYR cc_start: 0.7271 (m-80) cc_final: 0.6956 (m-80) REVERT: C 232 GLU cc_start: 0.8149 (tt0) cc_final: 0.7907 (tt0) REVERT: C 252 MET cc_start: 0.7910 (mmm) cc_final: 0.7327 (mmt) REVERT: C 432 TRP cc_start: 0.8492 (OUTLIER) cc_final: 0.6733 (m-90) REVERT: C 465 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7446 (mm) REVERT: C 506 GLU cc_start: 0.7564 (tp30) cc_final: 0.6896 (pm20) REVERT: C 569 MET cc_start: 0.6909 (tpp) cc_final: 0.6381 (mtm) REVERT: C 583 MET cc_start: 0.8994 (tpp) cc_final: 0.8669 (mmt) REVERT: C 768 LYS cc_start: 0.8360 (ttmt) cc_final: 0.7593 (tptt) REVERT: C 783 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7594 (tm-30) REVERT: C 784 ASN cc_start: 0.7473 (t0) cc_final: 0.7069 (m-40) REVERT: D 24 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7481 (mp) REVERT: D 37 TYR cc_start: 0.7234 (m-80) cc_final: 0.6913 (m-80) REVERT: D 232 GLU cc_start: 0.8152 (tt0) cc_final: 0.7920 (tt0) REVERT: D 252 MET cc_start: 0.7916 (mmm) cc_final: 0.7329 (mmt) REVERT: D 432 TRP cc_start: 0.8510 (OUTLIER) cc_final: 0.6735 (m-90) REVERT: D 465 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7444 (mm) REVERT: D 506 GLU cc_start: 0.7520 (tp30) cc_final: 0.6878 (pm20) REVERT: D 569 MET cc_start: 0.6966 (tpp) cc_final: 0.6458 (mtm) REVERT: D 583 MET cc_start: 0.8990 (tpp) cc_final: 0.8673 (mmt) REVERT: D 768 LYS cc_start: 0.8358 (ttmt) cc_final: 0.7591 (tptt) REVERT: D 783 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7557 (tm-30) REVERT: D 784 ASN cc_start: 0.7433 (t0) cc_final: 0.7027 (m-40) outliers start: 82 outliers final: 50 residues processed: 304 average time/residue: 0.1320 time to fit residues: 65.2835 Evaluate side-chains 286 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 225 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 468 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 780 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 3 optimal weight: 0.0970 chunk 224 optimal weight: 0.4980 chunk 92 optimal weight: 0.6980 chunk 172 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 222 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 192 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 140 optimal weight: 20.0000 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.135376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.096295 restraints weight = 31350.297| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.81 r_work: 0.3070 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23428 Z= 0.104 Angle : 0.497 10.450 31724 Z= 0.250 Chirality : 0.037 0.207 3612 Planarity : 0.003 0.027 3900 Dihedral : 10.114 113.529 3424 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.86 % Allowed : 15.45 % Favored : 81.69 % 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 are not related in a simple way. whole: 2.22 (0.16), residues: 2768 helix: 2.23 (0.11), residues: 1984 sheet: None (None), residues: 0 loop : -0.52 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 330 TYR 0.011 0.001 TYR C 488 PHE 0.013 0.001 PHE D 568 TRP 0.011 0.001 TRP A 432 HIS 0.003 0.000 HIS D 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (23412) covalent geometry : angle 0.49677 / 0.25 (31712) hydrogen bonds : bond 0.04247 / 2.87 ( 1416) hydrogen bonds : angle 3.27496 / 2.36 ( 4188) metal coordination : bond 0.00348 / 0.24 ( 16) metal coordination : angle 0.81126 / 0.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 228 time to evaluate : 0.702 Fit side-chains REVERT: A 24 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7421 (mp) REVERT: A 37 TYR cc_start: 0.7215 (m-80) cc_final: 0.6919 (m-80) REVERT: A 232 GLU cc_start: 0.8025 (tt0) cc_final: 0.7539 (tt0) REVERT: A 252 MET cc_start: 0.7848 (mmm) cc_final: 0.7273 (mmt) REVERT: A 459 VAL cc_start: 0.8158 (t) cc_final: 0.7823 (m) REVERT: A 506 GLU cc_start: 0.7501 (tp30) cc_final: 0.6886 (pm20) REVERT: A 569 MET cc_start: 0.6720 (tpp) cc_final: 0.6154 (mtm) REVERT: A 583 MET cc_start: 0.8865 (tpp) cc_final: 0.8534 (mmt) REVERT: A 768 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7537 (tptt) REVERT: A 784 ASN cc_start: 0.7389 (t0) cc_final: 0.6987 (m-40) REVERT: B 24 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7436 (mp) REVERT: B 37 TYR cc_start: 0.7129 (m-80) cc_final: 0.6834 (m-80) REVERT: B 232 GLU cc_start: 0.8064 (tt0) cc_final: 0.7578 (tt0) REVERT: B 252 MET cc_start: 0.7852 (mmm) cc_final: 0.7275 (mmt) REVERT: B 459 VAL cc_start: 0.8151 (t) cc_final: 0.7818 (m) REVERT: B 506 GLU cc_start: 0.7502 (tp30) cc_final: 0.6890 (pm20) REVERT: B 569 MET cc_start: 0.6692 (tpp) cc_final: 0.6120 (mtm) REVERT: B 583 MET cc_start: 0.8906 (tpp) cc_final: 0.8572 (mmt) REVERT: B 768 LYS cc_start: 0.8297 (ttmt) cc_final: 0.7534 (tptt) REVERT: B 782 LYS cc_start: 0.8371 (tmtt) cc_final: 0.7992 (ttmt) REVERT: B 784 ASN cc_start: 0.7371 (t0) cc_final: 0.6972 (m-40) REVERT: C 24 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7421 (mp) REVERT: C 37 TYR cc_start: 0.7224 (m-80) cc_final: 0.6928 (m-80) REVERT: C 232 GLU cc_start: 0.8025 (tt0) cc_final: 0.7538 (tt0) REVERT: C 252 MET cc_start: 0.7857 (mmm) cc_final: 0.7281 (mmt) REVERT: C 506 GLU cc_start: 0.7527 (tp30) cc_final: 0.6939 (pm20) REVERT: C 569 MET cc_start: 0.6740 (tpp) cc_final: 0.6170 (mtm) REVERT: C 583 MET cc_start: 0.8909 (tpp) cc_final: 0.8577 (mmt) REVERT: C 768 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7538 (tptt) REVERT: C 783 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7604 (tm-30) REVERT: C 784 ASN cc_start: 0.7490 (t0) cc_final: 0.7080 (m-40) REVERT: D 24 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7444 (mp) REVERT: D 37 TYR cc_start: 0.7205 (m-80) cc_final: 0.6906 (m-80) REVERT: D 232 GLU cc_start: 0.8058 (tt0) cc_final: 0.7572 (tt0) REVERT: D 252 MET cc_start: 0.7860 (mmm) cc_final: 0.7280 (mmt) REVERT: D 465 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7330 (mm) REVERT: D 506 GLU cc_start: 0.7500 (tp30) cc_final: 0.6896 (pm20) REVERT: D 569 MET cc_start: 0.6844 (tpp) cc_final: 0.6295 (mtm) REVERT: D 583 MET cc_start: 0.8866 (tpp) cc_final: 0.8538 (mmt) REVERT: D 768 LYS cc_start: 0.8299 (ttmt) cc_final: 0.7539 (tptt) REVERT: D 783 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7575 (tm-30) REVERT: D 784 ASN cc_start: 0.7432 (t0) cc_final: 0.7046 (m-40) outliers start: 68 outliers final: 51 residues processed: 274 average time/residue: 0.1293 time to fit residues: 58.1164 Evaluate side-chains 283 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 227 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 413 GLN Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 413 GLN Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 468 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 792 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 221 optimal weight: 0.5980 chunk 138 optimal weight: 4.9990 chunk 273 optimal weight: 1.9990 chunk 116 optimal weight: 0.0270 chunk 225 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.133201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.094053 restraints weight = 31386.350| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.81 r_work: 0.3025 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23428 Z= 0.127 Angle : 0.505 8.391 31724 Z= 0.255 Chirality : 0.037 0.204 3612 Planarity : 0.003 0.029 3900 Dihedral : 10.047 114.826 3424 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.24 % Allowed : 15.24 % Favored : 81.52 % 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 are not related in a simple way. whole: 2.16 (0.16), residues: 2768 helix: 2.17 (0.11), residues: 1984 sheet: None (None), residues: 0 loop : -0.51 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 514 TYR 0.011 0.001 TYR D 636 PHE 0.011 0.001 PHE C 572 TRP 0.010 0.002 TRP A 432 HIS 0.007 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (23412) covalent geometry : angle 0.50417 / 0.25 (31712) hydrogen bonds : bond 0.04443 / 3.01 ( 1416) hydrogen bonds : angle 3.27268 / 2.36 ( 4188) metal coordination : bond 0.00246 / 0.16 ( 16) metal coordination : angle 1.21579 / 0.75 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 239 time to evaluate : 0.876 Fit side-chains REVERT: A 24 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7423 (mp) REVERT: A 37 TYR cc_start: 0.7225 (m-80) cc_final: 0.7000 (m-80) REVERT: A 232 GLU cc_start: 0.8094 (tt0) cc_final: 0.7563 (tt0) REVERT: A 252 MET cc_start: 0.7835 (mmm) cc_final: 0.7245 (mmt) REVERT: A 432 TRP cc_start: 0.8437 (OUTLIER) cc_final: 0.7027 (m-90) REVERT: A 465 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7420 (mm) REVERT: A 506 GLU cc_start: 0.7500 (tp30) cc_final: 0.6979 (pm20) REVERT: A 569 MET cc_start: 0.6589 (tpp) cc_final: 0.6072 (mtm) REVERT: A 583 MET cc_start: 0.8907 (tpp) cc_final: 0.8569 (mmt) REVERT: A 646 MET cc_start: 0.7967 (mmt) cc_final: 0.7731 (mmt) REVERT: A 768 LYS cc_start: 0.8276 (ttmt) cc_final: 0.7524 (tptt) REVERT: A 783 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7618 (tm-30) REVERT: A 784 ASN cc_start: 0.7439 (t0) cc_final: 0.7057 (m-40) REVERT: B 24 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7417 (mp) REVERT: B 232 GLU cc_start: 0.8104 (tt0) cc_final: 0.7873 (tt0) REVERT: B 252 MET cc_start: 0.7815 (mmm) cc_final: 0.7238 (mmt) REVERT: B 432 TRP cc_start: 0.8433 (OUTLIER) cc_final: 0.7022 (m-90) REVERT: B 465 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7410 (mm) REVERT: B 506 GLU cc_start: 0.7496 (tp30) cc_final: 0.6978 (pm20) REVERT: B 569 MET cc_start: 0.6632 (tpp) cc_final: 0.6086 (mtm) REVERT: B 583 MET cc_start: 0.8922 (tpp) cc_final: 0.8584 (mmt) REVERT: B 612 SER cc_start: 0.9004 (t) cc_final: 0.8527 (m) REVERT: B 627 ASP cc_start: 0.8253 (t0) cc_final: 0.7704 (t0) REVERT: B 646 MET cc_start: 0.7965 (mmt) cc_final: 0.7736 (mmt) REVERT: B 768 LYS cc_start: 0.8269 (ttmt) cc_final: 0.7517 (tptt) REVERT: B 783 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7561 (tm-30) REVERT: B 784 ASN cc_start: 0.7459 (t0) cc_final: 0.7056 (m-40) REVERT: C 24 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7423 (mp) REVERT: C 37 TYR cc_start: 0.7226 (m-80) cc_final: 0.7005 (m-80) REVERT: C 169 MET cc_start: 0.8551 (mmt) cc_final: 0.8350 (mtp) REVERT: C 232 GLU cc_start: 0.8096 (tt0) cc_final: 0.7856 (tt0) REVERT: C 252 MET cc_start: 0.7845 (mmm) cc_final: 0.7253 (mmt) REVERT: C 432 TRP cc_start: 0.8422 (OUTLIER) cc_final: 0.7010 (m-90) REVERT: C 506 GLU cc_start: 0.7511 (tp30) cc_final: 0.6934 (pm20) REVERT: C 569 MET cc_start: 0.6597 (tpp) cc_final: 0.6076 (mtm) REVERT: C 583 MET cc_start: 0.8920 (tpp) cc_final: 0.8584 (mmt) REVERT: C 612 SER cc_start: 0.9005 (t) cc_final: 0.8529 (m) REVERT: C 627 ASP cc_start: 0.8223 (t0) cc_final: 0.8001 (t0) REVERT: C 646 MET cc_start: 0.7930 (mmt) cc_final: 0.7696 (mmt) REVERT: C 768 LYS cc_start: 0.8281 (ttmt) cc_final: 0.7527 (tptt) REVERT: C 783 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7551 (tm-30) REVERT: C 784 ASN cc_start: 0.7425 (t0) cc_final: 0.7021 (m-40) REVERT: D 24 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7423 (mp) REVERT: D 37 TYR cc_start: 0.7216 (m-80) cc_final: 0.6990 (m-80) REVERT: D 232 GLU cc_start: 0.8102 (tt0) cc_final: 0.7865 (tt0) REVERT: D 252 MET cc_start: 0.7841 (mmm) cc_final: 0.7245 (mmt) REVERT: D 432 TRP cc_start: 0.8426 (OUTLIER) cc_final: 0.7016 (m-90) REVERT: D 465 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7367 (mm) REVERT: D 506 GLU cc_start: 0.7499 (tp30) cc_final: 0.6984 (pm20) REVERT: D 569 MET cc_start: 0.6756 (tpp) cc_final: 0.6251 (mtm) REVERT: D 583 MET cc_start: 0.8918 (tpp) cc_final: 0.8585 (mmt) REVERT: D 768 LYS cc_start: 0.8285 (ttmt) cc_final: 0.7530 (tptt) REVERT: D 783 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7561 (tm-30) REVERT: D 784 ASN cc_start: 0.7430 (t0) cc_final: 0.7031 (m-40) outliers start: 77 outliers final: 51 residues processed: 298 average time/residue: 0.1295 time to fit residues: 63.8381 Evaluate side-chains 287 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 225 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 VAL Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 468 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 761 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 23 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 174 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 175 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 chunk 205 optimal weight: 0.4980 chunk 3 optimal weight: 0.1980 chunk 241 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.135009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.095903 restraints weight = 31495.625| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.82 r_work: 0.3053 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23428 Z= 0.106 Angle : 0.487 8.039 31724 Z= 0.245 Chirality : 0.037 0.178 3612 Planarity : 0.003 0.028 3900 Dihedral : 9.619 114.289 3418 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.99 % Allowed : 15.82 % Favored : 81.19 % 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 are not related in a simple way. whole: 2.33 (0.16), residues: 2768 helix: 2.29 (0.11), residues: 1984 sheet: None (None), residues: 0 loop : -0.42 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 514 TYR 0.013 0.001 TYR B 37 PHE 0.014 0.001 PHE D 568 TRP 0.010 0.001 TRP C 432 HIS 0.005 0.000 HIS D 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (23412) covalent geometry : angle 0.48726 / 0.25 (31712) hydrogen bonds : bond 0.04143 / 2.80 ( 1416) hydrogen bonds : angle 3.19417 / 2.31 ( 4188) metal coordination : bond 0.00263 / 0.18 ( 16) metal coordination : angle 0.82422 / 0.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 237 time to evaluate : 0.860 Fit side-chains REVERT: A 24 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7411 (mp) REVERT: A 37 TYR cc_start: 0.7197 (m-80) cc_final: 0.6901 (m-80) REVERT: A 232 GLU cc_start: 0.8037 (tt0) cc_final: 0.7554 (tt0) REVERT: A 252 MET cc_start: 0.7836 (mmm) cc_final: 0.7260 (mmt) REVERT: A 432 TRP cc_start: 0.8434 (OUTLIER) cc_final: 0.7172 (m-90) REVERT: A 465 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7389 (mm) REVERT: A 506 GLU cc_start: 0.7541 (tp30) cc_final: 0.6992 (pm20) REVERT: A 569 MET cc_start: 0.6612 (tpp) cc_final: 0.6019 (mtp) REVERT: A 583 MET cc_start: 0.8876 (tpp) cc_final: 0.8540 (mmt) REVERT: A 627 ASP cc_start: 0.8179 (t0) cc_final: 0.7932 (t0) REVERT: A 768 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7521 (tptt) REVERT: A 783 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7618 (tm-30) REVERT: A 784 ASN cc_start: 0.7439 (t0) cc_final: 0.7089 (m-40) REVERT: B 24 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7401 (mp) REVERT: B 232 GLU cc_start: 0.8045 (tt0) cc_final: 0.7562 (tt0) REVERT: B 252 MET cc_start: 0.7840 (mmm) cc_final: 0.7265 (mmt) REVERT: B 394 ASP cc_start: 0.8047 (t0) cc_final: 0.7729 (t0) REVERT: B 428 LEU cc_start: 0.7823 (tp) cc_final: 0.7598 (mt) REVERT: B 432 TRP cc_start: 0.8422 (OUTLIER) cc_final: 0.7049 (m-90) REVERT: B 465 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7375 (mm) REVERT: B 506 GLU cc_start: 0.7545 (tp30) cc_final: 0.7029 (pm20) REVERT: B 569 MET cc_start: 0.6549 (tpp) cc_final: 0.5924 (mtp) REVERT: B 627 ASP cc_start: 0.8226 (t0) cc_final: 0.7668 (t0) REVERT: B 768 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7526 (tptt) REVERT: B 782 LYS cc_start: 0.8391 (tptp) cc_final: 0.7918 (ttmt) REVERT: B 783 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7555 (tm-30) REVERT: B 784 ASN cc_start: 0.7433 (t0) cc_final: 0.7108 (m-40) REVERT: C 24 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7410 (mp) REVERT: C 37 TYR cc_start: 0.7202 (m-80) cc_final: 0.6905 (m-80) REVERT: C 232 GLU cc_start: 0.8039 (tt0) cc_final: 0.7556 (tt0) REVERT: C 252 MET cc_start: 0.7847 (mmm) cc_final: 0.7268 (mmt) REVERT: C 428 LEU cc_start: 0.7794 (tp) cc_final: 0.7564 (mt) REVERT: C 432 TRP cc_start: 0.8429 (OUTLIER) cc_final: 0.7061 (m-90) REVERT: C 506 GLU cc_start: 0.7526 (tp30) cc_final: 0.7004 (pm20) REVERT: C 569 MET cc_start: 0.6603 (tpp) cc_final: 0.6004 (mtp) REVERT: C 583 MET cc_start: 0.8879 (tpp) cc_final: 0.8542 (mmt) REVERT: C 627 ASP cc_start: 0.8224 (t0) cc_final: 0.7979 (t0) REVERT: C 768 LYS cc_start: 0.8274 (ttmt) cc_final: 0.7525 (tptt) REVERT: C 783 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7506 (tm-30) REVERT: C 784 ASN cc_start: 0.7473 (t0) cc_final: 0.7126 (m-40) REVERT: D 24 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7410 (mp) REVERT: D 37 TYR cc_start: 0.7211 (m-80) cc_final: 0.6916 (m-80) REVERT: D 232 GLU cc_start: 0.8044 (tt0) cc_final: 0.7563 (tt0) REVERT: D 252 MET cc_start: 0.7851 (mmm) cc_final: 0.7269 (mmt) REVERT: D 428 LEU cc_start: 0.7793 (tp) cc_final: 0.7567 (mt) REVERT: D 432 TRP cc_start: 0.8424 (OUTLIER) cc_final: 0.7057 (m-90) REVERT: D 465 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7333 (mm) REVERT: D 506 GLU cc_start: 0.7545 (tp30) cc_final: 0.6997 (pm20) REVERT: D 569 MET cc_start: 0.6531 (tpp) cc_final: 0.5898 (mtp) REVERT: D 583 MET cc_start: 0.8876 (tpp) cc_final: 0.8545 (mmt) REVERT: D 627 ASP cc_start: 0.8160 (t0) cc_final: 0.7634 (t0) REVERT: D 768 LYS cc_start: 0.8276 (ttmt) cc_final: 0.7525 (tptt) REVERT: D 783 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7597 (tm-30) REVERT: D 784 ASN cc_start: 0.7485 (t0) cc_final: 0.7140 (m-40) outliers start: 71 outliers final: 51 residues processed: 289 average time/residue: 0.1365 time to fit residues: 64.2556 Evaluate side-chains 289 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 227 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 413 GLN Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 565 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 468 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 761 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 87 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 249 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 213 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 413 GLN D 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.133663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.094450 restraints weight = 31255.034| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.82 r_work: 0.3029 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23428 Z= 0.122 Angle : 0.498 7.493 31724 Z= 0.251 Chirality : 0.037 0.169 3612 Planarity : 0.003 0.028 3900 Dihedral : 9.499 114.907 3418 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.69 % Allowed : 16.46 % Favored : 80.85 % 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 are not related in a simple way. whole: 2.27 (0.16), residues: 2768 helix: 2.23 (0.11), residues: 1984 sheet: None (None), residues: 0 loop : -0.40 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 514 TYR 0.011 0.001 TYR B 452 PHE 0.015 0.001 PHE C 572 TRP 0.010 0.001 TRP A 432 HIS 0.004 0.000 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (23412) covalent geometry : angle 0.49771 / 0.25 (31712) hydrogen bonds : bond 0.04329 / 2.93 ( 1416) hydrogen bonds : angle 3.22524 / 2.33 ( 4188) metal coordination : bond 0.00265 / 0.18 ( 16) metal coordination : angle 1.07961 / 0.65 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5536 Ramachandran restraints generated. 2768 Oldfield, 0 Emsley, 2768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 228 time to evaluate : 0.761 Fit side-chains REVERT: A 24 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7423 (mp) REVERT: A 37 TYR cc_start: 0.7142 (m-80) cc_final: 0.6930 (m-80) REVERT: A 232 GLU cc_start: 0.8074 (tt0) cc_final: 0.7839 (tt0) REVERT: A 252 MET cc_start: 0.7827 (mmm) cc_final: 0.7233 (mmt) REVERT: A 394 ASP cc_start: 0.8050 (t0) cc_final: 0.7749 (t0) REVERT: A 432 TRP cc_start: 0.8452 (OUTLIER) cc_final: 0.7117 (m-90) REVERT: A 445 TRP cc_start: 0.8043 (t-100) cc_final: 0.7761 (t60) REVERT: A 465 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7437 (mm) REVERT: A 506 GLU cc_start: 0.7525 (tp30) cc_final: 0.7016 (pm20) REVERT: A 569 MET cc_start: 0.6566 (tpp) cc_final: 0.6006 (mtp) REVERT: A 768 LYS cc_start: 0.8271 (ttmt) cc_final: 0.7521 (tptt) REVERT: A 783 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7631 (tm-30) REVERT: A 784 ASN cc_start: 0.7469 (t0) cc_final: 0.7095 (m-40) REVERT: B 24 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7406 (mp) REVERT: B 37 TYR cc_start: 0.7156 (m-80) cc_final: 0.6945 (m-80) REVERT: B 232 GLU cc_start: 0.8088 (tt0) cc_final: 0.7852 (tt0) REVERT: B 252 MET cc_start: 0.7833 (mmm) cc_final: 0.7236 (mmt) REVERT: B 394 ASP cc_start: 0.7994 (t0) cc_final: 0.7750 (t0) REVERT: B 432 TRP cc_start: 0.8443 (OUTLIER) cc_final: 0.7109 (m-90) REVERT: B 445 TRP cc_start: 0.7997 (t-100) cc_final: 0.7683 (t60) REVERT: B 465 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7418 (mm) REVERT: B 506 GLU cc_start: 0.7530 (tp30) cc_final: 0.7017 (pm20) REVERT: B 569 MET cc_start: 0.6574 (tpp) cc_final: 0.6016 (mtp) REVERT: B 627 ASP cc_start: 0.8235 (t0) cc_final: 0.7655 (t0) REVERT: B 768 LYS cc_start: 0.8271 (ttmt) cc_final: 0.7522 (tptt) REVERT: B 784 ASN cc_start: 0.7485 (t0) cc_final: 0.7152 (m-40) REVERT: C 24 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7398 (mp) REVERT: C 37 TYR cc_start: 0.7201 (m-80) cc_final: 0.6952 (m-80) REVERT: C 232 GLU cc_start: 0.8101 (tt0) cc_final: 0.7868 (tt0) REVERT: C 252 MET cc_start: 0.7829 (mmm) cc_final: 0.7235 (mmt) REVERT: C 394 ASP cc_start: 0.8063 (t0) cc_final: 0.7754 (t0) REVERT: C 432 TRP cc_start: 0.8438 (OUTLIER) cc_final: 0.7112 (m-90) REVERT: C 445 TRP cc_start: 0.7999 (t-100) cc_final: 0.7733 (t60) REVERT: C 506 GLU cc_start: 0.7522 (tp30) cc_final: 0.7018 (pm20) REVERT: C 569 MET cc_start: 0.6581 (tpp) cc_final: 0.6015 (mtp) REVERT: C 583 MET cc_start: 0.8943 (tpp) cc_final: 0.8607 (mmt) REVERT: C 768 LYS cc_start: 0.8272 (ttmt) cc_final: 0.7522 (tptt) REVERT: C 783 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7570 (tm-30) REVERT: C 784 ASN cc_start: 0.7467 (t0) cc_final: 0.7115 (m-40) REVERT: D 24 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7376 (mp) REVERT: D 37 TYR cc_start: 0.7159 (m-80) cc_final: 0.6946 (m-80) REVERT: D 232 GLU cc_start: 0.8112 (tt0) cc_final: 0.7878 (tt0) REVERT: D 252 MET cc_start: 0.7855 (mmm) cc_final: 0.7259 (mmt) REVERT: D 394 ASP cc_start: 0.8051 (t0) cc_final: 0.7753 (t0) REVERT: D 432 TRP cc_start: 0.8440 (OUTLIER) cc_final: 0.7106 (m-90) REVERT: D 445 TRP cc_start: 0.8016 (t-100) cc_final: 0.7746 (t60) REVERT: D 465 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7379 (mm) REVERT: D 506 GLU cc_start: 0.7531 (tp30) cc_final: 0.7021 (pm20) REVERT: D 569 MET cc_start: 0.6508 (tpp) cc_final: 0.5916 (mtp) REVERT: D 583 MET cc_start: 0.8906 (tpp) cc_final: 0.8575 (mmt) REVERT: D 627 ASP cc_start: 0.8165 (t0) cc_final: 0.7614 (t0) REVERT: D 768 LYS cc_start: 0.8274 (ttmt) cc_final: 0.7522 (tptt) REVERT: D 783 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7588 (tm-30) REVERT: D 784 ASN cc_start: 0.7486 (t0) cc_final: 0.7145 (m-40) outliers start: 64 outliers final: 46 residues processed: 276 average time/residue: 0.1314 time to fit residues: 59.5295 Evaluate side-chains 282 residues out of total 2488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 225 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 432 TRP Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 468 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 357 ILE Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 432 TRP Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 468 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 432 TRP Chi-restraints excluded: chain C residue 468 PHE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 357 ILE Chi-restraints excluded: chain D residue 366 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 432 TRP Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 468 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 761 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 20 optimal weight: 0.8980 chunk 277 optimal weight: 0.0970 chunk 5 optimal weight: 10.0000 chunk 64 optimal weight: 0.0970 chunk 55 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 134 optimal weight: 0.0870 chunk 232 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.4354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 413 GLN D 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.135675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.096613 restraints weight = 31069.954| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.83 r_work: 0.3062 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23428 Z= 0.102 Angle : 0.483 7.545 31724 Z= 0.243 Chirality : 0.036 0.161 3612 Planarity : 0.003 0.027 3900 Dihedral : 9.244 113.999 3412 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.61 % Allowed : 16.79 % Favored : 80.60 % 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 are not related in a simple way. whole: 2.42 (0.16), residues: 2768 helix: 2.34 (0.11), residues: 1984 sheet: None (None), residues: 0 loop : -0.30 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 514 TYR 0.013 0.001 TYR D 452 PHE 0.013 0.001 PHE D 568 TRP 0.010 0.001 TRP B 457 HIS 0.004 0.000 HIS D 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (23412) covalent geometry : angle 0.48246 / 0.24 (31712) hydrogen bonds : bond 0.04012 / 2.72 ( 1416) hydrogen bonds : angle 3.15470 / 2.28 ( 4188) metal coordination : bond 0.00241 / 0.16 ( 16) metal coordination : angle 0.76744 / 0.42 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3943.17 seconds wall clock time: 68 minutes 41.35 seconds (4121.35 seconds total)