Starting phenix.real_space_refine on Sun May 18 04:44:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ii3_60589/05_2025/9ii3_60589.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ii3_60589/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ii3_60589/05_2025/9ii3_60589.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ii3_60589/05_2025/9ii3_60589.map" model { file = "/net/cci-nas-00/data/ceres_data/9ii3_60589/05_2025/9ii3_60589.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ii3_60589/05_2025/9ii3_60589.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 6, 'TPO:plan-1': 1, 'ASP:plan': 9, 'GLU:plan': 3, 'ARG:plan': 10} 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: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} 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: {'GLN:plan1': 6, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4} 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: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 10} 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: 9.61, per 1000 atoms: 0.58 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: 4.22 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.93 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: 6.16 Time building geometry restraints manager: 4.85 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 834 \ or resid 901 or resid 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 or resid 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: 4.130 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: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 38.700 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.560 ------------------------------------------------------------------------------- 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 : 13.02 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (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 TRP 0.015 0.002 TRP B 303 HIS 0.005 0.001 HIS R 498 PHE 0.020 0.001 PHE R 275 TYR 0.018 0.001 TYR R 539 ARG 0.005 0.000 ARG B 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 2) link_NAG-ASN : angle 2.35797 ( 6) link_BETA1-4 : bond 0.00288 ( 2) link_BETA1-4 : angle 1.04024 ( 6) hydrogen bonds : bond 0.12885 ( 762) hydrogen bonds : angle 6.20683 ( 2238) SS BOND : bond 0.00244 ( 18) SS BOND : angle 1.34368 ( 36) covalent geometry : bond 0.00439 (16868) covalent geometry : angle 0.61812 (22978) *********************** 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 : 1.976 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: 0.3168 time to fit residues: 233.1803 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 : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 86 optimal weight: 0.0970 chunk 167 optimal weight: 0.5980 chunk 64 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 overall best weight: 1.4782 ------------------------------------------------------------------------------- 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 386 GLN A 122 ASN A 223 ASN 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 = 0.3956 r_free = 0.3956 target = 0.114631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.096278 restraints weight = 62157.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.097606 restraints weight = 38153.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.098477 restraints weight = 24197.686| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16890 Z= 0.208 Angle : 0.694 10.445 23026 Z= 0.355 Chirality : 0.046 0.179 2657 Planarity : 0.005 0.065 2898 Dihedral : 5.880 67.031 2543 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.49 % Allowed : 13.59 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.18), residues: 2121 helix: 0.90 (0.18), residues: 741 sheet: -0.74 (0.29), residues: 341 loop : -2.00 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 303 HIS 0.005 0.001 HIS A 159 PHE 0.027 0.002 PHE B 770 TYR 0.020 0.002 TYR B 384 ARG 0.007 0.001 ARG A 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 2) link_NAG-ASN : angle 3.70120 ( 6) link_BETA1-4 : bond 0.00472 ( 2) link_BETA1-4 : angle 2.34423 ( 6) hydrogen bonds : bond 0.04389 ( 762) hydrogen bonds : angle 5.26760 ( 2238) SS BOND : bond 0.00262 ( 18) SS BOND : angle 2.18625 ( 36) covalent geometry : bond 0.00453 (16868) covalent geometry : angle 0.68582 (22978) *********************** 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 377 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 335 time to evaluate : 1.907 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: symmetry clash revert: symmetry clash REVERT: R 199 LYS cc_start: 0.8573 (ttmt) cc_final: 0.8370 (mtpp) REVERT: R 204 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8401 (mt) REVERT: R 400 MET cc_start: 0.8408 (tpp) cc_final: 0.7937 (tpp) REVERT: R 499 TRP cc_start: 0.6985 (m100) cc_final: 0.5758 (m100) REVERT: R 537 TYR cc_start: 0.8687 (p90) cc_final: 0.8066 (p90) REVERT: R 630 PHE cc_start: 0.8791 (m-80) cc_final: 0.8554 (m-80) REVERT: R 674 LYS cc_start: 0.8440 (mttt) cc_final: 0.8130 (mmmt) REVERT: R 729 LYS cc_start: 0.8683 (mtpp) cc_final: 0.8446 (ttmm) REVERT: R 783 LEU cc_start: 0.8853 (mt) cc_final: 0.8558 (mt) REVERT: A 69 ASP cc_start: 0.9028 (m-30) cc_final: 0.8809 (m-30) REVERT: A 102 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8371 (mp0) REVERT: A 147 LYS cc_start: 0.8765 (mttt) cc_final: 0.8172 (mtpp) REVERT: A 200 GLU cc_start: 0.7240 (pp20) cc_final: 0.6386 (tp30) REVERT: A 219 HIS cc_start: 0.7815 (t-170) cc_final: 0.7196 (t-170) REVERT: A 248 GLN cc_start: 0.8444 (tt0) cc_final: 0.8016 (tt0) REVERT: S 71 ASP cc_start: 0.8153 (m-30) cc_final: 0.7441 (p0) REVERT: S 1030 PHE cc_start: 0.7583 (p90) cc_final: 0.7087 (p90) REVERT: S 1048 LEU cc_start: 0.8290 (mt) cc_final: 0.7961 (mt) REVERT: S 1101 ARG cc_start: 0.7772 (tmt170) cc_final: 0.7238 (ttt-90) REVERT: B 204 ILE cc_start: 0.8456 (mm) cc_final: 0.8214 (mt) REVERT: B 295 PHE cc_start: 0.6456 (m-80) cc_final: 0.6138 (m-80) REVERT: B 347 ARG cc_start: 0.6742 (mtm180) cc_final: 0.6475 (ttm170) REVERT: B 391 MET cc_start: 0.7700 (ppp) cc_final: 0.7194 (ttp) REVERT: B 479 SER cc_start: 0.7789 (OUTLIER) cc_final: 0.7467 (m) REVERT: B 593 MET cc_start: 0.1348 (OUTLIER) cc_final: 0.1117 (ptt) REVERT: B 754 TYR cc_start: 0.8413 (m-80) cc_final: 0.8185 (t80) REVERT: B 779 CYS cc_start: 0.8928 (m) cc_final: 0.8418 (m) REVERT: B 802 THR cc_start: 0.8738 (p) cc_final: 0.8479 (t) REVERT: B 803 MET cc_start: 0.8407 (mmm) cc_final: 0.7931 (mtp) REVERT: R 901 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7217 (mt-10) outliers start: 42 outliers final: 19 residues processed: 352 average time/residue: 0.2869 time to fit residues: 155.6356 Evaluate side-chains 311 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 288 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 ILE Chi-restraints excluded: chain R residue 204 ILE Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 384 TYR Chi-restraints excluded: chain R residue 454 VAL Chi-restraints excluded: chain R residue 479 SER Chi-restraints excluded: chain R residue 643 LEU Chi-restraints excluded: chain R residue 660 LEU Chi-restraints excluded: chain R residue 726 VAL Chi-restraints excluded: chain R residue 752 THR 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 233 ILE Chi-restraints excluded: chain S residue 1093 ASP 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 593 MET Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 773 PHE Chi-restraints excluded: chain B residue 786 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 126 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 177 optimal weight: 0.5980 chunk 186 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 678 GLN A 222 ASN S 90 GLN ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.113806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.095519 restraints weight = 61380.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.096311 restraints weight = 38942.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.097479 restraints weight = 26071.701| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 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 = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16890 Z= 0.192 Angle : 0.658 8.981 23026 Z= 0.337 Chirality : 0.045 0.179 2657 Planarity : 0.005 0.064 2898 Dihedral : 5.792 64.800 2543 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 2.55 % Allowed : 17.86 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.18), residues: 2121 helix: 0.79 (0.18), residues: 743 sheet: -1.01 (0.28), residues: 367 loop : -2.05 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 303 HIS 0.004 0.001 HIS A 159 PHE 0.036 0.002 PHE R 770 TYR 0.022 0.002 TYR B 384 ARG 0.010 0.001 ARG B 716 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 2) link_NAG-ASN : angle 3.27764 ( 6) link_BETA1-4 : bond 0.00385 ( 2) link_BETA1-4 : angle 2.17013 ( 6) hydrogen bonds : bond 0.04181 ( 762) hydrogen bonds : angle 5.04771 ( 2238) SS BOND : bond 0.00240 ( 18) SS BOND : angle 1.54427 ( 36) covalent geometry : bond 0.00428 (16868) covalent geometry : angle 0.65313 (22978) *********************** 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 348 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 305 time to evaluate : 2.022 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 400 MET cc_start: 0.8317 (tpp) cc_final: 0.7872 (tpp) REVERT: R 499 TRP cc_start: 0.6890 (m100) cc_final: 0.5969 (m100) REVERT: R 537 TYR cc_start: 0.8689 (p90) cc_final: 0.8082 (p90) REVERT: R 606 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8840 (tt) REVERT: R 630 PHE cc_start: 0.8815 (m-80) cc_final: 0.8496 (m-80) REVERT: R 674 LYS cc_start: 0.8439 (mttt) cc_final: 0.8155 (mmmt) REVERT: R 744 ASP cc_start: 0.8236 (m-30) cc_final: 0.7947 (t70) REVERT: R 822 LYS cc_start: 0.8113 (mmmt) cc_final: 0.7474 (mmmt) REVERT: A 52 ARG cc_start: 0.7490 (mtm180) cc_final: 0.7019 (mtm-85) REVERT: A 100 LEU cc_start: 0.9443 (mp) cc_final: 0.9114 (tt) REVERT: A 147 LYS cc_start: 0.8750 (mttt) cc_final: 0.8144 (mtpp) REVERT: A 306 LEU cc_start: 0.7007 (tp) cc_final: 0.6703 (tp) REVERT: S 103 THR cc_start: 0.8319 (t) cc_final: 0.7489 (m) REVERT: S 1030 PHE cc_start: 0.7469 (p90) cc_final: 0.6985 (p90) REVERT: S 1101 ARG cc_start: 0.7884 (tmt170) cc_final: 0.7386 (ttt-90) REVERT: B 70 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6998 (mm-30) REVERT: B 391 MET cc_start: 0.7661 (ppp) cc_final: 0.7178 (ttp) REVERT: B 479 SER cc_start: 0.7731 (OUTLIER) cc_final: 0.7483 (m) REVERT: B 593 MET cc_start: 0.1245 (ptt) cc_final: 0.1023 (ptt) REVERT: B 660 LEU cc_start: 0.8365 (tp) cc_final: 0.8053 (pp) REVERT: B 754 TYR cc_start: 0.8383 (m-80) cc_final: 0.8159 (t80) REVERT: B 765 PHE cc_start: 0.8103 (m-80) cc_final: 0.7893 (m-80) REVERT: B 775 MET cc_start: 0.7513 (tpp) cc_final: 0.7204 (tpp) REVERT: B 779 CYS cc_start: 0.8574 (m) cc_final: 0.8371 (m) REVERT: B 803 MET cc_start: 0.8373 (mmm) cc_final: 0.8006 (mpp) outliers start: 43 outliers final: 26 residues processed: 327 average time/residue: 0.2703 time to fit residues: 135.1387 Evaluate side-chains 306 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 278 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 ILE Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 241 ILE 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 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 606 LEU Chi-restraints excluded: chain R residue 726 VAL 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 223 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 1089 LEU Chi-restraints excluded: chain S residue 1093 ASP Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 764 ASN Chi-restraints excluded: chain B residue 773 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 116 optimal weight: 0.3980 chunk 156 optimal weight: 0.8980 chunk 170 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 141 optimal weight: 0.2980 chunk 169 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 60 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 90 GLN ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.115409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.096940 restraints weight = 61157.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.098481 restraints weight = 38108.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.100040 restraints weight = 22561.308| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3663 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3663 r_free = 0.3663 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3663 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16890 Z= 0.133 Angle : 0.629 9.249 23026 Z= 0.316 Chirality : 0.044 0.210 2657 Planarity : 0.004 0.064 2898 Dihedral : 5.606 64.330 2543 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.98 % Favored : 92.98 % Rotamer: Outliers : 1.90 % Allowed : 19.94 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.18), residues: 2121 helix: 0.84 (0.18), residues: 754 sheet: -0.92 (0.27), residues: 380 loop : -2.12 (0.19), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 303 HIS 0.006 0.001 HIS A 159 PHE 0.029 0.002 PHE R 789 TYR 0.042 0.001 TYR R 776 ARG 0.005 0.001 ARG R 331 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 2) link_NAG-ASN : angle 2.41040 ( 6) link_BETA1-4 : bond 0.00261 ( 2) link_BETA1-4 : angle 2.00808 ( 6) hydrogen bonds : bond 0.03983 ( 762) hydrogen bonds : angle 4.95536 ( 2238) SS BOND : bond 0.00191 ( 18) SS BOND : angle 1.49825 ( 36) covalent geometry : bond 0.00297 (16868) covalent geometry : angle 0.62479 (22978) *********************** 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 329 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 297 time to evaluate : 1.767 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: 0.8293 (tpp) cc_final: 0.8052 (tpt) REVERT: R 537 TYR cc_start: 0.8740 (p90) cc_final: 0.8120 (p90) REVERT: R 606 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8751 (tt) REVERT: R 630 PHE cc_start: 0.8763 (m-80) cc_final: 0.8448 (m-80) REVERT: R 674 LYS cc_start: 0.8411 (mttt) cc_final: 0.8104 (mmmt) REVERT: R 763 GLU cc_start: 0.7985 (tp30) cc_final: 0.7690 (mt-10) REVERT: R 775 MET cc_start: 0.8474 (mmp) cc_final: 0.7895 (mmt) REVERT: R 782 TRP cc_start: 0.7708 (m-10) cc_final: 0.7441 (m-10) REVERT: A 52 ARG cc_start: 0.7432 (mtm180) cc_final: 0.6984 (mtm-85) REVERT: A 69 ASP cc_start: 0.8991 (m-30) cc_final: 0.8650 (p0) REVERT: A 100 LEU cc_start: 0.9437 (mp) cc_final: 0.9121 (tt) REVERT: A 147 LYS cc_start: 0.8714 (mttt) cc_final: 0.8169 (ttmm) REVERT: A 306 LEU cc_start: 0.6984 (tp) cc_final: 0.6629 (tp) REVERT: S 7 GLN cc_start: 0.7428 (tt0) cc_final: 0.7186 (tt0) REVERT: S 39 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7953 (pt0) REVERT: S 40 LYS cc_start: 0.8939 (mmtp) cc_final: 0.8610 (mmtm) REVERT: S 1030 PHE cc_start: 0.7480 (p90) cc_final: 0.6970 (p90) REVERT: S 1042 GLN cc_start: 0.7779 (mt0) cc_final: 0.7502 (mt0) REVERT: S 1048 LEU cc_start: 0.8429 (mt) cc_final: 0.8109 (mt) REVERT: S 1101 ARG cc_start: 0.7649 (tmt170) cc_final: 0.7163 (ttt-90) REVERT: B 391 MET cc_start: 0.7591 (ppp) cc_final: 0.7049 (ttp) REVERT: B 463 MET cc_start: 0.6356 (ttm) cc_final: 0.5884 (tmm) REVERT: B 593 MET cc_start: 0.1142 (ptt) cc_final: 0.0933 (ptt) REVERT: B 660 LEU cc_start: 0.8372 (tp) cc_final: 0.8084 (pp) REVERT: B 754 TYR cc_start: 0.8373 (m-80) cc_final: 0.8150 (t80) REVERT: B 803 MET cc_start: 0.8390 (mmm) cc_final: 0.8053 (mpp) outliers start: 32 outliers final: 18 residues processed: 315 average time/residue: 0.2863 time to fit residues: 138.0651 Evaluate side-chains 287 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 267 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 214 SER 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 454 VAL Chi-restraints excluded: chain R residue 479 SER Chi-restraints excluded: chain R residue 606 LEU Chi-restraints excluded: chain R residue 726 VAL 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 149 PHE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 1089 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 404 LEU 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 49 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 179 optimal weight: 0.0770 overall best weight: 1.9742 ------------------------------------------------------------------------------- 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 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 38 GLN S 39 GLN S 90 GLN S1042 GLN ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.112593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.094437 restraints weight = 61982.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.095157 restraints weight = 35709.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.095978 restraints weight = 24689.611| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 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 = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 16890 Z= 0.229 Angle : 0.670 10.814 23026 Z= 0.347 Chirality : 0.045 0.180 2657 Planarity : 0.005 0.063 2898 Dihedral : 5.761 64.193 2543 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 3.50 % Allowed : 20.00 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.18), residues: 2121 helix: 0.63 (0.18), residues: 754 sheet: -1.06 (0.27), residues: 378 loop : -2.15 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 303 HIS 0.006 0.001 HIS A 159 PHE 0.023 0.002 PHE R 670 TYR 0.016 0.002 TYR R 796 ARG 0.010 0.001 ARG S1103 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 2) link_NAG-ASN : angle 3.32546 ( 6) link_BETA1-4 : bond 0.00125 ( 2) link_BETA1-4 : angle 2.19011 ( 6) hydrogen bonds : bond 0.04231 ( 762) hydrogen bonds : angle 5.07968 ( 2238) SS BOND : bond 0.00322 ( 18) SS BOND : angle 1.97775 ( 36) covalent geometry : bond 0.00513 (16868) covalent geometry : angle 0.66265 (22978) *********************** 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 337 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 278 time to evaluate : 2.061 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: 0.8508 (tpp) cc_final: 0.7964 (tpp) REVERT: R 537 TYR cc_start: 0.8698 (p90) cc_final: 0.8086 (p90) REVERT: R 606 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8836 (tt) REVERT: R 630 PHE cc_start: 0.8819 (m-80) cc_final: 0.8429 (m-80) REVERT: R 674 LYS cc_start: 0.8423 (mttt) cc_final: 0.8105 (mmmt) REVERT: R 702 MET cc_start: 0.8741 (mmm) cc_final: 0.8433 (mmm) REVERT: R 763 GLU cc_start: 0.8151 (tp30) cc_final: 0.7865 (mt-10) REVERT: R 775 MET cc_start: 0.8529 (mmp) cc_final: 0.7782 (mmt) REVERT: R 782 TRP cc_start: 0.7775 (m-10) cc_final: 0.7467 (m-10) REVERT: R 803 MET cc_start: 0.8260 (tpp) cc_final: 0.8006 (tpp) REVERT: A 99 ARG cc_start: 0.8364 (tpp-160) cc_final: 0.7883 (tpm170) REVERT: A 100 LEU cc_start: 0.9463 (mp) cc_final: 0.9159 (tt) REVERT: A 145 GLU cc_start: 0.7491 (mp0) cc_final: 0.7258 (mp0) REVERT: A 147 LYS cc_start: 0.8775 (mttt) cc_final: 0.8161 (mtpp) REVERT: A 240 ASP cc_start: 0.7705 (m-30) cc_final: 0.7293 (m-30) REVERT: A 306 LEU cc_start: 0.7022 (tp) cc_final: 0.6632 (tp) REVERT: S 90 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7618 (tm130) REVERT: S 1030 PHE cc_start: 0.7448 (p90) cc_final: 0.6967 (p90) REVERT: S 1048 LEU cc_start: 0.8451 (mt) cc_final: 0.8130 (mt) REVERT: S 1101 ARG cc_start: 0.8046 (tmt170) cc_final: 0.7618 (ttt-90) REVERT: B 391 MET cc_start: 0.7629 (ppp) cc_final: 0.7340 (ttp) REVERT: B 571 ARG cc_start: 0.6383 (tpm170) cc_final: 0.5617 (tpm170) REVERT: B 660 LEU cc_start: 0.8354 (tp) cc_final: 0.8075 (pp) REVERT: B 727 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8707 (tp) REVERT: B 779 CYS cc_start: 0.8926 (m) cc_final: 0.8648 (p) REVERT: B 803 MET cc_start: 0.8317 (mmm) cc_final: 0.8036 (mpp) outliers start: 59 outliers final: 41 residues processed: 312 average time/residue: 0.2686 time to fit residues: 128.9303 Evaluate side-chains 316 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 272 time to evaluate : 1.959 ------------------------------------------------------------------------------- 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 241 ILE Chi-restraints excluded: chain R residue 276 MET Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 322 THR Chi-restraints excluded: chain R residue 331 ARG 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 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 606 LEU Chi-restraints excluded: chain R residue 643 LEU Chi-restraints excluded: chain R residue 726 VAL Chi-restraints excluded: chain R residue 727 ILE Chi-restraints excluded: chain R residue 744 ASP 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 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 A residue 281 ASN Chi-restraints excluded: chain S residue 90 GLN Chi-restraints excluded: chain S residue 1020 SER Chi-restraints excluded: chain S residue 1049 GLU Chi-restraints excluded: chain S residue 1089 LEU Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 441 THR 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 Chi-restraints excluded: chain B residue 727 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 196 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 161 optimal weight: 0.0050 chunk 53 optimal weight: 8.9990 chunk 194 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN S 39 GLN S1042 GLN ** B 159 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 = 0.3935 r_free = 0.3935 target = 0.113393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.095709 restraints weight = 61582.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.096074 restraints weight = 36857.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.096802 restraints weight = 27063.902| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3604 r_free = 0.3604 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 = 0.3604 r_free = 0.3604 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16890 Z= 0.174 Angle : 0.642 9.586 23026 Z= 0.327 Chirality : 0.044 0.238 2657 Planarity : 0.004 0.061 2898 Dihedral : 5.680 64.464 2543 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.26 % Allowed : 21.42 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.18), residues: 2121 helix: 0.62 (0.18), residues: 755 sheet: -1.07 (0.27), residues: 373 loop : -2.17 (0.19), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 303 HIS 0.007 0.001 HIS A 159 PHE 0.021 0.002 PHE R 670 TYR 0.016 0.002 TYR B 569 ARG 0.004 0.000 ARG B 571 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 2) link_NAG-ASN : angle 2.70704 ( 6) link_BETA1-4 : bond 0.00268 ( 2) link_BETA1-4 : angle 2.06002 ( 6) hydrogen bonds : bond 0.04037 ( 762) hydrogen bonds : angle 4.95892 ( 2238) SS BOND : bond 0.00475 ( 18) SS BOND : angle 1.23994 ( 36) covalent geometry : bond 0.00389 (16868) covalent geometry : angle 0.63870 (22978) *********************** 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 337 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 282 time to evaluate : 1.972 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 276 MET cc_start: 0.7658 (ptt) cc_final: 0.7270 (ptt) REVERT: R 400 MET cc_start: 0.8409 (tpp) cc_final: 0.8186 (tpt) REVERT: R 537 TYR cc_start: 0.8675 (p90) cc_final: 0.8050 (p90) REVERT: R 606 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8444 (tt) REVERT: R 630 PHE cc_start: 0.8758 (m-80) cc_final: 0.8374 (m-80) REVERT: R 674 LYS cc_start: 0.8393 (mttt) cc_final: 0.8118 (mmmt) REVERT: R 702 MET cc_start: 0.8712 (mmm) cc_final: 0.8436 (mmm) REVERT: R 763 GLU cc_start: 0.8201 (tp30) cc_final: 0.7884 (mt-10) REVERT: R 764 ASN cc_start: 0.7555 (m-40) cc_final: 0.7327 (t0) REVERT: R 775 MET cc_start: 0.8550 (mmp) cc_final: 0.8214 (mmp) REVERT: R 782 TRP cc_start: 0.7792 (m-10) cc_final: 0.7499 (m-10) REVERT: A 52 ARG cc_start: 0.7329 (mtm180) cc_final: 0.6872 (mtm-85) REVERT: A 69 ASP cc_start: 0.9031 (m-30) cc_final: 0.8766 (p0) REVERT: A 99 ARG cc_start: 0.8357 (tpp-160) cc_final: 0.7899 (tpm170) REVERT: A 100 LEU cc_start: 0.9468 (mp) cc_final: 0.9181 (tt) REVERT: A 145 GLU cc_start: 0.7479 (mp0) cc_final: 0.7266 (mp0) REVERT: A 147 LYS cc_start: 0.8776 (mttt) cc_final: 0.8143 (mtpp) REVERT: A 306 LEU cc_start: 0.6969 (tp) cc_final: 0.6564 (tp) REVERT: S 39 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7722 (pt0) REVERT: S 1030 PHE cc_start: 0.7358 (p90) cc_final: 0.6832 (p90) REVERT: S 1042 GLN cc_start: 0.7976 (mt0) cc_final: 0.7551 (mt0) REVERT: S 1048 LEU cc_start: 0.8270 (mt) cc_final: 0.7975 (mt) REVERT: S 1049 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7814 (mm-30) REVERT: S 1101 ARG cc_start: 0.8088 (tmt170) cc_final: 0.7534 (ttt-90) REVERT: S 1103 ARG cc_start: 0.7559 (tmm160) cc_final: 0.7351 (ttt-90) REVERT: B 391 MET cc_start: 0.7591 (ppp) cc_final: 0.7266 (ttp) REVERT: B 521 MET cc_start: 0.7423 (ppp) cc_final: 0.7222 (ppp) REVERT: B 571 ARG cc_start: 0.6074 (tpm170) cc_final: 0.5796 (tpm170) REVERT: B 660 LEU cc_start: 0.8351 (tp) cc_final: 0.8060 (pp) REVERT: B 727 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8782 (tp) REVERT: B 766 ASN cc_start: 0.7977 (t0) cc_final: 0.7645 (t0) REVERT: B 803 MET cc_start: 0.8317 (mmm) cc_final: 0.8057 (mpp) outliers start: 55 outliers final: 37 residues processed: 309 average time/residue: 0.2657 time to fit residues: 126.0623 Evaluate side-chains 313 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 272 time to evaluate : 1.887 ------------------------------------------------------------------------------- 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 322 THR Chi-restraints excluded: chain R residue 331 ARG 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 407 MET Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 454 VAL Chi-restraints excluded: chain R residue 463 MET Chi-restraints excluded: chain R residue 479 SER Chi-restraints excluded: chain R residue 590 CYS Chi-restraints excluded: chain R residue 606 LEU Chi-restraints excluded: chain R residue 671 ASP Chi-restraints excluded: chain R residue 726 VAL Chi-restraints excluded: chain R residue 727 ILE Chi-restraints excluded: chain R residue 744 ASP Chi-restraints excluded: chain R residue 785 PHE Chi-restraints excluded: chain A residue 40 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 39 GLN Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 1049 GLU Chi-restraints excluded: chain S residue 1089 LEU Chi-restraints excluded: chain S residue 1093 ASP Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 537 TYR Chi-restraints excluded: chain B residue 628 MET Chi-restraints excluded: chain B residue 683 ILE Chi-restraints excluded: chain B residue 727 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 116 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 197 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 105 optimal weight: 0.2980 chunk 193 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 281 ASN S 90 GLN ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.113262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.094566 restraints weight = 61621.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.095922 restraints weight = 38540.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.097236 restraints weight = 24676.980| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 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 = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16890 Z= 0.145 Angle : 0.614 9.641 23026 Z= 0.311 Chirality : 0.043 0.192 2657 Planarity : 0.004 0.062 2898 Dihedral : 5.575 64.019 2543 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.32 % Allowed : 21.60 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.18), residues: 2121 helix: 0.65 (0.18), residues: 755 sheet: -1.05 (0.27), residues: 389 loop : -2.12 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 303 HIS 0.007 0.001 HIS A 159 PHE 0.020 0.002 PHE B 187 TYR 0.044 0.001 TYR R 776 ARG 0.004 0.000 ARG B 261 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 2) link_NAG-ASN : angle 2.32770 ( 6) link_BETA1-4 : bond 0.00303 ( 2) link_BETA1-4 : angle 1.98574 ( 6) hydrogen bonds : bond 0.03917 ( 762) hydrogen bonds : angle 4.89442 ( 2238) SS BOND : bond 0.00228 ( 18) SS BOND : angle 1.44009 ( 36) covalent geometry : bond 0.00325 (16868) covalent geometry : angle 0.60996 (22978) *********************** 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 338 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 282 time to evaluate : 1.935 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 276 MET cc_start: 0.7655 (ptt) cc_final: 0.7260 (ptt) REVERT: R 400 MET cc_start: 0.8434 (tpp) cc_final: 0.8191 (tpt) REVERT: R 537 TYR cc_start: 0.8713 (p90) cc_final: 0.8073 (p90) REVERT: R 606 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8543 (tt) REVERT: R 630 PHE cc_start: 0.8683 (m-80) cc_final: 0.8287 (m-80) REVERT: R 674 LYS cc_start: 0.8376 (mttt) cc_final: 0.8083 (mmmt) REVERT: R 702 MET cc_start: 0.8718 (mmm) cc_final: 0.8435 (mmm) REVERT: R 763 GLU cc_start: 0.8293 (tp30) cc_final: 0.7813 (mt-10) REVERT: R 764 ASN cc_start: 0.7552 (m-40) cc_final: 0.7256 (t0) REVERT: R 782 TRP cc_start: 0.7716 (m-10) cc_final: 0.7456 (m-10) REVERT: R 783 LEU cc_start: 0.8864 (mt) cc_final: 0.8559 (mt) REVERT: A 69 ASP cc_start: 0.9013 (m-30) cc_final: 0.8734 (p0) REVERT: A 99 ARG cc_start: 0.8323 (tpp-160) cc_final: 0.7910 (tpm170) REVERT: A 100 LEU cc_start: 0.9481 (mp) cc_final: 0.9196 (tt) REVERT: A 145 GLU cc_start: 0.7446 (mp0) cc_final: 0.7198 (mp0) REVERT: A 147 LYS cc_start: 0.8737 (mttt) cc_final: 0.8152 (ttmm) REVERT: A 306 LEU cc_start: 0.6898 (tp) cc_final: 0.6512 (tp) REVERT: S 39 GLN cc_start: 0.8341 (pp30) cc_final: 0.8070 (pp30) REVERT: S 1030 PHE cc_start: 0.7381 (p90) cc_final: 0.6813 (p90) REVERT: S 1101 ARG cc_start: 0.7927 (tmt170) cc_final: 0.7435 (ttt-90) REVERT: B 391 MET cc_start: 0.7623 (ppp) cc_final: 0.7228 (ttp) REVERT: B 463 MET cc_start: 0.6348 (ttm) cc_final: 0.5878 (tmm) REVERT: B 521 MET cc_start: 0.7545 (ppp) cc_final: 0.7245 (ppp) REVERT: B 660 LEU cc_start: 0.8332 (tp) cc_final: 0.8054 (pp) REVERT: B 727 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8785 (tp) REVERT: B 766 ASN cc_start: 0.7986 (t0) cc_final: 0.7751 (t0) REVERT: B 803 MET cc_start: 0.8355 (mmm) cc_final: 0.8061 (mpp) outliers start: 56 outliers final: 39 residues processed: 314 average time/residue: 0.2659 time to fit residues: 128.4120 Evaluate side-chains 305 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 264 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU 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 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 402 HIS Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 463 MET Chi-restraints excluded: chain R residue 474 VAL Chi-restraints excluded: chain R residue 479 SER Chi-restraints excluded: chain R residue 606 LEU Chi-restraints excluded: chain R residue 671 ASP Chi-restraints excluded: chain R residue 727 ILE Chi-restraints excluded: chain R residue 744 ASP 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 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 48 LEU Chi-restraints excluded: chain S residue 73 THR Chi-restraints excluded: chain S residue 1089 LEU Chi-restraints excluded: chain S residue 1093 ASP Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain B residue 400 MET Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 537 TYR Chi-restraints excluded: chain B residue 683 ILE Chi-restraints excluded: chain B residue 727 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 52 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 127 optimal weight: 6.9990 chunk 22 optimal weight: 0.2980 chunk 26 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 232 GLN S 39 GLN ** B 159 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 = 0.3927 r_free = 0.3927 target = 0.113808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.095439 restraints weight = 61226.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.096857 restraints weight = 37844.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.097647 restraints weight = 24111.141| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3588 |-occupancy refinement: start-------------------------------------------------| | 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 | |-----------------------------------------------------------------------------| |-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: 0.7376 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16890 Z= 0.134 Angle : 0.618 10.581 23026 Z= 0.313 Chirality : 0.044 0.205 2657 Planarity : 0.004 0.063 2898 Dihedral : 5.509 64.554 2543 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 2.85 % Allowed : 22.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.18), residues: 2121 helix: 0.69 (0.18), residues: 757 sheet: -0.99 (0.27), residues: 401 loop : -2.07 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 706 HIS 0.006 0.001 HIS A 159 PHE 0.022 0.001 PHE A 268 TYR 0.014 0.001 TYR B 384 ARG 0.006 0.000 ARG R 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 2) link_NAG-ASN : angle 2.10309 ( 6) link_BETA1-4 : bond 0.00349 ( 2) link_BETA1-4 : angle 1.95015 ( 6) hydrogen bonds : bond 0.03895 ( 762) hydrogen bonds : angle 4.86474 ( 2238) SS BOND : bond 0.00308 ( 18) SS BOND : angle 1.30974 ( 36) covalent geometry : bond 0.00299 (16868) covalent geometry : angle 0.61519 (22978) *********************** 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 320 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 272 time to evaluate : 1.968 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: R 276 MET cc_start: 0.7588 (ptt) cc_final: 0.7240 (ptt) REVERT: R 400 MET cc_start: 0.8393 (tpp) cc_final: 0.8118 (tpt) REVERT: R 422 MET cc_start: 0.6530 (mtt) cc_final: 0.6273 (mtt) REVERT: R 537 TYR cc_start: 0.8707 (p90) cc_final: 0.8070 (p90) REVERT: R 606 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8474 (tt) REVERT: R 630 PHE cc_start: 0.8696 (m-80) cc_final: 0.8308 (m-80) REVERT: R 674 LYS cc_start: 0.8376 (mttt) cc_final: 0.8107 (mmmt) REVERT: R 702 MET cc_start: 0.8690 (mmm) cc_final: 0.8409 (mmm) REVERT: R 763 GLU cc_start: 0.8310 (tp30) cc_final: 0.7814 (mt-10) REVERT: R 764 ASN cc_start: 0.7480 (m-40) cc_final: 0.7207 (t0) REVERT: R 775 MET cc_start: 0.8368 (mmp) cc_final: 0.7710 (mmt) REVERT: R 782 TRP cc_start: 0.7685 (m-10) cc_final: 0.7425 (m-10) REVERT: R 783 LEU cc_start: 0.8855 (mt) cc_final: 0.8543 (mt) REVERT: A 69 ASP cc_start: 0.8988 (m-30) cc_final: 0.8730 (p0) REVERT: A 99 ARG cc_start: 0.8328 (tpp-160) cc_final: 0.7913 (tpm170) REVERT: A 100 LEU cc_start: 0.9488 (mp) cc_final: 0.9174 (tt) REVERT: A 145 GLU cc_start: 0.7469 (mp0) cc_final: 0.7230 (mp0) REVERT: A 147 LYS cc_start: 0.8745 (mttt) cc_final: 0.8152 (ttmm) REVERT: A 306 LEU cc_start: 0.6926 (tp) cc_final: 0.6525 (tp) REVERT: S 1030 PHE cc_start: 0.7369 (p90) cc_final: 0.6814 (p90) REVERT: S 1101 ARG cc_start: 0.7931 (tmt170) cc_final: 0.7420 (ttt-90) REVERT: B 391 MET cc_start: 0.7594 (ppp) cc_final: 0.7220 (ttp) REVERT: B 463 MET cc_start: 0.6406 (ttm) cc_final: 0.5918 (tmm) REVERT: B 660 LEU cc_start: 0.8331 (tp) cc_final: 0.8074 (pp) REVERT: B 727 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8751 (tp) REVERT: B 766 ASN cc_start: 0.7962 (t0) cc_final: 0.7727 (t0) REVERT: B 803 MET cc_start: 0.8352 (mmm) cc_final: 0.8061 (mpp) outliers start: 48 outliers final: 36 residues processed: 302 average time/residue: 0.2570 time to fit residues: 121.0301 Evaluate side-chains 298 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 260 time to evaluate : 1.786 ------------------------------------------------------------------------------- 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 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 402 HIS Chi-restraints excluded: chain R residue 407 MET Chi-restraints excluded: chain R residue 463 MET Chi-restraints excluded: chain R residue 474 VAL Chi-restraints excluded: chain R residue 479 SER Chi-restraints excluded: chain R residue 606 LEU Chi-restraints excluded: chain R residue 671 ASP Chi-restraints excluded: chain R residue 727 ILE Chi-restraints excluded: chain R residue 744 ASP Chi-restraints excluded: chain R residue 785 PHE Chi-restraints excluded: chain A residue 40 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 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 1093 ASP Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 400 MET Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 509 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 727 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 150 optimal weight: 0.5980 chunk 146 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 182 optimal weight: 0.0570 chunk 207 optimal weight: 4.9990 chunk 177 optimal weight: 0.0870 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.114497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.096061 restraints weight = 61477.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.097948 restraints weight = 35965.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.098511 restraints weight = 21938.742| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 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 = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3608 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16890 Z= 0.127 Angle : 0.638 13.188 23026 Z= 0.320 Chirality : 0.044 0.235 2657 Planarity : 0.004 0.063 2898 Dihedral : 5.439 64.433 2543 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.43 % Allowed : 23.38 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.18), residues: 2121 helix: 0.72 (0.18), residues: 757 sheet: -0.95 (0.27), residues: 401 loop : -2.04 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 706 HIS 0.006 0.001 HIS A 159 PHE 0.029 0.001 PHE B 275 TYR 0.013 0.001 TYR B 754 ARG 0.006 0.000 ARG R 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 2) link_NAG-ASN : angle 1.88939 ( 6) link_BETA1-4 : bond 0.00547 ( 2) link_BETA1-4 : angle 1.89180 ( 6) hydrogen bonds : bond 0.03823 ( 762) hydrogen bonds : angle 4.87211 ( 2238) SS BOND : bond 0.00610 ( 18) SS BOND : angle 1.38409 ( 36) covalent geometry : bond 0.00281 (16868) covalent geometry : angle 0.63460 (22978) *********************** 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 317 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 276 time to evaluate : 2.016 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: R 276 MET cc_start: 0.7536 (ptt) cc_final: 0.7208 (ptt) REVERT: R 391 MET cc_start: 0.7857 (tmm) cc_final: 0.7037 (tmm) REVERT: R 400 MET cc_start: 0.8339 (tpp) cc_final: 0.8079 (tpt) REVERT: R 537 TYR cc_start: 0.8706 (p90) cc_final: 0.8054 (p90) REVERT: R 606 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8506 (tt) REVERT: R 630 PHE cc_start: 0.8645 (m-80) cc_final: 0.8261 (m-80) REVERT: R 674 LYS cc_start: 0.8381 (mttt) cc_final: 0.8109 (mmmt) REVERT: R 702 MET cc_start: 0.8607 (mmm) cc_final: 0.8355 (mmm) REVERT: R 763 GLU cc_start: 0.8326 (tp30) cc_final: 0.7827 (mt-10) REVERT: R 764 ASN cc_start: 0.7469 (m-40) cc_final: 0.7192 (t0) REVERT: R 775 MET cc_start: 0.8392 (mmp) cc_final: 0.7697 (mmt) REVERT: R 782 TRP cc_start: 0.7645 (m-10) cc_final: 0.7420 (m-10) REVERT: R 783 LEU cc_start: 0.8863 (mt) cc_final: 0.8547 (mt) REVERT: R 803 MET cc_start: 0.8333 (tpp) cc_final: 0.8104 (mmp) REVERT: A 69 ASP cc_start: 0.8988 (m-30) cc_final: 0.8712 (p0) REVERT: A 99 ARG cc_start: 0.8349 (tpp-160) cc_final: 0.7928 (tpm170) REVERT: A 100 LEU cc_start: 0.9496 (mp) cc_final: 0.9232 (tt) REVERT: A 145 GLU cc_start: 0.7454 (mp0) cc_final: 0.7192 (mp0) REVERT: A 147 LYS cc_start: 0.8726 (mttt) cc_final: 0.8140 (ttmm) REVERT: A 248 GLN cc_start: 0.8691 (tt0) cc_final: 0.8444 (tt0) REVERT: A 306 LEU cc_start: 0.6974 (tp) cc_final: 0.6588 (tp) REVERT: S 39 GLN cc_start: 0.8136 (pp30) cc_final: 0.7803 (pt0) REVERT: S 91 GLN cc_start: 0.8079 (pp30) cc_final: 0.7455 (pp30) REVERT: S 1030 PHE cc_start: 0.7431 (p90) cc_final: 0.6907 (p90) REVERT: S 1042 GLN cc_start: 0.8104 (mt0) cc_final: 0.7635 (mm-40) REVERT: S 1048 LEU cc_start: 0.8157 (mt) cc_final: 0.7919 (mt) REVERT: S 1049 GLU cc_start: 0.8310 (tp30) cc_final: 0.7454 (pm20) REVERT: S 1101 ARG cc_start: 0.7877 (tmt170) cc_final: 0.7451 (ttt-90) REVERT: B 272 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8635 (m) REVERT: B 391 MET cc_start: 0.7599 (ppp) cc_final: 0.7060 (ttp) REVERT: B 463 MET cc_start: 0.6350 (ttm) cc_final: 0.5939 (tmm) REVERT: B 521 MET cc_start: 0.7665 (ppp) cc_final: 0.7363 (ppp) REVERT: B 660 LEU cc_start: 0.8344 (tp) cc_final: 0.8086 (pp) REVERT: B 727 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8776 (tp) REVERT: B 766 ASN cc_start: 0.7876 (t0) cc_final: 0.7572 (t0) REVERT: B 803 MET cc_start: 0.8365 (mmm) cc_final: 0.8059 (mpp) outliers start: 41 outliers final: 33 residues processed: 302 average time/residue: 0.2465 time to fit residues: 116.1792 Evaluate side-chains 302 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 266 time to evaluate : 1.836 ------------------------------------------------------------------------------- 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 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 407 MET Chi-restraints excluded: chain R residue 415 THR Chi-restraints excluded: chain R residue 463 MET Chi-restraints excluded: chain R residue 474 VAL Chi-restraints excluded: chain R residue 479 SER Chi-restraints excluded: chain R residue 606 LEU 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 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 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 272 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 400 MET Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 488 GLU Chi-restraints excluded: chain B residue 509 CYS Chi-restraints excluded: chain B residue 537 TYR Chi-restraints excluded: chain B residue 683 ILE Chi-restraints excluded: chain B residue 727 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 122 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 212 optimal weight: 8.9990 chunk 179 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 213 optimal weight: 0.0870 chunk 211 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 GLN ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.110993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.090423 restraints weight = 61859.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.092413 restraints weight = 36241.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.093541 restraints weight = 24544.442| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3525 |-occupancy refinement: start-------------------------------------------------| | 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 | |-----------------------------------------------------------------------------| |-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: 0.7505 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 16890 Z= 0.249 Angle : 0.725 15.900 23026 Z= 0.371 Chirality : 0.046 0.217 2657 Planarity : 0.005 0.068 2898 Dihedral : 5.719 64.084 2543 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 2.73 % Allowed : 23.68 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.18), residues: 2121 helix: 0.51 (0.18), residues: 755 sheet: -1.10 (0.27), residues: 394 loop : -2.10 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 706 HIS 0.007 0.001 HIS A 159 PHE 0.033 0.002 PHE B 295 TYR 0.025 0.002 TYR B 754 ARG 0.019 0.001 ARG S1041 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 2) link_NAG-ASN : angle 2.83089 ( 6) link_BETA1-4 : bond 0.00124 ( 2) link_BETA1-4 : angle 2.08682 ( 6) hydrogen bonds : bond 0.04228 ( 762) hydrogen bonds : angle 5.15909 ( 2238) SS BOND : bond 0.00389 ( 18) SS BOND : angle 1.59986 ( 36) covalent geometry : bond 0.00552 (16868) covalent geometry : angle 0.72077 (22978) ********************** 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 307 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 261 time to evaluate : 1.919 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: R 276 MET cc_start: 0.7648 (ptt) cc_final: 0.7315 (ptt) REVERT: R 400 MET cc_start: 0.8523 (tpp) cc_final: 0.7937 (tpp) REVERT: R 537 TYR cc_start: 0.8634 (p90) cc_final: 0.7986 (p90) REVERT: R 606 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8614 (tt) REVERT: R 630 PHE cc_start: 0.8666 (m-80) cc_final: 0.8230 (m-80) REVERT: R 674 LYS cc_start: 0.8382 (mttt) cc_final: 0.8103 (mmmt) REVERT: R 702 MET cc_start: 0.8707 (mmm) cc_final: 0.8408 (mmm) REVERT: R 763 GLU cc_start: 0.8407 (tp30) cc_final: 0.7954 (mt-10) REVERT: R 764 ASN cc_start: 0.7862 (m-40) cc_final: 0.7633 (t0) REVERT: R 783 LEU cc_start: 0.8858 (mt) cc_final: 0.8549 (mt) REVERT: R 803 MET cc_start: 0.8317 (tpp) cc_final: 0.7951 (mmp) REVERT: A 69 ASP cc_start: 0.8971 (m-30) cc_final: 0.8758 (p0) REVERT: A 145 GLU cc_start: 0.7520 (mp0) cc_final: 0.7291 (mp0) REVERT: A 147 LYS cc_start: 0.8788 (mttt) cc_final: 0.8124 (mtpp) REVERT: A 248 GLN cc_start: 0.8758 (tt0) cc_final: 0.8417 (tt0) REVERT: A 306 LEU cc_start: 0.6924 (tp) cc_final: 0.6523 (tp) REVERT: S 1042 GLN cc_start: 0.8064 (mt0) cc_final: 0.7578 (mm-40) REVERT: S 1049 GLU cc_start: 0.8377 (tp30) cc_final: 0.7478 (pm20) REVERT: S 1101 ARG cc_start: 0.8021 (tmt170) cc_final: 0.7590 (ttt-90) REVERT: B 463 MET cc_start: 0.6545 (ttm) cc_final: 0.6044 (tmm) REVERT: B 660 LEU cc_start: 0.8261 (tp) cc_final: 0.8041 (pp) REVERT: B 727 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8790 (tp) REVERT: B 803 MET cc_start: 0.8476 (mmm) cc_final: 0.8071 (mpp) outliers start: 46 outliers final: 37 residues processed: 289 average time/residue: 0.2524 time to fit residues: 114.2199 Evaluate side-chains 291 residues out of total 1880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 252 time to evaluate : 1.774 ------------------------------------------------------------------------------- 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 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 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 606 LEU Chi-restraints excluded: chain R residue 727 ILE Chi-restraints excluded: chain R residue 744 ASP Chi-restraints excluded: chain R residue 785 PHE Chi-restraints excluded: chain R residue 814 VAL 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 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 B residue 60 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 404 LEU 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 488 GLU Chi-restraints excluded: chain B residue 509 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 727 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 17 optimal weight: 2.9990 chunk 207 optimal weight: 0.0670 chunk 134 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 177 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 HIS ** B 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.113563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.095202 restraints weight = 61184.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.096366 restraints weight = 38525.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.097486 restraints weight = 24300.539| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 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 = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16890 Z= 0.140 Angle : 0.675 14.853 23026 Z= 0.337 Chirality : 0.045 0.239 2657 Planarity : 0.004 0.060 2898 Dihedral : 5.516 65.276 2543 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.20 % Allowed : 24.45 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.18), residues: 2121 helix: 0.66 (0.18), residues: 749 sheet: -1.02 (0.27), residues: 388 loop : -2.04 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 706 HIS 0.006 0.001 HIS A 159 PHE 0.024 0.002 PHE R 785 TYR 0.022 0.001 TYR B 754 ARG 0.013 0.001 ARG B 571 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 2) link_NAG-ASN : angle 1.97719 ( 6) link_BETA1-4 : bond 0.00421 ( 2) link_BETA1-4 : angle 1.89582 ( 6) hydrogen bonds : bond 0.03965 ( 762) hydrogen bonds : angle 4.99179 ( 2238) SS BOND : bond 0.00304 ( 18) SS BOND : angle 1.22277 ( 36) covalent geometry : bond 0.00310 (16868) covalent geometry : angle 0.67263 (22978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5623.89 seconds wall clock time: 99 minutes 26.60 seconds (5966.60 seconds total)