Starting phenix.real_space_refine on Sun Aug 24 03:07:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ii3_60589/08_2025/9ii3_60589.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ii3_60589/08_2025/9ii3_60589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ii3_60589/08_2025/9ii3_60589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ii3_60589/08_2025/9ii3_60589.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ii3_60589/08_2025/9ii3_60589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ii3_60589/08_2025/9ii3_60589.map" } resolution = 3.9 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= 0.004 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 100 5.16 5 C 10614 2.51 5 N 2736 2.21 5 O 3035 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16488 Number of models: 1 Model: "" Number of chains: 10 Chain: "R" Number of atoms: 6159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 6159 Classifications: {'peptide': 803} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 33, 'TRANS': 769} Chain breaks: 3 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 10, 'ASP:plan': 9, 'TYR:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 3, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 138 Chain: "A" Number of atoms: 2630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2630 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 27, 'TRANS': 319} Chain breaks: 3 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 4, 'GLU:plan': 10, 'ARG:plan': 4, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 88 Chain: "S" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1592 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 6, 'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 5977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 5977 Classifications: {'peptide': 782} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 31, 'TRANS': 750} Chain breaks: 3 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 290 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 10, 'ASP:plan': 11, 'TYR:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 4, 'ASN:plan1': 6, 'HIS:plan': 2, 'TRP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 157 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C1 NAG C 2 " occ=0.60 ... (12 atoms not shown) pdb=" O7 NAG C 2 " occ=0.60 residue: pdb=" C1 NAG D 2 " occ=0.60 ... (12 atoms not shown) pdb=" O7 NAG D 2 " occ=0.60 Time building chain proxies: 4.08, per 1000 atoms: 0.25 Number of scatterers: 16488 At special positions: 0 Unit cell: (97.65, 108.81, 252.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 3 15.00 O 3035 8.00 N 2736 7.00 C 10614 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS R 57 " - pdb=" SG CYS R 99 " distance=2.03 Simple disulfide: pdb=" SG CYS R 361 " - pdb=" SG CYS R 373 " distance=2.03 Simple disulfide: pdb=" SG CYS R 412 " - pdb=" SG CYS R 419 " distance=2.03 Simple disulfide: pdb=" SG CYS R 509 " - pdb=" SG CYS R 528 " distance=2.03 Simple disulfide: pdb=" SG CYS R 513 " - pdb=" SG CYS R 531 " distance=2.03 Simple disulfide: pdb=" SG CYS R 534 " - pdb=" SG CYS R 546 " distance=2.03 Simple disulfide: pdb=" SG CYS R 549 " - pdb=" SG CYS R 562 " distance=2.03 Simple disulfide: pdb=" SG CYS R 641 " - pdb=" SG CYS R 730 " distance=2.03 Simple disulfide: pdb=" SG CYS S 24 " - pdb=" SG CYS S 89 " distance=2.03 Simple disulfide: pdb=" SG CYS S1025 " - pdb=" SG CYS S1099 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.04 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS B 412 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 509 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 513 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 546 " distance=2.03 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 641 " - pdb=" SG CYS B 730 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG C 1 " - " ASN R 209 " " NAG D 1 " - " ASN B 209 " Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 759.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4068 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 25 sheets defined 37.8% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'R' and resid 64 through 82 removed outlier: 3.664A pdb=" N ARG R 68 " --> pdb=" O ARG R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 114 Processing helix chain 'R' and resid 115 through 121 removed outlier: 3.822A pdb=" N LYS R 119 " --> pdb=" O ALA R 115 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL R 120 " --> pdb=" O SER R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 163 removed outlier: 4.005A pdb=" N LEU R 163 " --> pdb=" O ASN R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 180 Processing helix chain 'R' and resid 193 through 208 removed outlier: 4.286A pdb=" N GLN R 197 " --> pdb=" O PRO R 193 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE R 208 " --> pdb=" O ILE R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 237 Processing helix chain 'R' and resid 254 through 265 Processing helix chain 'R' and resid 277 through 291 Processing helix chain 'R' and resid 307 through 311 removed outlier: 3.823A pdb=" N LYS R 311 " --> pdb=" O SER R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 330 through 338 removed outlier: 3.723A pdb=" N ASP R 334 " --> pdb=" O VAL R 330 " (cutoff:3.500A) Processing helix chain 'R' and resid 350 through 359 Processing helix chain 'R' and resid 389 through 412 Processing helix chain 'R' and resid 426 through 434 Processing helix chain 'R' and resid 493 through 497 removed outlier: 3.648A pdb=" N ILE R 497 " --> pdb=" O VAL R 494 " (cutoff:3.500A) Processing helix chain 'R' and resid 577 through 601 Processing helix chain 'R' and resid 604 through 633 removed outlier: 3.534A pdb=" N LYS R 608 " --> pdb=" O THR R 604 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY R 611 " --> pdb=" O VAL R 607 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG R 612 " --> pdb=" O LYS R 608 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N GLU R 613 " --> pdb=" O ALA R 609 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU R 614 " --> pdb=" O SER R 610 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR R 629 " --> pdb=" O SER R 625 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE R 630 " --> pdb=" O TYR R 626 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE R 631 " --> pdb=" O CYS R 627 " (cutoff:3.500A) Processing helix chain 'R' and resid 637 through 672 removed outlier: 3.834A pdb=" N GLY R 672 " --> pdb=" O ARG R 668 " (cutoff:3.500A) Processing helix chain 'R' and resid 683 through 710 removed outlier: 3.576A pdb=" N SER R 687 " --> pdb=" O ILE R 683 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN R 688 " --> pdb=" O SER R 684 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N VAL R 689 " --> pdb=" O PRO R 685 " (cutoff:3.500A) Processing helix chain 'R' and resid 733 through 758 removed outlier: 4.794A pdb=" N TYR R 743 " --> pdb=" O ILE R 739 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP R 744 " --> pdb=" O SER R 740 " (cutoff:3.500A) Processing helix chain 'R' and resid 762 through 792 removed outlier: 6.035A pdb=" N ALA R 768 " --> pdb=" O ASN R 764 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS R 769 " --> pdb=" O PHE R 765 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE R 770 " --> pdb=" O ASN R 766 " (cutoff:3.500A) Proline residue: R 787 - end of helix Processing helix chain 'R' and resid 796 through 829 removed outlier: 4.584A pdb=" N ALA R 820 " --> pdb=" O GLY R 816 " (cutoff:3.500A) Proline residue: R 821 - end of helix Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'S' and resid 1091 through 1093 No H-bonds generated for 'chain 'S' and resid 1091 through 1093' Processing helix chain 'B' and resid 63 through 82 removed outlier: 3.645A pdb=" N GLN B 67 " --> pdb=" O ASP B 63 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG B 68 " --> pdb=" O ARG B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 121 removed outlier: 4.603A pdb=" N ALA B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N SER B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 163 removed outlier: 3.930A pdb=" N LEU B 163 " --> pdb=" O ASN B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 193 through 208 removed outlier: 4.076A pdb=" N GLN B 197 " --> pdb=" O PRO B 193 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 237 Processing helix chain 'B' and resid 254 through 265 Processing helix chain 'B' and resid 277 through 291 Processing helix chain 'B' and resid 307 through 311 Processing helix chain 'B' and resid 330 through 339 Processing helix chain 'B' and resid 350 through 359 Processing helix chain 'B' and resid 389 through 412 Processing helix chain 'B' and resid 419 through 424 removed outlier: 4.142A pdb=" N ILE B 424 " --> pdb=" O ASP B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 434 Processing helix chain 'B' and resid 493 through 497 Processing helix chain 'B' and resid 577 through 601 Processing helix chain 'B' and resid 604 through 610 Processing helix chain 'B' and resid 611 through 633 removed outlier: 3.821A pdb=" N THR B 629 " --> pdb=" O SER B 625 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE B 630 " --> pdb=" O TYR B 626 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE B 631 " --> pdb=" O CYS B 627 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE B 633 " --> pdb=" O THR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 671 Processing helix chain 'B' and resid 683 through 710 removed outlier: 3.549A pdb=" N SER B 687 " --> pdb=" O ILE B 683 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL B 689 " --> pdb=" O PRO B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 758 removed outlier: 3.582A pdb=" N MET B 737 " --> pdb=" O LYS B 733 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR B 743 " --> pdb=" O ILE B 739 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASP B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 793 Proline residue: B 787 - end of helix Processing helix chain 'B' and resid 795 through 829 removed outlier: 4.532A pdb=" N ALA B 820 " --> pdb=" O GLY B 816 " (cutoff:3.500A) Proline residue: B 821 - end of helix Processing sheet with id=AA1, first strand: chain 'R' and resid 32 through 35 removed outlier: 6.253A pdb=" N LEU R 39 " --> pdb=" O GLY R 92 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N HIS R 94 " --> pdb=" O LEU R 39 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU R 41 " --> pdb=" O HIS R 94 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU R 96 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY R 43 " --> pdb=" O LEU R 96 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL R 40 " --> pdb=" O GLY R 144 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE R 146 " --> pdb=" O VAL R 40 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLY R 42 " --> pdb=" O ILE R 146 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N ILE R 169 " --> pdb=" O ALA R 143 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL R 145 " --> pdb=" O ILE R 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 214 through 217 removed outlier: 6.995A pdb=" N SER R 214 " --> pdb=" O VAL R 273 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N PHE R 275 " --> pdb=" O SER R 214 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL R 216 " --> pdb=" O PHE R 275 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL R 272 " --> pdb=" O VAL R 298 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TRP R 297 " --> pdb=" O ILE R 321 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU R 323 " --> pdb=" O TRP R 297 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA R 299 " --> pdb=" O LEU R 323 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N LEU R 325 " --> pdb=" O ALA R 299 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR R 466 " --> pdb=" O HIS R 485 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N HIS R 485 " --> pdb=" O TYR R 466 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL R 468 " --> pdb=" O VAL R 483 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 518 through 521 Processing sheet with id=AA4, first strand: chain 'R' and resid 538 through 542 removed outlier: 6.881A pdb=" N THR R 545 " --> pdb=" O ALA R 541 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 553 through 555 Processing sheet with id=AA6, first strand: chain 'R' and resid 714 through 718 Processing sheet with id=AA7, first strand: chain 'R' and resid 836 through 837 removed outlier: 7.340A pdb=" N HIS R 837 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N PHE A 80 " --> pdb=" O HIS R 837 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ARG A 76 " --> pdb=" O TYR A 63 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N TYR A 63 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASP A 78 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE A 61 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE A 80 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A 52 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 9.327A pdb=" N VAL A 142 " --> pdb=" O LYS A 170 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N LYS A 170 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 171 " --> pdb=" O PHE A 27 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 9 through 11 Processing sheet with id=AA9, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AB1, first strand: chain 'A' and resid 183 through 187 Processing sheet with id=AB2, first strand: chain 'A' and resid 207 through 208 removed outlier: 3.832A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ILE A 231 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU A 257 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE A 233 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N MET A 255 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL A 235 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 5 through 6 Processing sheet with id=AB4, first strand: chain 'S' and resid 54 through 55 removed outlier: 6.634A pdb=" N TRP S 36 " --> pdb=" O LEU S 48 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR S 50 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 54 through 55 removed outlier: 6.634A pdb=" N TRP S 36 " --> pdb=" O LEU S 48 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR S 50 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 1008 through 1010 Processing sheet with id=AB7, first strand: chain 'S' and resid 1060 through 1063 removed outlier: 5.442A pdb=" N TRP S1050 " --> pdb=" O ARG S1041 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG S1041 " --> pdb=" O TRP S1050 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR S1112 " --> pdb=" O ARG S1101 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ARG S1103 " --> pdb=" O LEU S1110 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LEU S1110 " --> pdb=" O ARG S1103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 1060 through 1063 removed outlier: 5.442A pdb=" N TRP S1050 " --> pdb=" O ARG S1041 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG S1041 " --> pdb=" O TRP S1050 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR S1117 " --> pdb=" O TYR S1097 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 32 through 35 removed outlier: 6.322A pdb=" N LEU B 39 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N HIS B 94 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU B 41 " --> pdb=" O HIS B 94 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU B 96 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY B 43 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL B 40 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE B 146 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N GLY B 42 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N ILE B 169 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL B 145 " --> pdb=" O ILE B 169 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 49 Processing sheet with id=AC2, first strand: chain 'B' and resid 240 through 246 removed outlier: 5.633A pdb=" N VAL B 213 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR B 243 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N TYR B 212 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N VAL B 273 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N SER B 214 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N PHE B 275 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL B 216 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL B 272 " --> pdb=" O THR B 296 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 321 through 325 removed outlier: 6.751A pdb=" N TYR B 466 " --> pdb=" O HIS B 485 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N HIS B 485 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL B 468 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN B 470 " --> pdb=" O LEU B 481 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU B 481 " --> pdb=" O ASN B 470 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 519 through 521 Processing sheet with id=AC5, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.948A pdb=" N THR B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 553 through 555 Processing sheet with id=AC7, first strand: chain 'B' and resid 567 through 568 removed outlier: 3.973A pdb=" N LEU B 728 " --> pdb=" O ASP B 568 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 2238 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: 3.48 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2640 1.30 - 1.43: 4566 1.43 - 1.56: 9517 1.56 - 1.69: 11 1.69 - 1.82: 134 Bond restraints: 16868 Sorted by residual: bond pdb=" C7 NAG D 2 " pdb=" N2 NAG D 2 " ideal model delta sigma weight residual 1.346 1.477 -0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" C7 NAG C 2 " pdb=" N2 NAG C 2 " ideal model delta sigma weight residual 1.346 1.477 -0.131 2.00e-02 2.50e+03 4.30e+01 bond pdb=" C7 NAG C 1 " pdb=" N2 NAG C 1 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.13e+01 bond pdb=" C7 NAG D 1 " pdb=" N2 NAG D 1 " ideal model delta sigma weight residual 1.346 1.474 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" OG1 TPO R 860 " pdb=" P TPO R 860 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.80e+01 ... (remaining 16863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 22791 2.67 - 5.35: 173 5.35 - 8.02: 12 8.02 - 10.69: 1 10.69 - 13.37: 1 Bond angle restraints: 22978 Sorted by residual: angle pdb=" CB TPO R 860 " pdb=" OG1 TPO R 860 " pdb=" P TPO R 860 " ideal model delta sigma weight residual 119.31 105.94 13.37 3.00e+00 1.11e-01 1.99e+01 angle pdb=" OG1 TPO R 860 " pdb=" P TPO R 860 " pdb=" O1P TPO R 860 " ideal model delta sigma weight residual 100.43 109.26 -8.83 3.00e+00 1.11e-01 8.65e+00 angle pdb=" N PHE B 765 " pdb=" CA PHE B 765 " pdb=" C PHE B 765 " ideal model delta sigma weight residual 110.80 105.37 5.43 2.13e+00 2.20e-01 6.49e+00 angle pdb=" CA CYS R 730 " pdb=" CB CYS R 730 " pdb=" SG CYS R 730 " ideal model delta sigma weight residual 114.40 120.24 -5.84 2.30e+00 1.89e-01 6.45e+00 angle pdb=" N SER B 300 " pdb=" CA SER B 300 " pdb=" C SER B 300 " ideal model delta sigma weight residual 108.34 111.64 -3.30 1.31e+00 5.83e-01 6.34e+00 ... (remaining 22973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.64: 9206 16.64 - 33.27: 807 33.27 - 49.91: 151 49.91 - 66.55: 23 66.55 - 83.18: 11 Dihedral angle restraints: 10198 sinusoidal: 3892 harmonic: 6306 Sorted by residual: dihedral pdb=" CB CYS B 513 " pdb=" SG CYS B 513 " pdb=" SG CYS B 531 " pdb=" CB CYS B 531 " ideal model delta sinusoidal sigma weight residual 93.00 176.18 -83.18 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" CB CYS R 513 " pdb=" SG CYS R 513 " pdb=" SG CYS R 531 " pdb=" CB CYS R 531 " ideal model delta sinusoidal sigma weight residual 93.00 160.87 -67.87 1 1.00e+01 1.00e-02 5.98e+01 dihedral pdb=" CB CYS B 534 " pdb=" SG CYS B 534 " pdb=" SG CYS B 546 " pdb=" CB CYS B 546 " ideal model delta sinusoidal sigma weight residual -86.00 -152.51 66.51 1 1.00e+01 1.00e-02 5.77e+01 ... (remaining 10195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1777 0.037 - 0.074: 624 0.074 - 0.110: 200 0.110 - 0.147: 52 0.147 - 0.184: 4 Chirality restraints: 2657 Sorted by residual: chirality pdb=" CA GLN B 108 " pdb=" N GLN B 108 " pdb=" C GLN B 108 " pdb=" CB GLN B 108 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.46e-01 chirality pdb=" CB ILE A 233 " pdb=" CA ILE A 233 " pdb=" CG1 ILE A 233 " pdb=" CG2 ILE A 233 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CA ILE R 532 " pdb=" N ILE R 532 " pdb=" C ILE R 532 " pdb=" CB ILE R 532 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.08e-01 ... (remaining 2654 not shown) Planarity restraints: 2900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 445 " 0.043 5.00e-02 4.00e+02 6.52e-02 6.79e+00 pdb=" N PRO R 446 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO R 446 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 446 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 113 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.87e+00 pdb=" N PRO A 114 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 114 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 114 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 445 " -0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO B 446 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 446 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 446 " -0.030 5.00e-02 4.00e+02 ... (remaining 2897 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 327 2.67 - 3.23: 16283 3.23 - 3.78: 26110 3.78 - 4.34: 34432 4.34 - 4.90: 56044 Nonbonded interactions: 133196 Sorted by model distance: nonbonded pdb=" OG1 THR A 56 " pdb=" OD1 ASN A 83 " model vdw 2.110 3.040 nonbonded pdb=" O LEU R 44 " pdb=" OH TYR R 171 " model vdw 2.114 3.040 nonbonded pdb=" OG SER R 625 " pdb=" OG SER R 651 " model vdw 2.117 3.040 nonbonded pdb=" O ASP B 449 " pdb=" OG SER B 452 " model vdw 2.190 3.040 nonbonded pdb=" O VAL A 253 " pdb=" ND2 ASN A 281 " model vdw 2.191 3.120 ... (remaining 133191 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 30 through 113 or (resid 114 through 115 and (name N or na \ me CA or name C or name O or name CB )) or resid 116 through 137 or (resid 138 a \ nd (name N or name CA or name C or name O or name CB )) or resid 139 through 902 \ )) selection = (chain 'R' and (resid 30 through 572 or (resid 573 through 578 and (name N or na \ me CA or name C or name O or name CB )) or resid 579 through 667 or (resid 668 t \ hrough 671 and (name N or name CA or name C or name O or name CB )) or (resid 68 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 682 through \ 834 or resid 901 through 902)) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.33 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.770 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.070 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 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 : 0.004 0.131 16890 Z= 0.219 Angle : 0.621 13.367 23026 Z= 0.325 Chirality : 0.043 0.184 2657 Planarity : 0.004 0.065 2898 Dihedral : 12.817 80.452 6076 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.19), residues: 2121 helix: 1.13 (0.19), residues: 735 sheet: -0.68 (0.29), residues: 358 loop : -1.95 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.018 0.001 TYR R 539 PHE 0.020 0.001 PHE R 275 TRP 0.015 0.002 TRP B 303 HIS 0.005 0.001 HIS R 498 Details of bonding type rmsd covalent geometry : bond 0.00439 (16868) covalent geometry : angle 0.61812 (22978) SS BOND : bond 0.00244 ( 18) SS BOND : angle 1.34368 ( 36) hydrogen bonds : bond 0.12885 ( 762) hydrogen bonds : angle 6.20683 ( 2238) link_BETA1-4 : bond 0.00288 ( 2) link_BETA1-4 : angle 1.04024 ( 6) link_NAG-ASN : bond 0.00421 ( 2) link_NAG-ASN : angle 2.35797 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 507 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 340 LEU cc_start: 0.7931 (mt) cc_final: 0.7690 (mt) REVERT: R 400 MET cc_start: 0.8000 (tpp) cc_final: 0.7747 (tpp) REVERT: R 499 TRP cc_start: 0.7132 (m100) cc_final: 0.6240 (m100) REVERT: R 537 TYR cc_start: 0.8503 (p90) cc_final: 0.7912 (p90) REVERT: R 606 LEU cc_start: 0.9215 (tt) cc_final: 0.8566 (tt) REVERT: R 630 PHE cc_start: 0.8751 (m-80) cc_final: 0.8520 (m-80) REVERT: R 674 LYS cc_start: 0.8436 (mttt) cc_final: 0.8164 (mmmt) REVERT: R 734 ASP cc_start: 0.7808 (m-30) cc_final: 0.7533 (m-30) REVERT: R 783 LEU cc_start: 0.8869 (mt) cc_final: 0.8480 (mt) REVERT: A 147 LYS cc_start: 0.8708 (mttt) cc_final: 0.8188 (ttmm) REVERT: A 362 HIS cc_start: 0.7678 (m90) cc_final: 0.7476 (m90) REVERT: S 50 TYR cc_start: 0.7605 (p90) cc_final: 0.7327 (p90) REVERT: S 83 ASP cc_start: 0.8134 (m-30) cc_final: 0.7603 (p0) REVERT: S 103 THR cc_start: 0.8346 (t) cc_final: 0.7529 (m) REVERT: S 1101 ARG cc_start: 0.7751 (tmt170) cc_final: 0.7236 (ttt-90) REVERT: B 204 ILE cc_start: 0.8391 (mm) cc_final: 0.8159 (mt) REVERT: B 347 ARG cc_start: 0.6741 (mtm180) cc_final: 0.6345 (ttm170) REVERT: B 358 LYS cc_start: 0.8421 (tttp) cc_final: 0.7876 (tttp) REVERT: B 400 MET cc_start: 0.7315 (tpp) cc_final: 0.6924 (tpt) REVERT: B 717 TYR cc_start: 0.9228 (t80) cc_final: 0.8933 (t80) REVERT: B 727 ILE cc_start: 0.9257 (mt) cc_final: 0.9053 (pt) REVERT: B 775 MET cc_start: 0.8398 (mmm) cc_final: 0.8084 (tpp) REVERT: B 779 CYS cc_start: 0.8932 (m) cc_final: 0.8294 (m) REVERT: R 901 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6369 (mt-10) outliers start: 0 outliers final: 0 residues processed: 507 average time/residue: 0.1327 time to fit residues: 98.0253 Evaluate side-chains 315 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 8.9990 chunk 212 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 232 GLN R 328 GLN R 678 GLN A 122 ASN A 223 ASN ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS ** S 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.110018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.092188 restraints weight = 62163.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.092274 restraints weight = 37100.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.092896 restraints weight = 27118.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.093069 restraints weight = 24233.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.093197 restraints weight = 21647.822| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.128 16890 Z= 0.407 Angle : 0.874 9.874 23026 Z= 0.457 Chirality : 0.050 0.182 2657 Planarity : 0.006 0.066 2898 Dihedral : 6.501 66.406 2543 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 3.32 % Allowed : 15.73 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.17), residues: 2121 helix: 0.33 (0.18), residues: 736 sheet: -1.27 (0.27), residues: 364 loop : -2.23 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 99 TYR 0.024 0.003 TYR B 384 PHE 0.035 0.003 PHE S1105 TRP 0.022 0.003 TRP B 303 HIS 0.007 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00898 (16868) covalent geometry : angle 0.86436 (22978) SS BOND : bond 0.00740 ( 18) SS BOND : angle 2.29919 ( 36) hydrogen bonds : bond 0.05069 ( 762) hydrogen bonds : angle 5.72838 ( 2238) link_BETA1-4 : bond 0.00701 ( 2) link_BETA1-4 : angle 2.84876 ( 6) link_NAG-ASN : bond 0.00781 ( 2) link_NAG-ASN : angle 5.34249 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 329 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 233 GLU cc_start: 0.8612 (tp30) cc_final: 0.8354 (tp30) REVERT: R 400 MET cc_start: 0.8725 (tpp) cc_final: 0.7950 (tpp) REVERT: R 537 TYR cc_start: 0.8729 (p90) cc_final: 0.8113 (p90) REVERT: R 606 LEU cc_start: 0.9244 (tt) cc_final: 0.8211 (tt) REVERT: R 630 PHE cc_start: 0.8863 (m-80) cc_final: 0.8567 (m-80) REVERT: R 674 LYS cc_start: 0.8479 (mttt) cc_final: 0.8124 (mmmt) REVERT: R 729 LYS cc_start: 0.8724 (mtpp) cc_final: 0.8468 (ttmm) REVERT: R 744 ASP cc_start: 0.8390 (m-30) cc_final: 0.8111 (t70) REVERT: R 809 LEU cc_start: 0.8941 (tp) cc_final: 0.8721 (mp) REVERT: R 822 LYS cc_start: 0.8636 (mtpp) cc_final: 0.8430 (mmmt) REVERT: A 69 ASP cc_start: 0.9171 (m-30) cc_final: 0.8951 (m-30) REVERT: A 102 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8445 (mp0) REVERT: A 145 GLU cc_start: 0.7450 (mp0) cc_final: 0.7205 (mp0) REVERT: A 147 LYS cc_start: 0.8794 (mttt) cc_final: 0.8173 (ttmm) REVERT: A 248 GLN cc_start: 0.8440 (tt0) cc_final: 0.8009 (tt0) REVERT: S 49 ILE cc_start: 0.8593 (mm) cc_final: 0.8391 (mm) REVERT: S 71 ASP cc_start: 0.8170 (m-30) cc_final: 0.7422 (p0) REVERT: S 1030 PHE cc_start: 0.7629 (p90) cc_final: 0.7006 (p90) REVERT: S 1101 ARG cc_start: 0.8155 (tmt170) cc_final: 0.7504 (ttt-90) REVERT: B 113 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8154 (p) REVERT: B 194 ASP cc_start: 0.7765 (t0) cc_final: 0.7509 (t0) REVERT: B 201 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8157 (ttm) REVERT: B 204 ILE cc_start: 0.8540 (mm) cc_final: 0.8290 (mt) REVERT: B 241 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8280 (mm) REVERT: B 295 PHE cc_start: 0.6626 (m-80) cc_final: 0.6234 (m-80) REVERT: B 347 ARG cc_start: 0.6853 (mtm180) cc_final: 0.6596 (ttm170) REVERT: B 391 MET cc_start: 0.7633 (ppp) cc_final: 0.7172 (ttp) REVERT: B 593 MET cc_start: 0.1543 (ptt) cc_final: 0.1318 (ptt) REVERT: B 754 TYR cc_start: 0.8486 (m-80) cc_final: 0.8258 (t80) REVERT: B 775 MET cc_start: 0.8459 (mmm) cc_final: 0.8184 (tpp) REVERT: B 779 CYS cc_start: 0.8932 (m) cc_final: 0.8391 (m) REVERT: B 803 MET cc_start: 0.8434 (mmm) cc_final: 0.8036 (mtp) outliers start: 56 outliers final: 29 residues processed: 360 average time/residue: 0.1165 time to fit residues: 64.4745 Evaluate side-chains 319 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 286 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 ILE Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 348 ASN Chi-restraints excluded: chain R residue 384 TYR Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 454 VAL Chi-restraints excluded: chain R residue 479 SER Chi-restraints excluded: chain R residue 585 CYS Chi-restraints excluded: chain R residue 590 CYS Chi-restraints excluded: chain R residue 643 LEU Chi-restraints excluded: chain R residue 727 ILE Chi-restraints excluded: chain R residue 749 ILE Chi-restraints excluded: chain R residue 752 THR Chi-restraints excluded: chain R residue 785 PHE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 773 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 187 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 98 optimal weight: 8.9990 chunk 182 optimal weight: 0.5980 chunk 141 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN B 764 ASN ** B 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.114250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.096130 restraints weight = 62337.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.097190 restraints weight = 37056.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.098083 restraints weight = 25026.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.098353 restraints weight = 19894.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.098615 restraints weight = 17204.133| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3645 r_free = 0.3645 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16890 Z= 0.145 Angle : 0.658 9.195 23026 Z= 0.334 Chirality : 0.045 0.183 2657 Planarity : 0.005 0.060 2898 Dihedral : 5.901 65.312 2543 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.02 % Allowed : 19.76 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.18), residues: 2121 helix: 0.68 (0.18), residues: 742 sheet: -0.94 (0.28), residues: 377 loop : -2.18 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 161 TYR 0.020 0.002 TYR R 796 PHE 0.020 0.002 PHE R 670 TRP 0.016 0.001 TRP B 303 HIS 0.008 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00324 (16868) covalent geometry : angle 0.65390 (22978) SS BOND : bond 0.00183 ( 18) SS BOND : angle 1.51810 ( 36) hydrogen bonds : bond 0.04193 ( 762) hydrogen bonds : angle 5.05788 ( 2238) link_BETA1-4 : bond 0.00533 ( 2) link_BETA1-4 : angle 2.06117 ( 6) link_NAG-ASN : bond 0.00404 ( 2) link_NAG-ASN : angle 2.79850 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 322 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 400 MET cc_start: 0.8332 (tpp) cc_final: 0.8117 (tpt) REVERT: R 537 TYR cc_start: 0.8721 (p90) cc_final: 0.8120 (p90) REVERT: R 630 PHE cc_start: 0.8791 (m-80) cc_final: 0.8460 (m-80) REVERT: R 674 LYS cc_start: 0.8425 (mttt) cc_final: 0.8138 (mmmt) REVERT: R 763 GLU cc_start: 0.8457 (tp30) cc_final: 0.7892 (mt-10) REVERT: A 10 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8403 (mtmt) REVERT: A 52 ARG cc_start: 0.7334 (mtm180) cc_final: 0.6910 (mtm-85) REVERT: A 69 ASP cc_start: 0.9022 (m-30) cc_final: 0.8578 (m-30) REVERT: A 100 LEU cc_start: 0.9414 (mp) cc_final: 0.9089 (tt) REVERT: A 147 LYS cc_start: 0.8726 (mttt) cc_final: 0.8108 (mtpp) REVERT: A 248 GLN cc_start: 0.8426 (tt0) cc_final: 0.8057 (tt0) REVERT: A 306 LEU cc_start: 0.7127 (tp) cc_final: 0.6827 (tp) REVERT: S 71 ASP cc_start: 0.8155 (m-30) cc_final: 0.7479 (p0) REVERT: S 103 THR cc_start: 0.8291 (t) cc_final: 0.7447 (m) REVERT: S 1021 LEU cc_start: 0.8356 (tp) cc_final: 0.8137 (tp) REVERT: S 1030 PHE cc_start: 0.7454 (p90) cc_final: 0.6921 (p90) REVERT: S 1041 ARG cc_start: 0.7948 (ptt180) cc_final: 0.7679 (ptt180) REVERT: S 1101 ARG cc_start: 0.7761 (tmt170) cc_final: 0.7286 (ttt-90) REVERT: B 204 ILE cc_start: 0.8472 (mm) cc_final: 0.8236 (mt) REVERT: B 297 TRP cc_start: 0.7585 (m100) cc_final: 0.7205 (m100) REVERT: B 301 ASP cc_start: 0.8070 (t0) cc_final: 0.7857 (t0) REVERT: B 347 ARG cc_start: 0.6768 (mtm180) cc_final: 0.6511 (ttm170) REVERT: B 391 MET cc_start: 0.7643 (ppp) cc_final: 0.7294 (ttp) REVERT: B 479 SER cc_start: 0.7749 (p) cc_final: 0.7440 (m) REVERT: B 660 LEU cc_start: 0.8399 (tp) cc_final: 0.8120 (pp) REVERT: B 754 TYR cc_start: 0.8390 (m-80) cc_final: 0.8173 (t80) REVERT: B 779 CYS cc_start: 0.8872 (m) cc_final: 0.8380 (m) REVERT: B 803 MET cc_start: 0.8421 (mmm) cc_final: 0.8032 (mpp) outliers start: 34 outliers final: 19 residues processed: 334 average time/residue: 0.1210 time to fit residues: 61.5746 Evaluate side-chains 304 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 284 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 ILE Chi-restraints excluded: chain R residue 285 ILE Chi-restraints excluded: chain R residue 348 ASN Chi-restraints excluded: chain R residue 384 TYR Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 632 PHE Chi-restraints excluded: chain R residue 643 LEU Chi-restraints excluded: chain R residue 785 PHE Chi-restraints excluded: chain R residue 798 VAL Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain S residue 1089 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 764 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 50 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 147 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 232 GLN ** R 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 678 GLN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** B 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.112114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.094281 restraints weight = 61534.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.094548 restraints weight = 38294.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.095389 restraints weight = 27711.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.095721 restraints weight = 21933.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.095903 restraints weight = 19010.614| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 16890 Z= 0.238 Angle : 0.697 9.515 23026 Z= 0.358 Chirality : 0.046 0.208 2657 Planarity : 0.005 0.062 2898 Dihedral : 5.988 64.740 2543 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.39 % Favored : 91.56 % Rotamer: Outliers : 3.26 % Allowed : 20.71 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.18), residues: 2121 helix: 0.56 (0.18), residues: 744 sheet: -1.04 (0.27), residues: 376 loop : -2.20 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 331 TYR 0.040 0.002 TYR R 776 PHE 0.021 0.002 PHE S1105 TRP 0.014 0.002 TRP R 303 HIS 0.005 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00534 (16868) covalent geometry : angle 0.69117 (22978) SS BOND : bond 0.00341 ( 18) SS BOND : angle 1.65734 ( 36) hydrogen bonds : bond 0.04379 ( 762) hydrogen bonds : angle 5.19575 ( 2238) link_BETA1-4 : bond 0.00204 ( 2) link_BETA1-4 : angle 2.15969 ( 6) link_NAG-ASN : bond 0.00336 ( 2) link_NAG-ASN : angle 3.46018 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 295 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 400 MET cc_start: 0.8496 (tpp) cc_final: 0.7998 (tpp) REVERT: R 537 TYR cc_start: 0.8750 (p90) cc_final: 0.8148 (p90) REVERT: R 630 PHE cc_start: 0.8761 (m-80) cc_final: 0.8405 (m-80) REVERT: R 674 LYS cc_start: 0.8442 (mttt) cc_final: 0.8133 (mmmt) REVERT: R 763 GLU cc_start: 0.8466 (tp30) cc_final: 0.7902 (mt-10) REVERT: R 775 MET cc_start: 0.8520 (mmp) cc_final: 0.7761 (mmt) REVERT: R 783 LEU cc_start: 0.8830 (mt) cc_final: 0.8509 (mt) REVERT: R 822 LYS cc_start: 0.8340 (mtpp) cc_final: 0.8103 (mmmt) REVERT: A 52 ARG cc_start: 0.7314 (mtm180) cc_final: 0.6842 (mtt90) REVERT: A 69 ASP cc_start: 0.9076 (m-30) cc_final: 0.8636 (m-30) REVERT: A 100 LEU cc_start: 0.9439 (mp) cc_final: 0.9125 (tt) REVERT: A 145 GLU cc_start: 0.7483 (mp0) cc_final: 0.7105 (mp0) REVERT: A 147 LYS cc_start: 0.8766 (mttt) cc_final: 0.8166 (ttmm) REVERT: A 240 ASP cc_start: 0.7826 (m-30) cc_final: 0.7620 (m-30) REVERT: A 306 LEU cc_start: 0.7117 (tp) cc_final: 0.6767 (tp) REVERT: S 1030 PHE cc_start: 0.7490 (p90) cc_final: 0.6999 (p90) REVERT: S 1101 ARG cc_start: 0.7920 (tmt170) cc_final: 0.7396 (ttt-90) REVERT: B 164 PHE cc_start: 0.7249 (m-80) cc_final: 0.7040 (m-80) REVERT: B 204 ILE cc_start: 0.8501 (mm) cc_final: 0.8273 (mt) REVERT: B 347 ARG cc_start: 0.6868 (mtm180) cc_final: 0.6577 (ttm170) REVERT: B 571 ARG cc_start: 0.6264 (tpm170) cc_final: 0.6061 (tpm170) REVERT: B 660 LEU cc_start: 0.8419 (tp) cc_final: 0.8158 (pp) REVERT: B 754 TYR cc_start: 0.8357 (m-80) cc_final: 0.8146 (t80) REVERT: B 803 MET cc_start: 0.8366 (mmm) cc_final: 0.8029 (mpp) outliers start: 55 outliers final: 39 residues processed: 323 average time/residue: 0.1129 time to fit residues: 55.9786 Evaluate side-chains 312 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 273 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 285 ILE Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 327 SER Chi-restraints excluded: chain R residue 348 ASN Chi-restraints excluded: chain R residue 384 TYR Chi-restraints excluded: chain R residue 393 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 454 VAL Chi-restraints excluded: chain R residue 479 SER Chi-restraints excluded: chain R residue 590 CYS Chi-restraints excluded: chain R residue 632 PHE Chi-restraints excluded: chain R residue 726 VAL Chi-restraints excluded: chain R residue 727 ILE Chi-restraints excluded: chain R residue 749 ILE Chi-restraints excluded: chain R residue 785 PHE Chi-restraints excluded: chain R residue 798 VAL Chi-restraints excluded: chain R residue 800 THR Chi-restraints excluded: chain R residue 818 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 1020 SER Chi-restraints excluded: chain S residue 1089 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 537 TYR Chi-restraints excluded: chain B residue 683 ILE Chi-restraints excluded: chain B residue 707 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 102 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 678 GLN ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN ** B 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.112807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.095402 restraints weight = 61640.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.095203 restraints weight = 40672.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.096250 restraints weight = 27960.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.096524 restraints weight = 22813.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.096570 restraints weight = 20115.818| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3601 r_free = 0.3601 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16890 Z= 0.187 Angle : 0.657 9.471 23026 Z= 0.337 Chirality : 0.045 0.206 2657 Planarity : 0.005 0.061 2898 Dihedral : 5.888 64.819 2543 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.09 % Allowed : 22.26 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.18), residues: 2121 helix: 0.50 (0.18), residues: 750 sheet: -1.09 (0.27), residues: 378 loop : -2.25 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 331 TYR 0.016 0.002 TYR S 50 PHE 0.025 0.002 PHE R 670 TRP 0.029 0.002 TRP R 499 HIS 0.006 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00416 (16868) covalent geometry : angle 0.65044 (22978) SS BOND : bond 0.00290 ( 18) SS BOND : angle 1.89905 ( 36) hydrogen bonds : bond 0.04200 ( 762) hydrogen bonds : angle 5.07219 ( 2238) link_BETA1-4 : bond 0.00427 ( 2) link_BETA1-4 : angle 2.19234 ( 6) link_NAG-ASN : bond 0.00321 ( 2) link_NAG-ASN : angle 2.77830 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 291 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 400 MET cc_start: 0.8456 (tpp) cc_final: 0.8027 (tpp) REVERT: R 537 TYR cc_start: 0.8743 (p90) cc_final: 0.8122 (p90) REVERT: R 630 PHE cc_start: 0.8722 (m-80) cc_final: 0.8359 (m-80) REVERT: R 674 LYS cc_start: 0.8431 (mttt) cc_final: 0.8122 (mmmt) REVERT: R 763 GLU cc_start: 0.8454 (tp30) cc_final: 0.7912 (mt-10) REVERT: R 775 MET cc_start: 0.8530 (mmp) cc_final: 0.8179 (mmp) REVERT: R 822 LYS cc_start: 0.8340 (mtpp) cc_final: 0.8134 (mmmt) REVERT: A 52 ARG cc_start: 0.7327 (mtm180) cc_final: 0.6851 (mtt90) REVERT: A 69 ASP cc_start: 0.9084 (m-30) cc_final: 0.8650 (m-30) REVERT: A 99 ARG cc_start: 0.8331 (tpp-160) cc_final: 0.7982 (tpm170) REVERT: A 100 LEU cc_start: 0.9470 (mp) cc_final: 0.9175 (tt) REVERT: A 145 GLU cc_start: 0.7495 (mp0) cc_final: 0.7116 (mp0) REVERT: A 147 LYS cc_start: 0.8770 (mttt) cc_final: 0.8168 (ttmm) REVERT: A 306 LEU cc_start: 0.7028 (tp) cc_final: 0.6628 (tp) REVERT: S 1030 PHE cc_start: 0.7469 (p90) cc_final: 0.6973 (p90) REVERT: S 1042 GLN cc_start: 0.8093 (mt0) cc_final: 0.7824 (mt0) REVERT: S 1101 ARG cc_start: 0.7877 (tmt170) cc_final: 0.7371 (ttt-90) REVERT: B 204 ILE cc_start: 0.8476 (mm) cc_final: 0.8257 (mt) REVERT: B 241 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8347 (mm) REVERT: B 301 ASP cc_start: 0.8151 (t0) cc_final: 0.7932 (t0) REVERT: B 347 ARG cc_start: 0.6837 (mtm180) cc_final: 0.6565 (ttm170) REVERT: B 400 MET cc_start: 0.9144 (tpp) cc_final: 0.8389 (tpt) REVERT: B 660 LEU cc_start: 0.8341 (tp) cc_final: 0.8060 (pp) REVERT: B 803 MET cc_start: 0.8343 (mmm) cc_final: 0.8046 (mpp) outliers start: 52 outliers final: 34 residues processed: 322 average time/residue: 0.1176 time to fit residues: 57.4098 Evaluate side-chains 305 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 270 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 285 ILE Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 322 THR Chi-restraints excluded: chain R residue 327 SER Chi-restraints excluded: chain R residue 348 ASN Chi-restraints excluded: chain R residue 384 TYR Chi-restraints excluded: chain R residue 393 VAL Chi-restraints excluded: chain R residue 402 HIS Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 454 VAL Chi-restraints excluded: chain R residue 479 SER Chi-restraints excluded: chain R residue 632 PHE Chi-restraints excluded: chain R residue 727 ILE Chi-restraints excluded: chain R residue 749 ILE Chi-restraints excluded: chain R residue 785 PHE Chi-restraints excluded: chain R residue 800 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain S residue 1089 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 537 TYR Chi-restraints excluded: chain B residue 683 ILE Chi-restraints excluded: chain B residue 707 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 187 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 232 GLN ** R 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 328 GLN ** R 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.110861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.093915 restraints weight = 61903.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.093643 restraints weight = 36881.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.094055 restraints weight = 28458.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.094291 restraints weight = 24607.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.094469 restraints weight = 22610.402| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 16890 Z= 0.268 Angle : 0.722 13.031 23026 Z= 0.372 Chirality : 0.046 0.147 2657 Planarity : 0.005 0.063 2898 Dihedral : 6.055 65.029 2543 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 4.93 % Allowed : 22.26 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.18), residues: 2121 helix: 0.38 (0.18), residues: 750 sheet: -1.14 (0.27), residues: 378 loop : -2.31 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 716 TYR 0.016 0.002 TYR S1097 PHE 0.025 0.002 PHE S1105 TRP 0.030 0.002 TRP B 706 HIS 0.006 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00597 (16868) covalent geometry : angle 0.71821 (22978) SS BOND : bond 0.00336 ( 18) SS BOND : angle 1.39453 ( 36) hydrogen bonds : bond 0.04481 ( 762) hydrogen bonds : angle 5.21635 ( 2238) link_BETA1-4 : bond 0.00142 ( 2) link_BETA1-4 : angle 2.29637 ( 6) link_NAG-ASN : bond 0.00396 ( 2) link_NAG-ASN : angle 3.21585 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 279 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 204 ILE cc_start: 0.8637 (mt) cc_final: 0.8388 (mt) REVERT: R 400 MET cc_start: 0.8521 (tpp) cc_final: 0.7882 (tpp) REVERT: R 537 TYR cc_start: 0.8694 (p90) cc_final: 0.8050 (p90) REVERT: R 630 PHE cc_start: 0.8749 (m-80) cc_final: 0.8366 (m-80) REVERT: R 674 LYS cc_start: 0.8436 (mttt) cc_final: 0.8150 (mmmt) REVERT: R 783 LEU cc_start: 0.8855 (mt) cc_final: 0.8556 (mt) REVERT: A 69 ASP cc_start: 0.9111 (m-30) cc_final: 0.8675 (m-30) REVERT: A 99 ARG cc_start: 0.8337 (tpp-160) cc_final: 0.7872 (tpm170) REVERT: A 100 LEU cc_start: 0.9478 (mp) cc_final: 0.9191 (tt) REVERT: A 145 GLU cc_start: 0.7498 (mp0) cc_final: 0.7175 (mp0) REVERT: A 147 LYS cc_start: 0.8800 (mttt) cc_final: 0.8159 (ttmm) REVERT: A 306 LEU cc_start: 0.7045 (tp) cc_final: 0.6672 (tp) REVERT: S 86 THR cc_start: 0.8920 (m) cc_final: 0.8546 (p) REVERT: S 1030 PHE cc_start: 0.7491 (p90) cc_final: 0.6960 (p90) REVERT: S 1101 ARG cc_start: 0.8018 (tmt170) cc_final: 0.7470 (ttt-90) REVERT: B 104 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7756 (t80) REVERT: B 204 ILE cc_start: 0.8532 (mm) cc_final: 0.8319 (mt) REVERT: B 228 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: B 241 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8306 (mm) REVERT: B 295 PHE cc_start: 0.6683 (m-80) cc_final: 0.6252 (m-80) REVERT: B 537 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.7827 (p90) REVERT: B 571 ARG cc_start: 0.6432 (tpm170) cc_final: 0.5876 (tpm170) REVERT: B 660 LEU cc_start: 0.8388 (tp) cc_final: 0.8101 (pp) REVERT: B 803 MET cc_start: 0.8303 (mmm) cc_final: 0.8045 (mpp) outliers start: 83 outliers final: 56 residues processed: 332 average time/residue: 0.0970 time to fit residues: 50.3040 Evaluate side-chains 329 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 269 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 ILE Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 285 ILE Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 322 THR Chi-restraints excluded: chain R residue 327 SER Chi-restraints excluded: chain R residue 348 ASN Chi-restraints excluded: chain R residue 354 PHE Chi-restraints excluded: chain R residue 384 TYR Chi-restraints excluded: chain R residue 393 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 454 VAL Chi-restraints excluded: chain R residue 474 VAL Chi-restraints excluded: chain R residue 479 SER Chi-restraints excluded: chain R residue 483 VAL Chi-restraints excluded: chain R residue 590 CYS Chi-restraints excluded: chain R residue 606 LEU Chi-restraints excluded: chain R residue 727 ILE Chi-restraints excluded: chain R residue 729 LYS Chi-restraints excluded: chain R residue 744 ASP Chi-restraints excluded: chain R residue 749 ILE Chi-restraints excluded: chain R residue 785 PHE Chi-restraints excluded: chain R residue 798 VAL Chi-restraints excluded: chain R residue 818 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 1020 SER Chi-restraints excluded: chain S residue 1089 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 336 TYR Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 537 TYR Chi-restraints excluded: chain B residue 683 ILE Chi-restraints excluded: chain B residue 754 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 154 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 chunk 193 optimal weight: 10.0000 chunk 140 optimal weight: 0.5980 chunk 177 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 209 optimal weight: 0.2980 chunk 184 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN B 306 GLN ** B 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.111990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.094161 restraints weight = 60479.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.095126 restraints weight = 33437.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.095840 restraints weight = 22848.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.096149 restraints weight = 19285.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.096718 restraints weight = 17071.167| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16890 Z= 0.154 Angle : 0.684 10.522 23026 Z= 0.345 Chirality : 0.044 0.193 2657 Planarity : 0.005 0.059 2898 Dihedral : 5.871 64.810 2543 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.68 % Allowed : 24.21 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.18), residues: 2121 helix: 0.57 (0.18), residues: 750 sheet: -1.06 (0.27), residues: 380 loop : -2.26 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 331 TYR 0.014 0.001 TYR B 569 PHE 0.038 0.002 PHE R 789 TRP 0.025 0.002 TRP B 706 HIS 0.005 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00344 (16868) covalent geometry : angle 0.67552 (22978) SS BOND : bond 0.00416 ( 18) SS BOND : angle 2.54834 ( 36) hydrogen bonds : bond 0.04156 ( 762) hydrogen bonds : angle 5.06762 ( 2238) link_BETA1-4 : bond 0.00237 ( 2) link_BETA1-4 : angle 2.11345 ( 6) link_NAG-ASN : bond 0.00383 ( 2) link_NAG-ASN : angle 2.20196 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 287 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 537 TYR cc_start: 0.8649 (p90) cc_final: 0.8001 (p90) REVERT: R 630 PHE cc_start: 0.8670 (m-80) cc_final: 0.8254 (m-80) REVERT: R 674 LYS cc_start: 0.8377 (mttt) cc_final: 0.8100 (mmmt) REVERT: R 715 ARG cc_start: 0.7415 (ttp-110) cc_final: 0.6423 (ttp-110) REVERT: R 763 GLU cc_start: 0.8456 (tp30) cc_final: 0.8011 (tt0) REVERT: R 775 MET cc_start: 0.8473 (mmp) cc_final: 0.7647 (mmt) REVERT: R 783 LEU cc_start: 0.8855 (mt) cc_final: 0.8531 (mt) REVERT: R 803 MET cc_start: 0.8152 (tpp) cc_final: 0.7943 (tpp) REVERT: R 833 ASN cc_start: 0.8418 (p0) cc_final: 0.7883 (p0) REVERT: A 69 ASP cc_start: 0.8977 (m-30) cc_final: 0.8525 (m-30) REVERT: A 99 ARG cc_start: 0.8284 (tpp-160) cc_final: 0.8001 (tpm170) REVERT: A 100 LEU cc_start: 0.9457 (mp) cc_final: 0.9186 (tt) REVERT: A 145 GLU cc_start: 0.7446 (mp0) cc_final: 0.7016 (mp0) REVERT: A 147 LYS cc_start: 0.8751 (mttt) cc_final: 0.8091 (ttmm) REVERT: A 306 LEU cc_start: 0.6927 (tp) cc_final: 0.6543 (tp) REVERT: S 39 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7761 (pt0) REVERT: S 1030 PHE cc_start: 0.7469 (p90) cc_final: 0.6934 (p90) REVERT: S 1101 ARG cc_start: 0.7759 (tmt170) cc_final: 0.7254 (ttt-90) REVERT: B 104 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7576 (t80) REVERT: B 204 ILE cc_start: 0.8502 (mm) cc_final: 0.8281 (mt) REVERT: B 241 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8232 (mm) REVERT: B 400 MET cc_start: 0.9109 (tpp) cc_final: 0.8787 (tpt) REVERT: B 422 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6507 (ptp) REVERT: B 571 ARG cc_start: 0.6157 (tpm170) cc_final: 0.5871 (tpm170) REVERT: B 660 LEU cc_start: 0.8327 (tp) cc_final: 0.8045 (pp) REVERT: B 803 MET cc_start: 0.8340 (mmm) cc_final: 0.8052 (mpp) outliers start: 62 outliers final: 36 residues processed: 329 average time/residue: 0.1031 time to fit residues: 52.9148 Evaluate side-chains 306 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 266 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 285 ILE Chi-restraints excluded: chain R residue 322 THR Chi-restraints excluded: chain R residue 348 ASN Chi-restraints excluded: chain R residue 384 TYR Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 454 VAL Chi-restraints excluded: chain R residue 474 VAL Chi-restraints excluded: chain R residue 479 SER Chi-restraints excluded: chain R residue 632 PHE Chi-restraints excluded: chain R residue 730 CYS Chi-restraints excluded: chain R residue 785 PHE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 1020 SER Chi-restraints excluded: chain S residue 1089 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 513 CYS Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 537 TYR Chi-restraints excluded: chain B residue 683 ILE Chi-restraints excluded: chain B residue 754 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 18 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 chunk 180 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 799 GLN A 222 ASN ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1104 GLN ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.110539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.092423 restraints weight = 61250.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.093487 restraints weight = 35782.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.094181 restraints weight = 23398.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.094466 restraints weight = 18828.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.094642 restraints weight = 18042.480| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 16890 Z= 0.227 Angle : 0.711 10.351 23026 Z= 0.363 Chirality : 0.045 0.205 2657 Planarity : 0.005 0.060 2898 Dihedral : 5.949 64.476 2543 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 3.98 % Allowed : 24.75 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.18), residues: 2121 helix: 0.51 (0.18), residues: 749 sheet: -1.24 (0.27), residues: 387 loop : -2.28 (0.19), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 715 TYR 0.045 0.002 TYR R 776 PHE 0.024 0.002 PHE B 337 TRP 0.021 0.002 TRP B 706 HIS 0.005 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00506 (16868) covalent geometry : angle 0.70411 (22978) SS BOND : bond 0.00316 ( 18) SS BOND : angle 2.24815 ( 36) hydrogen bonds : bond 0.04296 ( 762) hydrogen bonds : angle 5.17886 ( 2238) link_BETA1-4 : bond 0.00227 ( 2) link_BETA1-4 : angle 2.10030 ( 6) link_NAG-ASN : bond 0.00330 ( 2) link_NAG-ASN : angle 2.67228 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 269 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 537 TYR cc_start: 0.8726 (p90) cc_final: 0.8062 (p90) REVERT: R 630 PHE cc_start: 0.8684 (m-80) cc_final: 0.8276 (m-80) REVERT: R 674 LYS cc_start: 0.8336 (mttt) cc_final: 0.8045 (mmmt) REVERT: R 702 MET cc_start: 0.8776 (mmm) cc_final: 0.8465 (mmm) REVERT: R 763 GLU cc_start: 0.8516 (tp30) cc_final: 0.7916 (tt0) REVERT: R 775 MET cc_start: 0.8511 (mmp) cc_final: 0.7674 (mmt) REVERT: R 833 ASN cc_start: 0.8471 (p0) cc_final: 0.7886 (p0) REVERT: A 69 ASP cc_start: 0.9027 (m-30) cc_final: 0.8581 (m-30) REVERT: A 99 ARG cc_start: 0.8321 (tpp-160) cc_final: 0.8021 (tpm170) REVERT: A 100 LEU cc_start: 0.9476 (mp) cc_final: 0.9217 (tt) REVERT: A 145 GLU cc_start: 0.7467 (mp0) cc_final: 0.7218 (mp0) REVERT: A 147 LYS cc_start: 0.8769 (mttt) cc_final: 0.8099 (ttmm) REVERT: A 306 LEU cc_start: 0.6990 (tp) cc_final: 0.6596 (tp) REVERT: S 1030 PHE cc_start: 0.7500 (p90) cc_final: 0.6936 (p90) REVERT: S 1101 ARG cc_start: 0.7855 (tmt170) cc_final: 0.7328 (ttt-90) REVERT: B 104 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.7747 (t80) REVERT: B 204 ILE cc_start: 0.8559 (mm) cc_final: 0.8341 (mt) REVERT: B 241 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8299 (mm) REVERT: B 400 MET cc_start: 0.9087 (tpp) cc_final: 0.8607 (tpt) REVERT: B 422 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6720 (ptp) REVERT: B 537 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.8034 (p90) REVERT: B 571 ARG cc_start: 0.6127 (tpm170) cc_final: 0.5848 (tpm170) REVERT: B 660 LEU cc_start: 0.8384 (tp) cc_final: 0.8096 (pp) REVERT: B 803 MET cc_start: 0.8356 (mmm) cc_final: 0.8046 (mpp) outliers start: 67 outliers final: 49 residues processed: 312 average time/residue: 0.1065 time to fit residues: 52.4965 Evaluate side-chains 313 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 260 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 285 ILE Chi-restraints excluded: chain R residue 322 THR Chi-restraints excluded: chain R residue 327 SER Chi-restraints excluded: chain R residue 348 ASN Chi-restraints excluded: chain R residue 384 TYR Chi-restraints excluded: chain R residue 393 VAL Chi-restraints excluded: chain R residue 397 VAL Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 454 VAL Chi-restraints excluded: chain R residue 474 VAL Chi-restraints excluded: chain R residue 479 SER Chi-restraints excluded: chain R residue 590 CYS Chi-restraints excluded: chain R residue 727 ILE Chi-restraints excluded: chain R residue 730 CYS Chi-restraints excluded: chain R residue 749 ILE Chi-restraints excluded: chain R residue 785 PHE Chi-restraints excluded: chain R residue 818 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 1020 SER Chi-restraints excluded: chain S residue 1089 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 201 MET Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 336 TYR Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 398 TYR Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 513 CYS Chi-restraints excluded: chain B residue 526 VAL Chi-restraints excluded: chain B residue 537 TYR Chi-restraints excluded: chain B residue 683 ILE Chi-restraints excluded: chain B residue 754 TYR Chi-restraints excluded: chain B residue 771 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 196 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 147 optimal weight: 0.8980 chunk 152 optimal weight: 0.6980 chunk 158 optimal weight: 0.0170 chunk 9 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 191 optimal weight: 20.0000 chunk 165 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 799 GLN A 222 ASN ** B 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.113137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.095053 restraints weight = 60808.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.096319 restraints weight = 34908.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.097051 restraints weight = 22157.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.097427 restraints weight = 18490.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.097911 restraints weight = 16259.206| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3613 r_free = 0.3613 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16890 Z= 0.137 Angle : 0.677 13.545 23026 Z= 0.338 Chirality : 0.044 0.193 2657 Planarity : 0.004 0.057 2898 Dihedral : 5.671 63.933 2543 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 3.03 % Allowed : 25.70 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.18), residues: 2121 helix: 0.70 (0.18), residues: 744 sheet: -1.04 (0.27), residues: 387 loop : -2.16 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 501 TYR 0.043 0.001 TYR R 776 PHE 0.033 0.002 PHE R 789 TRP 0.023 0.002 TRP B 706 HIS 0.005 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00305 (16868) covalent geometry : angle 0.67153 (22978) SS BOND : bond 0.00253 ( 18) SS BOND : angle 2.04226 ( 36) hydrogen bonds : bond 0.04001 ( 762) hydrogen bonds : angle 4.96519 ( 2238) link_BETA1-4 : bond 0.00460 ( 2) link_BETA1-4 : angle 1.95204 ( 6) link_NAG-ASN : bond 0.00459 ( 2) link_NAG-ASN : angle 1.70609 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 273 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 400 MET cc_start: 0.8274 (tpp) cc_final: 0.7780 (tpt) REVERT: R 537 TYR cc_start: 0.8683 (p90) cc_final: 0.8015 (p90) REVERT: R 630 PHE cc_start: 0.8657 (m-80) cc_final: 0.8232 (m-80) REVERT: R 674 LYS cc_start: 0.8305 (mttt) cc_final: 0.8033 (mmmt) REVERT: R 702 MET cc_start: 0.8723 (mmm) cc_final: 0.8420 (mmm) REVERT: R 763 GLU cc_start: 0.8482 (tp30) cc_final: 0.7862 (tt0) REVERT: R 775 MET cc_start: 0.8449 (mmp) cc_final: 0.7646 (mmt) REVERT: R 783 LEU cc_start: 0.8854 (mt) cc_final: 0.8530 (mt) REVERT: A 99 ARG cc_start: 0.8300 (tpp-160) cc_final: 0.8001 (tpm170) REVERT: A 100 LEU cc_start: 0.9471 (mp) cc_final: 0.9185 (tt) REVERT: A 145 GLU cc_start: 0.7377 (mp0) cc_final: 0.7139 (mp0) REVERT: A 147 LYS cc_start: 0.8727 (mttt) cc_final: 0.8059 (mtpp) REVERT: A 306 LEU cc_start: 0.6953 (tp) cc_final: 0.6557 (tp) REVERT: S 91 GLN cc_start: 0.8297 (pp30) cc_final: 0.7736 (pp30) REVERT: S 1049 GLU cc_start: 0.8480 (tp30) cc_final: 0.8158 (tp30) REVERT: S 1101 ARG cc_start: 0.7664 (tmt170) cc_final: 0.7137 (ttt-90) REVERT: B 104 TYR cc_start: 0.7980 (OUTLIER) cc_final: 0.7556 (t80) REVERT: B 154 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.8244 (p) REVERT: B 204 ILE cc_start: 0.8437 (mm) cc_final: 0.8215 (mt) REVERT: B 228 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: B 400 MET cc_start: 0.8995 (tpp) cc_final: 0.8523 (tpt) REVERT: B 422 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6518 (ptp) REVERT: B 479 SER cc_start: 0.7650 (p) cc_final: 0.7356 (m) REVERT: B 660 LEU cc_start: 0.8420 (tp) cc_final: 0.8149 (pp) REVERT: B 803 MET cc_start: 0.8370 (mmm) cc_final: 0.8074 (mpp) outliers start: 51 outliers final: 38 residues processed: 306 average time/residue: 0.1132 time to fit residues: 54.3570 Evaluate side-chains 301 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 259 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 285 ILE Chi-restraints excluded: chain R residue 322 THR Chi-restraints excluded: chain R residue 327 SER Chi-restraints excluded: chain R residue 348 ASN Chi-restraints excluded: chain R residue 354 PHE Chi-restraints excluded: chain R residue 384 TYR Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 474 VAL Chi-restraints excluded: chain R residue 632 PHE Chi-restraints excluded: chain R residue 727 ILE Chi-restraints excluded: chain R residue 730 CYS Chi-restraints excluded: chain R residue 744 ASP Chi-restraints excluded: chain R residue 785 PHE Chi-restraints excluded: chain R residue 786 LEU Chi-restraints excluded: chain R residue 798 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 66 GLU Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 1020 SER Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 513 CYS Chi-restraints excluded: chain B residue 537 TYR Chi-restraints excluded: chain B residue 683 ILE Chi-restraints excluded: chain B residue 771 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 169 optimal weight: 0.4980 chunk 82 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 167 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 chunk 162 optimal weight: 0.0670 chunk 141 optimal weight: 0.0000 chunk 36 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.6924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 232 GLN ** R 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 GLN ** B 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.113225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.095400 restraints weight = 61390.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.096317 restraints weight = 33986.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.096796 restraints weight = 24152.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.097035 restraints weight = 21781.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.097289 restraints weight = 19014.026| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3597 r_free = 0.3597 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16890 Z= 0.137 Angle : 0.679 11.413 23026 Z= 0.340 Chirality : 0.044 0.175 2657 Planarity : 0.005 0.061 2898 Dihedral : 5.560 63.146 2543 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.73 % Allowed : 26.41 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.18), residues: 2121 helix: 0.70 (0.18), residues: 742 sheet: -0.95 (0.27), residues: 384 loop : -2.12 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG R 715 TYR 0.044 0.002 TYR R 776 PHE 0.037 0.002 PHE B 275 TRP 0.045 0.002 TRP R 499 HIS 0.004 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00305 (16868) covalent geometry : angle 0.67455 (22978) SS BOND : bond 0.00251 ( 18) SS BOND : angle 1.85350 ( 36) hydrogen bonds : bond 0.03964 ( 762) hydrogen bonds : angle 4.98807 ( 2238) link_BETA1-4 : bond 0.00435 ( 2) link_BETA1-4 : angle 1.89979 ( 6) link_NAG-ASN : bond 0.00393 ( 2) link_NAG-ASN : angle 1.87753 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 266 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 400 MET cc_start: 0.8260 (tpp) cc_final: 0.7884 (tpt) REVERT: R 537 TYR cc_start: 0.8599 (p90) cc_final: 0.7942 (p90) REVERT: R 630 PHE cc_start: 0.8664 (m-80) cc_final: 0.8252 (m-80) REVERT: R 674 LYS cc_start: 0.8301 (mttt) cc_final: 0.8041 (mmmt) REVERT: R 682 PHE cc_start: 0.7451 (t80) cc_final: 0.7221 (t80) REVERT: R 702 MET cc_start: 0.8720 (mmm) cc_final: 0.8424 (mmm) REVERT: R 763 GLU cc_start: 0.8493 (tp30) cc_final: 0.7847 (tt0) REVERT: R 775 MET cc_start: 0.8471 (mmp) cc_final: 0.7685 (mmt) REVERT: A 69 ASP cc_start: 0.8972 (m-30) cc_final: 0.8628 (p0) REVERT: A 99 ARG cc_start: 0.8321 (tpp-160) cc_final: 0.8011 (tpm170) REVERT: A 100 LEU cc_start: 0.9485 (mp) cc_final: 0.9230 (tt) REVERT: A 147 LYS cc_start: 0.8772 (mttt) cc_final: 0.8143 (ttmm) REVERT: A 270 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7791 (mmtm) REVERT: A 306 LEU cc_start: 0.6911 (tp) cc_final: 0.6523 (tp) REVERT: S 91 GLN cc_start: 0.8418 (pp30) cc_final: 0.7874 (pp30) REVERT: S 1101 ARG cc_start: 0.7725 (tmt170) cc_final: 0.7207 (ttt-90) REVERT: B 104 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7633 (t80) REVERT: B 154 SER cc_start: 0.8861 (OUTLIER) cc_final: 0.8257 (p) REVERT: B 204 ILE cc_start: 0.8462 (mm) cc_final: 0.8236 (mt) REVERT: B 400 MET cc_start: 0.8962 (tpp) cc_final: 0.8493 (tpt) REVERT: B 422 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6837 (ptp) REVERT: B 479 SER cc_start: 0.7671 (p) cc_final: 0.7386 (m) REVERT: B 571 ARG cc_start: 0.5957 (tpm170) cc_final: 0.5747 (tpm170) REVERT: B 660 LEU cc_start: 0.8364 (tp) cc_final: 0.8094 (pp) REVERT: B 803 MET cc_start: 0.8227 (mmm) cc_final: 0.8026 (mpp) outliers start: 46 outliers final: 34 residues processed: 299 average time/residue: 0.1049 time to fit residues: 49.7160 Evaluate side-chains 296 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 258 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 216 VAL Chi-restraints excluded: chain R residue 285 ILE Chi-restraints excluded: chain R residue 322 THR Chi-restraints excluded: chain R residue 327 SER Chi-restraints excluded: chain R residue 348 ASN Chi-restraints excluded: chain R residue 354 PHE Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 474 VAL Chi-restraints excluded: chain R residue 632 PHE Chi-restraints excluded: chain R residue 641 CYS Chi-restraints excluded: chain R residue 727 ILE Chi-restraints excluded: chain R residue 730 CYS Chi-restraints excluded: chain R residue 744 ASP Chi-restraints excluded: chain R residue 785 PHE Chi-restraints excluded: chain R residue 786 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 1020 SER Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 513 CYS Chi-restraints excluded: chain B residue 537 TYR Chi-restraints excluded: chain B residue 683 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 210 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 15 optimal weight: 0.0670 chunk 125 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 180 optimal weight: 0.2980 overall best weight: 1.4724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 232 GLN ** R 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.112828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.095063 restraints weight = 61628.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.095505 restraints weight = 37068.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.096454 restraints weight = 26199.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.096727 restraints weight = 21271.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.096973 restraints weight = 18452.432| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16890 Z= 0.189 Angle : 0.700 9.936 23026 Z= 0.356 Chirality : 0.045 0.186 2657 Planarity : 0.005 0.060 2898 Dihedral : 5.649 62.990 2543 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.03 % Allowed : 26.47 % Favored : 70.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.18), residues: 2121 helix: 0.63 (0.18), residues: 740 sheet: -1.15 (0.26), residues: 417 loop : -2.07 (0.19), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 571 TYR 0.024 0.002 TYR B 754 PHE 0.020 0.002 PHE R 670 TRP 0.034 0.002 TRP R 499 HIS 0.005 0.001 HIS A 159 Details of bonding type rmsd covalent geometry : bond 0.00422 (16868) covalent geometry : angle 0.69513 (22978) SS BOND : bond 0.00304 ( 18) SS BOND : angle 1.81250 ( 36) hydrogen bonds : bond 0.04171 ( 762) hydrogen bonds : angle 5.11168 ( 2238) link_BETA1-4 : bond 0.00251 ( 2) link_BETA1-4 : angle 1.98320 ( 6) link_NAG-ASN : bond 0.00274 ( 2) link_NAG-ASN : angle 2.32328 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2587.17 seconds wall clock time: 45 minutes 48.33 seconds (2748.33 seconds total)