Starting phenix.real_space_refine on Wed Jul 30 04:48:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ceb_7463/07_2025/6ceb_7463_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ceb_7463/07_2025/6ceb_7463.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ceb_7463/07_2025/6ceb_7463.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ceb_7463/07_2025/6ceb_7463.map" model { file = "/net/cci-nas-00/data/ceres_data/6ceb_7463/07_2025/6ceb_7463_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ceb_7463/07_2025/6ceb_7463_neut.cif" } resolution = 4.7 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= 0.003 sd= 0.054 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 7417 2.51 5 N 1969 2.21 5 O 2240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11722 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 5500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5500 Classifications: {'peptide': 682} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 645} Chain breaks: 5 Chain: "B" Number of atoms: 4540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4540 Classifications: {'peptide': 562} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 4 Chain: "M" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 243 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 27} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "L" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 240 Classifications: {'peptide': 30} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "N" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 163 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "O" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 240 Classifications: {'peptide': 30} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "P" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 243 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 27} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" 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: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "A" 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: "B" 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 Time building chain proxies: 7.71, per 1000 atoms: 0.66 Number of scatterers: 11722 At special positions: 0 Unit cell: (91.3, 149.6, 154, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 2240 8.00 N 1969 7.00 C 7417 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.02 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 786 " - pdb=" SG CYS A 795 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.02 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.02 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS K 6 " - pdb=" SG CYS K 11 " distance=2.03 Simple disulfide: pdb=" SG CYS N 6 " - pdb=" SG CYS N 11 " 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 D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG Q 1 " - " NAG Q 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG E 1 " - " FUC E 3 " " NAG G 1 " - " FUC G 2 " " NAG H 1 " - " FUC H 3 " " NAG J 1 " - " FUC J 3 " " NAG R 1 " - " FUC R 2 " NAG-ASN " NAG A1014 " - " ASN A 16 " " NAG B1014 " - " ASN B 16 " " NAG C 1 " - " ASN A 25 " " NAG D 1 " - " ASN A 111 " " NAG E 1 " - " ASN A 255 " " NAG F 1 " - " ASN A 397 " " NAG G 1 " - " ASN A 418 " " NAG H 1 " - " ASN B 25 " " NAG I 1 " - " ASN B 111 " " NAG J 1 " - " ASN B 255 " " NAG Q 1 " - " ASN B 397 " " NAG R 1 " - " ASN B 418 " Time building additional restraints: 2.88 Conformation dependent library (CDL) restraints added in 1.5 seconds 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2656 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 29 sheets defined 17.6% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.648A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU A 24 " --> pdb=" O HIS A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 48 removed outlier: 3.628A pdb=" N ARG A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASP A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 48' Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.592A pdb=" N ASP A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN A 143 " --> pdb=" O VAL A 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 139 through 143' Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 221 through 224 Processing helix chain 'A' and resid 255 through 264 removed outlier: 3.847A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS A 263 " --> pdb=" O CYS A 259 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 350 through 356 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.834A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.815A pdb=" N GLN A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 498 No H-bonds generated for 'chain 'A' and resid 496 through 498' Processing helix chain 'A' and resid 638 through 644 removed outlier: 3.569A pdb=" N PHE A 642 " --> pdb=" O SER A 639 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU A 643 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 644 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 24 removed outlier: 3.741A pdb=" N HIS B 21 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU B 24 " --> pdb=" O HIS B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 removed outlier: 4.017A pdb=" N ARG B 47 " --> pdb=" O PRO B 43 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 48' Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.639A pdb=" N ASN B 143 " --> pdb=" O VAL B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 264 removed outlier: 3.759A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS B 263 " --> pdb=" O CYS B 259 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS B 264 " --> pdb=" O GLN B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 329 through 331 No H-bonds generated for 'chain 'B' and resid 329 through 331' Processing helix chain 'B' and resid 350 through 357 removed outlier: 3.738A pdb=" N ASN B 357 " --> pdb=" O GLU B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.834A pdb=" N ILE B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 452 removed outlier: 3.528A pdb=" N ARG B 451 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 448 through 452' Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'M' and resid 692 through 715 removed outlier: 3.539A pdb=" N LEU M 696 " --> pdb=" O ILE M 692 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU M 709 " --> pdb=" O PHE M 705 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL M 715 " --> pdb=" O ASN M 711 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 7 Processing helix chain 'K' and resid 12 through 18 removed outlier: 3.792A pdb=" N ASN K 18 " --> pdb=" O TYR K 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 20 Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 12 through 18 removed outlier: 3.792A pdb=" N ASN N 18 " --> pdb=" O TYR N 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 20 Processing helix chain 'P' and resid 692 through 715 removed outlier: 3.538A pdb=" N LEU P 696 " --> pdb=" O ILE P 692 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU P 709 " --> pdb=" O PHE P 705 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL P 715 " --> pdb=" O ASN P 711 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 6.647A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A 93 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLU A 120 " --> pdb=" O LEU A 93 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE A 95 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ASN A 122 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N VAL A 146 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE A 119 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASN A 148 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LYS A 121 " --> pdb=" O ASN A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 Processing sheet with id=AA4, first strand: chain 'A' and resid 212 through 216 removed outlier: 4.765A pdb=" N LEU A 213 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N CYS A 228 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ASN A 215 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 231 through 232 removed outlier: 3.607A pdb=" N PHE A 231 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 252 through 254 removed outlier: 3.514A pdb=" N ARG A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N HIS A 247 " --> pdb=" O CYS A 284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 321 removed outlier: 3.686A pdb=" N LEU A 314 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N SER A 339 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N GLU A 316 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 10.129A pdb=" N ILE A 341 " --> pdb=" O GLU A 316 " (cutoff:3.500A) removed outlier: 9.462A pdb=" N GLU A 318 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 363 through 364 Processing sheet with id=AB1, first strand: chain 'A' and resid 402 through 403 removed outlier: 6.452A pdb=" N ALA A 402 " --> pdb=" O HIS A 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 471 through 472 removed outlier: 6.395A pdb=" N GLU A 471 " --> pdb=" O LYS A 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 475 through 480 removed outlier: 3.811A pdb=" N LEU A 487 " --> pdb=" O TRP A 551 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TRP A 551 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 532 through 534 Processing sheet with id=AB5, first strand: chain 'A' and resid 602 through 604 Processing sheet with id=AB6, first strand: chain 'A' and resid 759 through 762 Processing sheet with id=AB7, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.731A pdb=" N LEU B 33 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N PHE B 64 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE B 35 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL B 66 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU B 37 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASN B 122 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN B 148 " --> pdb=" O LYS B 121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AB9, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AC1, first strand: chain 'B' and resid 212 through 216 removed outlier: 4.576A pdb=" N LEU B 213 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N CYS B 228 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASN B 215 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 231 through 233 removed outlier: 3.539A pdb=" N PHE B 231 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.525A pdb=" N ARG B 252 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N HIS B 247 " --> pdb=" O CYS B 284 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 292 through 293 Processing sheet with id=AC5, first strand: chain 'B' and resid 318 through 321 Processing sheet with id=AC6, first strand: chain 'B' and resid 335 through 336 removed outlier: 3.760A pdb=" N ILE B 336 " --> pdb=" O GLU B 363 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 387 through 388 Processing sheet with id=AC8, first strand: chain 'B' and resid 402 through 403 removed outlier: 6.622A pdb=" N ALA B 402 " --> pdb=" O HIS B 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 471 through 472 removed outlier: 6.301A pdb=" N GLU B 471 " --> pdb=" O LYS B 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 475 through 480 Processing sheet with id=AD2, first strand: chain 'B' and resid 532 through 534 230 hydrogen bonds defined for protein. 591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.69 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3729 1.34 - 1.46: 2850 1.46 - 1.58: 5292 1.58 - 1.70: 0 1.70 - 1.83: 115 Bond restraints: 11986 Sorted by residual: bond pdb=" C5 FUC G 2 " pdb=" O5 FUC G 2 " ideal model delta sigma weight residual 1.423 1.471 -0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" C5 FUC R 2 " pdb=" O5 FUC R 2 " ideal model delta sigma weight residual 1.423 1.468 -0.045 2.00e-02 2.50e+03 5.07e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.560 -0.041 2.00e-02 2.50e+03 4.23e+00 bond pdb=" C1 BMA I 3 " pdb=" C2 BMA I 3 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.90e+00 bond pdb=" CA ASN B 405 " pdb=" CB ASN B 405 " ideal model delta sigma weight residual 1.527 1.493 0.034 1.75e-02 3.27e+03 3.77e+00 ... (remaining 11981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 15383 2.07 - 4.14: 705 4.14 - 6.21: 120 6.21 - 8.28: 23 8.28 - 10.35: 3 Bond angle restraints: 16234 Sorted by residual: angle pdb=" C HIS B 1 " pdb=" N LEU B 2 " pdb=" CA LEU B 2 " ideal model delta sigma weight residual 121.54 131.89 -10.35 1.91e+00 2.74e-01 2.94e+01 angle pdb=" C HIS A 1 " pdb=" N LEU A 2 " pdb=" CA LEU A 2 " ideal model delta sigma weight residual 121.54 131.14 -9.60 1.91e+00 2.74e-01 2.53e+01 angle pdb=" CA ASP A 591 " pdb=" C ASP A 591 " pdb=" O ASP A 591 " ideal model delta sigma weight residual 117.94 120.79 -2.85 5.80e-01 2.97e+00 2.41e+01 angle pdb=" C ASP A 591 " pdb=" CA ASP A 591 " pdb=" CB ASP A 591 " ideal model delta sigma weight residual 117.07 110.09 6.98 1.44e+00 4.82e-01 2.35e+01 angle pdb=" N GLY B 10 " pdb=" CA GLY B 10 " pdb=" C GLY B 10 " ideal model delta sigma weight residual 110.97 118.48 -7.51 1.56e+00 4.11e-01 2.32e+01 ... (remaining 16229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 7385 21.75 - 43.51: 211 43.51 - 65.26: 18 65.26 - 87.02: 21 87.02 - 108.77: 8 Dihedral angle restraints: 7643 sinusoidal: 3538 harmonic: 4105 Sorted by residual: dihedral pdb=" CA CYS B 468 " pdb=" C CYS B 468 " pdb=" N GLU B 469 " pdb=" CA GLU B 469 " ideal model delta harmonic sigma weight residual 180.00 -133.50 -46.50 0 5.00e+00 4.00e-02 8.65e+01 dihedral pdb=" CA CYS A 468 " pdb=" C CYS A 468 " pdb=" N GLU A 469 " pdb=" CA GLU A 469 " ideal model delta harmonic sigma weight residual -180.00 -135.96 -44.04 0 5.00e+00 4.00e-02 7.76e+01 dihedral pdb=" CA VAL P 715 " pdb=" C VAL P 715 " pdb=" N PRO P 716 " pdb=" CA PRO P 716 " ideal model delta harmonic sigma weight residual 180.00 138.45 41.55 0 5.00e+00 4.00e-02 6.90e+01 ... (remaining 7640 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1652 0.090 - 0.181: 191 0.181 - 0.271: 11 0.271 - 0.362: 4 0.362 - 0.452: 4 Chirality restraints: 1862 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 418 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 418 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 397 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.30e+00 ... (remaining 1859 not shown) Planarity restraints: 2062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL M 715 " 0.064 5.00e-02 4.00e+02 9.77e-02 1.53e+01 pdb=" N PRO M 716 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO M 716 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO M 716 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL P 715 " -0.064 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO P 716 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO P 716 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO P 716 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL P 715 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.91e+00 pdb=" C VAL P 715 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL P 715 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO P 716 " -0.015 2.00e-02 2.50e+03 ... (remaining 2059 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.01: 1 2.01 - 2.73: 871 2.73 - 3.46: 16598 3.46 - 4.18: 28856 4.18 - 4.90: 47535 Nonbonded interactions: 93861 Sorted by model distance: nonbonded pdb=" N THR A 560 " pdb=" OG1 THR A 590 " model vdw 1.288 3.120 nonbonded pdb=" N TRP A 559 " pdb=" O ASP A 591 " model vdw 2.146 3.120 nonbonded pdb=" CA THR A 560 " pdb=" OG1 THR A 590 " model vdw 2.249 3.470 nonbonded pdb=" O THR A 593 " pdb=" ND2 ASN A 787 " model vdw 2.283 3.120 nonbonded pdb=" O SER A 323 " pdb=" OG SER A 326 " model vdw 2.288 3.040 ... (remaining 93856 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 'C' and resid 1 through 2) selection = (chain 'D' and resid 1 through 2) selection = (chain 'E' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) } ncs_group { reference = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) } ncs_group { reference = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'M' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.940 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 29.420 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 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 : 0.006 0.066 12045 Z= 0.301 Angle : 1.055 12.507 16380 Z= 0.551 Chirality : 0.060 0.452 1862 Planarity : 0.007 0.098 2050 Dihedral : 11.439 108.769 4894 Min Nonbonded Distance : 1.288 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.81 % Favored : 87.97 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 4.41 % Twisted General : 0.68 % 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: -3.39 (0.20), residues: 1372 helix: -2.41 (0.29), residues: 180 sheet: -0.68 (0.35), residues: 200 loop : -2.78 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 251 HIS 0.014 0.003 HIS A 429 PHE 0.040 0.004 PHE P 714 TYR 0.026 0.003 TYR N 19 ARG 0.008 0.001 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 12) link_NAG-ASN : angle 4.65761 ( 36) link_BETA1-4 : bond 0.00605 ( 10) link_BETA1-4 : angle 3.55580 ( 30) hydrogen bonds : bond 0.17943 ( 230) hydrogen bonds : angle 9.38196 ( 591) link_BETA1-6 : bond 0.00511 ( 6) link_BETA1-6 : angle 2.18023 ( 18) SS BOND : bond 0.00431 ( 31) SS BOND : angle 1.28113 ( 62) covalent geometry : bond 0.00608 (11986) covalent geometry : angle 1.02002 (16234) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.411 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: A 62 LEU cc_start: 0.9790 (tt) cc_final: 0.9560 (mt) REVERT: A 101 LEU cc_start: 0.9692 (tp) cc_final: 0.9385 (mt) REVERT: A 110 MET cc_start: 0.9009 (mmt) cc_final: 0.8644 (mmm) REVERT: A 120 GLU cc_start: 0.9675 (tt0) cc_final: 0.8604 (mt-10) REVERT: A 137 LEU cc_start: 0.9415 (mp) cc_final: 0.9098 (tp) REVERT: A 294 MET cc_start: 0.8938 (ppp) cc_final: 0.8595 (ppp) REVERT: A 350 LEU cc_start: 0.9507 (mt) cc_final: 0.9131 (mm) REVERT: A 353 GLU cc_start: 0.9678 (mt-10) cc_final: 0.9443 (mp0) REVERT: A 442 MET cc_start: 0.9785 (ttt) cc_final: 0.9557 (tmm) REVERT: B 101 LEU cc_start: 0.9869 (tp) cc_final: 0.9656 (mt) REVERT: B 110 MET cc_start: 0.9688 (mmt) cc_final: 0.9237 (mmm) REVERT: B 120 GLU cc_start: 0.9642 (tt0) cc_final: 0.8981 (mt-10) REVERT: B 294 MET cc_start: 0.9548 (ppp) cc_final: 0.8887 (ppp) REVERT: B 376 LEU cc_start: 0.9512 (mt) cc_final: 0.8991 (tt) REVERT: B 442 MET cc_start: 0.9779 (ttt) cc_final: 0.9434 (tmm) REVERT: B 487 LEU cc_start: 0.9855 (mt) cc_final: 0.9565 (mm) REVERT: B 551 TRP cc_start: 0.9378 (t-100) cc_final: 0.8091 (t-100) REVERT: M 706 GLU cc_start: 0.9385 (mm-30) cc_final: 0.8874 (mm-30) REVERT: L 26 TYR cc_start: 0.8399 (t80) cc_final: 0.7847 (t80) REVERT: O 3 ASN cc_start: 0.9625 (t160) cc_final: 0.9344 (m-40) REVERT: O 26 TYR cc_start: 0.8996 (t80) cc_final: 0.8637 (t80) REVERT: P 707 ASP cc_start: 0.9517 (t70) cc_final: 0.9293 (m-30) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2899 time to fit residues: 69.0034 Evaluate side-chains 94 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 30.0000 chunk 109 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 HIS A 187 HIS ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN A 410 GLN A 417 HIS A 594 ASN B 78 ASN B 100 HIS B 108 ASN B 187 HIS ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN ** M 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 ASN L 4 GLN O 10 HIS P 711 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.034209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.022678 restraints weight = 120362.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.023450 restraints weight = 84268.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.024012 restraints weight = 65149.944| |-----------------------------------------------------------------------------| r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12045 Z= 0.177 Angle : 0.763 9.668 16380 Z= 0.374 Chirality : 0.047 0.263 1862 Planarity : 0.006 0.093 2050 Dihedral : 9.994 67.794 2130 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.21), residues: 1372 helix: -1.86 (0.30), residues: 201 sheet: -0.74 (0.34), residues: 210 loop : -2.37 (0.20), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 414 HIS 0.008 0.001 HIS A 1 PHE 0.019 0.002 PHE A 497 TYR 0.030 0.002 TYR K 19 ARG 0.004 0.000 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00569 ( 12) link_NAG-ASN : angle 3.34755 ( 36) link_BETA1-4 : bond 0.00335 ( 10) link_BETA1-4 : angle 2.71050 ( 30) hydrogen bonds : bond 0.04474 ( 230) hydrogen bonds : angle 7.54424 ( 591) link_BETA1-6 : bond 0.00251 ( 6) link_BETA1-6 : angle 1.65052 ( 18) SS BOND : bond 0.00283 ( 31) SS BOND : angle 0.98824 ( 62) covalent geometry : bond 0.00371 (11986) covalent geometry : angle 0.73651 (16234) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.478 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: A 33 LEU cc_start: 0.9710 (tp) cc_final: 0.9219 (tp) REVERT: A 93 LEU cc_start: 0.9694 (tp) cc_final: 0.9488 (tp) REVERT: A 101 LEU cc_start: 0.9709 (tp) cc_final: 0.9362 (mt) REVERT: A 109 LEU cc_start: 0.9746 (tp) cc_final: 0.9543 (tp) REVERT: A 110 MET cc_start: 0.8992 (mmt) cc_final: 0.8533 (mmm) REVERT: A 120 GLU cc_start: 0.9655 (tt0) cc_final: 0.8585 (mt-10) REVERT: A 137 LEU cc_start: 0.9474 (mp) cc_final: 0.9104 (tp) REVERT: A 294 MET cc_start: 0.8873 (ppp) cc_final: 0.8511 (ppp) REVERT: A 350 LEU cc_start: 0.9558 (mt) cc_final: 0.9199 (pp) REVERT: A 353 GLU cc_start: 0.9709 (mt-10) cc_final: 0.9486 (pm20) REVERT: A 504 MET cc_start: 0.9690 (mmp) cc_final: 0.9315 (mmm) REVERT: A 553 MET cc_start: 0.9597 (tpt) cc_final: 0.9377 (tpp) REVERT: B 62 LEU cc_start: 0.9848 (tt) cc_final: 0.9639 (tt) REVERT: B 101 LEU cc_start: 0.9815 (tp) cc_final: 0.9603 (mt) REVERT: B 110 MET cc_start: 0.9493 (mmt) cc_final: 0.9140 (mmm) REVERT: B 120 GLU cc_start: 0.9627 (tt0) cc_final: 0.9049 (mt-10) REVERT: B 294 MET cc_start: 0.9538 (ppp) cc_final: 0.9060 (ppp) REVERT: B 376 LEU cc_start: 0.9529 (mt) cc_final: 0.9029 (tt) REVERT: B 442 MET cc_start: 0.9789 (ttt) cc_final: 0.9448 (tmm) REVERT: B 487 LEU cc_start: 0.9871 (mt) cc_final: 0.9468 (mm) REVERT: B 551 TRP cc_start: 0.9086 (t-100) cc_final: 0.8485 (t-100) REVERT: B 553 MET cc_start: 0.9763 (mmm) cc_final: 0.9504 (mmm) REVERT: B 559 TRP cc_start: 0.8175 (m-10) cc_final: 0.7852 (m100) REVERT: M 706 GLU cc_start: 0.9502 (mm-30) cc_final: 0.9037 (tp30) REVERT: L 15 LEU cc_start: 0.9800 (mm) cc_final: 0.9549 (pp) REVERT: L 26 TYR cc_start: 0.8558 (t80) cc_final: 0.7895 (t80) REVERT: O 6 LEU cc_start: 0.8765 (mt) cc_final: 0.8553 (tp) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2505 time to fit residues: 42.0850 Evaluate side-chains 95 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 137 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN B 1 HIS B 78 ASN B 108 ASN B 144 HIS ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN ** M 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN P 710 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.034034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.022425 restraints weight = 122625.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.023221 restraints weight = 85378.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.023806 restraints weight = 65667.385| |-----------------------------------------------------------------------------| r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12045 Z= 0.144 Angle : 0.706 8.261 16380 Z= 0.345 Chirality : 0.046 0.250 1862 Planarity : 0.005 0.063 2050 Dihedral : 8.669 57.417 2130 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.22), residues: 1372 helix: -1.37 (0.33), residues: 195 sheet: -0.97 (0.35), residues: 206 loop : -2.16 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 551 HIS 0.007 0.001 HIS A 1 PHE 0.015 0.001 PHE P 714 TYR 0.020 0.001 TYR K 19 ARG 0.013 0.001 ARG A 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00427 ( 12) link_NAG-ASN : angle 3.06486 ( 36) link_BETA1-4 : bond 0.00380 ( 10) link_BETA1-4 : angle 2.63240 ( 30) hydrogen bonds : bond 0.04060 ( 230) hydrogen bonds : angle 7.00484 ( 591) link_BETA1-6 : bond 0.00351 ( 6) link_BETA1-6 : angle 1.37494 ( 18) SS BOND : bond 0.00279 ( 31) SS BOND : angle 1.21777 ( 62) covalent geometry : bond 0.00301 (11986) covalent geometry : angle 0.67970 (16234) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.307 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: A 98 MET cc_start: 0.8526 (mmp) cc_final: 0.8217 (mmm) REVERT: A 101 LEU cc_start: 0.9680 (tp) cc_final: 0.9225 (mt) REVERT: A 120 GLU cc_start: 0.9613 (tt0) cc_final: 0.8668 (mt-10) REVERT: A 137 LEU cc_start: 0.9496 (mp) cc_final: 0.9157 (tp) REVERT: A 294 MET cc_start: 0.8853 (ppp) cc_final: 0.8481 (ppp) REVERT: A 340 LEU cc_start: 0.9791 (tt) cc_final: 0.9459 (mp) REVERT: A 408 LEU cc_start: 0.9602 (tp) cc_final: 0.8972 (tp) REVERT: A 442 MET cc_start: 0.9711 (tmm) cc_final: 0.9509 (tmm) REVERT: A 504 MET cc_start: 0.9671 (mmp) cc_final: 0.9222 (mmp) REVERT: A 553 MET cc_start: 0.9581 (tpt) cc_final: 0.9291 (tpp) REVERT: B 101 LEU cc_start: 0.9820 (tp) cc_final: 0.9599 (mt) REVERT: B 109 LEU cc_start: 0.9799 (mt) cc_final: 0.9593 (mt) REVERT: B 110 MET cc_start: 0.9491 (mmt) cc_final: 0.9159 (mmm) REVERT: B 120 GLU cc_start: 0.9613 (tt0) cc_final: 0.9279 (mm-30) REVERT: B 294 MET cc_start: 0.9518 (ppp) cc_final: 0.9035 (ppp) REVERT: B 376 LEU cc_start: 0.9536 (mt) cc_final: 0.9057 (tt) REVERT: B 442 MET cc_start: 0.9786 (ttt) cc_final: 0.9430 (tmm) REVERT: B 455 ASN cc_start: 0.9296 (m110) cc_final: 0.8998 (m110) REVERT: B 487 LEU cc_start: 0.9807 (mt) cc_final: 0.9408 (mm) REVERT: B 553 MET cc_start: 0.9752 (mmm) cc_final: 0.9436 (tpp) REVERT: M 706 GLU cc_start: 0.9472 (mm-30) cc_final: 0.9238 (mt-10) REVERT: M 708 TYR cc_start: 0.9593 (t80) cc_final: 0.9286 (t80) REVERT: M 710 HIS cc_start: 0.9638 (m90) cc_final: 0.9372 (m-70) REVERT: O 6 LEU cc_start: 0.8929 (mt) cc_final: 0.8664 (tp) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2384 time to fit residues: 37.3705 Evaluate side-chains 90 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 18 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 1 HIS A 32 HIS ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.033615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.022125 restraints weight = 121313.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.022904 restraints weight = 84669.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.023470 restraints weight = 65342.035| |-----------------------------------------------------------------------------| r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12045 Z= 0.142 Angle : 0.689 11.495 16380 Z= 0.334 Chirality : 0.046 0.245 1862 Planarity : 0.004 0.059 2050 Dihedral : 7.990 58.762 2130 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.22), residues: 1372 helix: -1.25 (0.35), residues: 188 sheet: -0.80 (0.35), residues: 214 loop : -2.01 (0.20), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 551 HIS 0.007 0.001 HIS A 1 PHE 0.014 0.001 PHE P 714 TYR 0.020 0.001 TYR K 19 ARG 0.003 0.000 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 12) link_NAG-ASN : angle 3.56857 ( 36) link_BETA1-4 : bond 0.00353 ( 10) link_BETA1-4 : angle 2.49642 ( 30) hydrogen bonds : bond 0.03720 ( 230) hydrogen bonds : angle 6.85978 ( 591) link_BETA1-6 : bond 0.00325 ( 6) link_BETA1-6 : angle 1.36776 ( 18) SS BOND : bond 0.00226 ( 31) SS BOND : angle 0.81872 ( 62) covalent geometry : bond 0.00301 (11986) covalent geometry : angle 0.65936 (16234) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.286 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: A 33 LEU cc_start: 0.9536 (tp) cc_final: 0.9301 (tp) REVERT: A 98 MET cc_start: 0.8723 (mmp) cc_final: 0.8165 (mmm) REVERT: A 101 LEU cc_start: 0.9571 (tp) cc_final: 0.9297 (mt) REVERT: A 120 GLU cc_start: 0.9610 (tt0) cc_final: 0.9179 (mt-10) REVERT: A 137 LEU cc_start: 0.9462 (mp) cc_final: 0.9156 (tp) REVERT: A 294 MET cc_start: 0.8819 (ppp) cc_final: 0.8459 (ppp) REVERT: A 340 LEU cc_start: 0.9799 (tt) cc_final: 0.9449 (mp) REVERT: A 442 MET cc_start: 0.9703 (tmm) cc_final: 0.9493 (tmm) REVERT: A 504 MET cc_start: 0.9697 (mmp) cc_final: 0.9243 (mmp) REVERT: A 553 MET cc_start: 0.9591 (tpt) cc_final: 0.9277 (tpp) REVERT: B 98 MET cc_start: 0.8885 (mmm) cc_final: 0.8601 (mmm) REVERT: B 101 LEU cc_start: 0.9817 (tp) cc_final: 0.9545 (mp) REVERT: B 109 LEU cc_start: 0.9800 (mt) cc_final: 0.9591 (mp) REVERT: B 110 MET cc_start: 0.9479 (mmt) cc_final: 0.9166 (mmm) REVERT: B 120 GLU cc_start: 0.9633 (tt0) cc_final: 0.9088 (mt-10) REVERT: B 294 MET cc_start: 0.9580 (ppp) cc_final: 0.9074 (ppp) REVERT: B 376 LEU cc_start: 0.9540 (mt) cc_final: 0.9051 (tt) REVERT: B 442 MET cc_start: 0.9785 (ttt) cc_final: 0.9421 (tmm) REVERT: B 455 ASN cc_start: 0.9326 (m110) cc_final: 0.9029 (m110) REVERT: B 487 LEU cc_start: 0.9805 (mt) cc_final: 0.9411 (mm) REVERT: B 504 MET cc_start: 0.9359 (tpt) cc_final: 0.9056 (tpt) REVERT: B 559 TRP cc_start: 0.8727 (m-10) cc_final: 0.8455 (m100) REVERT: M 703 LYS cc_start: 0.9591 (tptm) cc_final: 0.9029 (tppt) REVERT: M 706 GLU cc_start: 0.9459 (mm-30) cc_final: 0.9205 (mt-10) REVERT: M 710 HIS cc_start: 0.9665 (m90) cc_final: 0.9366 (m-70) REVERT: L 15 LEU cc_start: 0.9765 (mm) cc_final: 0.9526 (pp) REVERT: O 6 LEU cc_start: 0.8918 (mt) cc_final: 0.8636 (tp) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.2303 time to fit residues: 35.0370 Evaluate side-chains 84 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 128 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 HIS B 34 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.033644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.022244 restraints weight = 119068.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.023006 restraints weight = 83399.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.023575 restraints weight = 64592.440| |-----------------------------------------------------------------------------| r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12045 Z= 0.123 Angle : 0.657 9.949 16380 Z= 0.320 Chirality : 0.045 0.246 1862 Planarity : 0.004 0.057 2050 Dihedral : 7.385 59.599 2130 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.23), residues: 1372 helix: -1.11 (0.35), residues: 188 sheet: -0.76 (0.34), residues: 215 loop : -1.92 (0.21), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 493 HIS 0.003 0.001 HIS B 32 PHE 0.011 0.001 PHE P 714 TYR 0.019 0.001 TYR N 19 ARG 0.003 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 12) link_NAG-ASN : angle 3.17779 ( 36) link_BETA1-4 : bond 0.00348 ( 10) link_BETA1-4 : angle 2.32536 ( 30) hydrogen bonds : bond 0.03537 ( 230) hydrogen bonds : angle 6.49008 ( 591) link_BETA1-6 : bond 0.00370 ( 6) link_BETA1-6 : angle 1.33276 ( 18) SS BOND : bond 0.00224 ( 31) SS BOND : angle 0.79821 ( 62) covalent geometry : bond 0.00261 (11986) covalent geometry : angle 0.63167 (16234) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.702 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: A 33 LEU cc_start: 0.9503 (tp) cc_final: 0.9246 (tp) REVERT: A 98 MET cc_start: 0.8814 (mmp) cc_final: 0.8336 (mmm) REVERT: A 101 LEU cc_start: 0.9546 (tp) cc_final: 0.9243 (mt) REVERT: A 120 GLU cc_start: 0.9675 (tt0) cc_final: 0.9220 (mt-10) REVERT: A 137 LEU cc_start: 0.9455 (mp) cc_final: 0.9157 (tp) REVERT: A 294 MET cc_start: 0.8769 (ppp) cc_final: 0.8445 (ppp) REVERT: A 340 LEU cc_start: 0.9806 (tt) cc_final: 0.9444 (mp) REVERT: A 504 MET cc_start: 0.9688 (mmp) cc_final: 0.9273 (mmp) REVERT: A 553 MET cc_start: 0.9585 (tpt) cc_final: 0.9303 (tpp) REVERT: B 98 MET cc_start: 0.8895 (mmm) cc_final: 0.8560 (mmm) REVERT: B 101 LEU cc_start: 0.9816 (tp) cc_final: 0.9541 (mp) REVERT: B 109 LEU cc_start: 0.9809 (mt) cc_final: 0.9598 (mp) REVERT: B 110 MET cc_start: 0.9495 (mmt) cc_final: 0.9187 (mmm) REVERT: B 120 GLU cc_start: 0.9630 (tt0) cc_final: 0.9171 (mt-10) REVERT: B 294 MET cc_start: 0.9548 (ppp) cc_final: 0.9057 (ppp) REVERT: B 376 LEU cc_start: 0.9549 (mt) cc_final: 0.9065 (tt) REVERT: B 442 MET cc_start: 0.9789 (ttt) cc_final: 0.9401 (tmm) REVERT: B 455 ASN cc_start: 0.9327 (m110) cc_final: 0.9029 (m110) REVERT: B 559 TRP cc_start: 0.8677 (m-10) cc_final: 0.8399 (m100) REVERT: M 703 LYS cc_start: 0.9583 (tptm) cc_final: 0.9085 (tppt) REVERT: M 706 GLU cc_start: 0.9460 (mm-30) cc_final: 0.9211 (mt-10) REVERT: M 710 HIS cc_start: 0.9656 (m90) cc_final: 0.9361 (m-70) REVERT: L 15 LEU cc_start: 0.9763 (mm) cc_final: 0.9526 (pp) REVERT: O 6 LEU cc_start: 0.8872 (mt) cc_final: 0.8598 (tp) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2336 time to fit residues: 34.1450 Evaluate side-chains 83 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 21 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 62 optimal weight: 0.0050 chunk 64 optimal weight: 9.9990 overall best weight: 3.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 HIS ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.031924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.021068 restraints weight = 130188.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.021797 restraints weight = 91321.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.022334 restraints weight = 70938.745| |-----------------------------------------------------------------------------| r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12045 Z= 0.223 Angle : 0.770 9.023 16380 Z= 0.373 Chirality : 0.046 0.228 1862 Planarity : 0.005 0.057 2050 Dihedral : 7.457 59.620 2130 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.05 % Favored : 86.95 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.22), residues: 1372 helix: -1.48 (0.33), residues: 200 sheet: -0.89 (0.33), residues: 218 loop : -1.94 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 551 HIS 0.007 0.002 HIS B 100 PHE 0.015 0.002 PHE B 89 TYR 0.023 0.002 TYR N 19 ARG 0.007 0.001 ARG A 47 Details of bonding type rmsd link_NAG-ASN : bond 0.00508 ( 12) link_NAG-ASN : angle 3.24092 ( 36) link_BETA1-4 : bond 0.00315 ( 10) link_BETA1-4 : angle 2.36354 ( 30) hydrogen bonds : bond 0.03918 ( 230) hydrogen bonds : angle 6.81531 ( 591) link_BETA1-6 : bond 0.00350 ( 6) link_BETA1-6 : angle 1.57285 ( 18) SS BOND : bond 0.00302 ( 31) SS BOND : angle 0.94036 ( 62) covalent geometry : bond 0.00458 (11986) covalent geometry : angle 0.74741 (16234) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LEU cc_start: 0.9727 (tp) cc_final: 0.9465 (tp) REVERT: A 98 MET cc_start: 0.8873 (mmp) cc_final: 0.8362 (mmm) REVERT: A 101 LEU cc_start: 0.9612 (tp) cc_final: 0.9231 (mt) REVERT: A 120 GLU cc_start: 0.9725 (tt0) cc_final: 0.9253 (mt-10) REVERT: A 137 LEU cc_start: 0.9485 (mp) cc_final: 0.9120 (tt) REVERT: A 294 MET cc_start: 0.8839 (ppp) cc_final: 0.8431 (ppp) REVERT: A 340 LEU cc_start: 0.9813 (tt) cc_final: 0.9377 (mp) REVERT: A 434 LEU cc_start: 0.9455 (mt) cc_final: 0.9198 (mt) REVERT: A 504 MET cc_start: 0.9591 (mmp) cc_final: 0.9115 (mmp) REVERT: A 553 MET cc_start: 0.9617 (tpt) cc_final: 0.9349 (tpp) REVERT: B 38 MET cc_start: 0.8681 (mtt) cc_final: 0.8458 (mtt) REVERT: B 98 MET cc_start: 0.8744 (mmm) cc_final: 0.8513 (mmm) REVERT: B 101 LEU cc_start: 0.9826 (tp) cc_final: 0.9621 (mt) REVERT: B 110 MET cc_start: 0.9495 (mmt) cc_final: 0.9223 (mmm) REVERT: B 120 GLU cc_start: 0.9657 (tt0) cc_final: 0.9199 (mt-10) REVERT: B 294 MET cc_start: 0.9522 (ppp) cc_final: 0.8927 (ppp) REVERT: B 376 LEU cc_start: 0.9520 (mt) cc_final: 0.9012 (tt) REVERT: B 442 MET cc_start: 0.9803 (ttt) cc_final: 0.9425 (tmm) REVERT: B 455 ASN cc_start: 0.9438 (m110) cc_final: 0.9150 (m110) REVERT: M 703 LYS cc_start: 0.9575 (tptm) cc_final: 0.9105 (tptt) REVERT: M 706 GLU cc_start: 0.9541 (mm-30) cc_final: 0.9210 (mt-10) REVERT: M 710 HIS cc_start: 0.9678 (m90) cc_final: 0.9292 (m90) REVERT: O 6 LEU cc_start: 0.9015 (mt) cc_final: 0.8715 (tp) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.2336 time to fit residues: 32.4997 Evaluate side-chains 74 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 101 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 117 optimal weight: 0.0870 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN P 710 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.033151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2476 r_free = 0.2476 target = 0.021770 restraints weight = 123377.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.022539 restraints weight = 85869.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.023133 restraints weight = 65938.110| |-----------------------------------------------------------------------------| r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12045 Z= 0.112 Angle : 0.647 7.924 16380 Z= 0.316 Chirality : 0.046 0.251 1862 Planarity : 0.004 0.061 2050 Dihedral : 7.126 58.012 2130 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.22), residues: 1372 helix: -1.24 (0.34), residues: 195 sheet: -0.90 (0.33), residues: 215 loop : -1.79 (0.21), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 493 HIS 0.010 0.001 HIS P 710 PHE 0.033 0.001 PHE A 89 TYR 0.022 0.001 TYR N 19 ARG 0.004 0.000 ARG A 780 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 12) link_NAG-ASN : angle 2.94058 ( 36) link_BETA1-4 : bond 0.00398 ( 10) link_BETA1-4 : angle 2.17797 ( 30) hydrogen bonds : bond 0.03421 ( 230) hydrogen bonds : angle 6.30357 ( 591) link_BETA1-6 : bond 0.00394 ( 6) link_BETA1-6 : angle 1.40303 ( 18) SS BOND : bond 0.00208 ( 31) SS BOND : angle 0.76222 ( 62) covalent geometry : bond 0.00243 (11986) covalent geometry : angle 0.62503 (16234) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.329 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: A 33 LEU cc_start: 0.9463 (tp) cc_final: 0.9248 (tp) REVERT: A 98 MET cc_start: 0.8794 (mmp) cc_final: 0.8361 (mmm) REVERT: A 101 LEU cc_start: 0.9541 (tp) cc_final: 0.9277 (mt) REVERT: A 120 GLU cc_start: 0.9705 (tt0) cc_final: 0.9151 (mt-10) REVERT: A 137 LEU cc_start: 0.9476 (mp) cc_final: 0.9165 (tp) REVERT: A 294 MET cc_start: 0.8852 (ppp) cc_final: 0.8509 (ppp) REVERT: A 340 LEU cc_start: 0.9806 (tt) cc_final: 0.9372 (mp) REVERT: A 434 LEU cc_start: 0.9283 (mt) cc_final: 0.8928 (mt) REVERT: A 504 MET cc_start: 0.9659 (mmp) cc_final: 0.9282 (mmp) REVERT: A 553 MET cc_start: 0.9612 (tpt) cc_final: 0.9272 (tpp) REVERT: B 38 MET cc_start: 0.8851 (mtt) cc_final: 0.8638 (mtt) REVERT: B 101 LEU cc_start: 0.9825 (tp) cc_final: 0.9619 (mt) REVERT: B 110 MET cc_start: 0.9488 (mmt) cc_final: 0.9200 (mmm) REVERT: B 294 MET cc_start: 0.9556 (ppp) cc_final: 0.9048 (ppp) REVERT: B 376 LEU cc_start: 0.9567 (mt) cc_final: 0.9105 (tt) REVERT: B 442 MET cc_start: 0.9802 (ttt) cc_final: 0.9417 (tmm) REVERT: B 455 ASN cc_start: 0.9404 (m110) cc_final: 0.9106 (m110) REVERT: M 703 LYS cc_start: 0.9565 (tptm) cc_final: 0.9102 (tptt) REVERT: M 706 GLU cc_start: 0.9501 (mm-30) cc_final: 0.9159 (mt-10) REVERT: M 710 HIS cc_start: 0.9643 (m90) cc_final: 0.9242 (m90) REVERT: L 13 GLU cc_start: 0.9741 (mm-30) cc_final: 0.9536 (mm-30) REVERT: L 15 LEU cc_start: 0.9761 (mm) cc_final: 0.9531 (pp) REVERT: P 706 GLU cc_start: 0.9633 (pt0) cc_final: 0.9384 (pp20) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2126 time to fit residues: 29.9142 Evaluate side-chains 79 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 113 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 86 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.033237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.021750 restraints weight = 122612.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.022549 restraints weight = 85029.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.023141 restraints weight = 65331.723| |-----------------------------------------------------------------------------| r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12045 Z= 0.105 Angle : 0.635 8.145 16380 Z= 0.309 Chirality : 0.045 0.244 1862 Planarity : 0.004 0.059 2050 Dihedral : 6.758 55.452 2130 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.23), residues: 1372 helix: -0.87 (0.36), residues: 188 sheet: -0.69 (0.34), residues: 213 loop : -1.74 (0.21), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 493 HIS 0.003 0.001 HIS O 5 PHE 0.055 0.001 PHE P 714 TYR 0.033 0.001 TYR M 708 ARG 0.004 0.000 ARG A 47 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 12) link_NAG-ASN : angle 2.81424 ( 36) link_BETA1-4 : bond 0.00402 ( 10) link_BETA1-4 : angle 2.10800 ( 30) hydrogen bonds : bond 0.03337 ( 230) hydrogen bonds : angle 6.04622 ( 591) link_BETA1-6 : bond 0.00367 ( 6) link_BETA1-6 : angle 1.38003 ( 18) SS BOND : bond 0.00286 ( 31) SS BOND : angle 0.78303 ( 62) covalent geometry : bond 0.00231 (11986) covalent geometry : angle 0.61352 (16234) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.9472 (tp) cc_final: 0.9248 (tp) REVERT: A 98 MET cc_start: 0.8865 (mmp) cc_final: 0.8441 (mmm) REVERT: A 101 LEU cc_start: 0.9519 (tp) cc_final: 0.9230 (mt) REVERT: A 120 GLU cc_start: 0.9680 (tt0) cc_final: 0.9216 (mt-10) REVERT: A 137 LEU cc_start: 0.9455 (mp) cc_final: 0.9157 (tp) REVERT: A 294 MET cc_start: 0.8806 (ppp) cc_final: 0.8507 (ppp) REVERT: A 340 LEU cc_start: 0.9792 (tt) cc_final: 0.9365 (mp) REVERT: A 434 LEU cc_start: 0.9300 (mt) cc_final: 0.8945 (mt) REVERT: A 504 MET cc_start: 0.9665 (mmp) cc_final: 0.9232 (mmp) REVERT: A 553 MET cc_start: 0.9630 (tpt) cc_final: 0.9326 (tpp) REVERT: B 101 LEU cc_start: 0.9831 (tp) cc_final: 0.9631 (mt) REVERT: B 110 MET cc_start: 0.9479 (mmt) cc_final: 0.9192 (mmm) REVERT: B 120 GLU cc_start: 0.9620 (tt0) cc_final: 0.9139 (mt-10) REVERT: B 294 MET cc_start: 0.9540 (ppp) cc_final: 0.9069 (ppp) REVERT: B 376 LEU cc_start: 0.9552 (mt) cc_final: 0.9079 (tt) REVERT: B 442 MET cc_start: 0.9804 (ttt) cc_final: 0.9434 (tmm) REVERT: B 455 ASN cc_start: 0.9393 (m110) cc_final: 0.9096 (m110) REVERT: M 703 LYS cc_start: 0.9560 (tptm) cc_final: 0.9085 (tptt) REVERT: M 706 GLU cc_start: 0.9508 (mm-30) cc_final: 0.9210 (mt-10) REVERT: M 710 HIS cc_start: 0.9632 (m90) cc_final: 0.9339 (m-70) REVERT: L 13 GLU cc_start: 0.9765 (mm-30) cc_final: 0.9564 (mm-30) REVERT: L 15 LEU cc_start: 0.9765 (mm) cc_final: 0.9539 (pp) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2337 time to fit residues: 32.0092 Evaluate side-chains 76 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN A 429 HIS ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 HIS B 276 GLN L 4 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.032233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.021249 restraints weight = 128811.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.022020 restraints weight = 89028.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.022576 restraints weight = 68276.480| |-----------------------------------------------------------------------------| r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12045 Z= 0.203 Angle : 0.748 14.194 16380 Z= 0.358 Chirality : 0.046 0.224 1862 Planarity : 0.005 0.060 2050 Dihedral : 7.020 54.645 2130 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.81 % Favored : 88.19 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.22), residues: 1372 helix: -1.27 (0.33), residues: 200 sheet: -0.77 (0.33), residues: 214 loop : -1.74 (0.21), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 414 HIS 0.006 0.002 HIS B 100 PHE 0.054 0.002 PHE P 714 TYR 0.026 0.002 TYR P 708 ARG 0.004 0.001 ARG A 47 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 12) link_NAG-ASN : angle 3.72351 ( 36) link_BETA1-4 : bond 0.00319 ( 10) link_BETA1-4 : angle 2.21812 ( 30) hydrogen bonds : bond 0.03719 ( 230) hydrogen bonds : angle 6.36269 ( 591) link_BETA1-6 : bond 0.00297 ( 6) link_BETA1-6 : angle 1.46895 ( 18) SS BOND : bond 0.00279 ( 31) SS BOND : angle 0.88543 ( 62) covalent geometry : bond 0.00424 (11986) covalent geometry : angle 0.72114 (16234) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8924 (mmp) cc_final: 0.8451 (mmm) REVERT: A 101 LEU cc_start: 0.9611 (tp) cc_final: 0.9240 (mt) REVERT: A 110 MET cc_start: 0.8948 (mmm) cc_final: 0.8562 (mmm) REVERT: A 120 GLU cc_start: 0.9729 (tt0) cc_final: 0.9149 (mt-10) REVERT: A 137 LEU cc_start: 0.9496 (mp) cc_final: 0.9162 (tt) REVERT: A 294 MET cc_start: 0.8703 (ppp) cc_final: 0.8335 (ppp) REVERT: A 434 LEU cc_start: 0.9424 (mt) cc_final: 0.9116 (mt) REVERT: A 504 MET cc_start: 0.9600 (mmp) cc_final: 0.9193 (mmm) REVERT: A 553 MET cc_start: 0.9662 (tpt) cc_final: 0.9347 (tpp) REVERT: B 98 MET cc_start: 0.8790 (mmm) cc_final: 0.8297 (mmm) REVERT: B 101 LEU cc_start: 0.9846 (tp) cc_final: 0.9584 (mp) REVERT: B 294 MET cc_start: 0.9559 (ppp) cc_final: 0.9019 (ppp) REVERT: B 376 LEU cc_start: 0.9555 (mt) cc_final: 0.9066 (tt) REVERT: B 442 MET cc_start: 0.9815 (ttt) cc_final: 0.9409 (tmm) REVERT: B 455 ASN cc_start: 0.9466 (m110) cc_final: 0.9177 (m110) REVERT: M 703 LYS cc_start: 0.9571 (tptm) cc_final: 0.9085 (tptt) REVERT: M 706 GLU cc_start: 0.9581 (mm-30) cc_final: 0.9276 (mt-10) REVERT: M 710 HIS cc_start: 0.9656 (m90) cc_final: 0.9349 (m-70) REVERT: L 15 LEU cc_start: 0.9770 (mm) cc_final: 0.9516 (pp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2209 time to fit residues: 30.9154 Evaluate side-chains 73 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 30 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 85 optimal weight: 0.1980 chunk 79 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.031972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.021083 restraints weight = 128413.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.021859 restraints weight = 88402.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.022400 restraints weight = 67630.106| |-----------------------------------------------------------------------------| r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12045 Z= 0.192 Angle : 0.727 11.346 16380 Z= 0.351 Chirality : 0.046 0.405 1862 Planarity : 0.005 0.059 2050 Dihedral : 7.067 52.002 2130 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.22), residues: 1372 helix: -1.33 (0.33), residues: 201 sheet: -0.80 (0.33), residues: 219 loop : -1.72 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 493 HIS 0.006 0.001 HIS B 417 PHE 0.039 0.002 PHE P 714 TYR 0.038 0.002 TYR M 708 ARG 0.006 0.001 ARG B 345 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 12) link_NAG-ASN : angle 3.70326 ( 36) link_BETA1-4 : bond 0.00339 ( 10) link_BETA1-4 : angle 2.21474 ( 30) hydrogen bonds : bond 0.03636 ( 230) hydrogen bonds : angle 6.45867 ( 591) link_BETA1-6 : bond 0.00304 ( 6) link_BETA1-6 : angle 1.51122 ( 18) SS BOND : bond 0.00280 ( 31) SS BOND : angle 0.86799 ( 62) covalent geometry : bond 0.00398 (11986) covalent geometry : angle 0.69887 (16234) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2744 Ramachandran restraints generated. 1372 Oldfield, 0 Emsley, 1372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 1.465 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: A 33 LEU cc_start: 0.9564 (tp) cc_final: 0.9336 (tp) REVERT: A 98 MET cc_start: 0.8891 (mmp) cc_final: 0.8432 (mmm) REVERT: A 101 LEU cc_start: 0.9579 (tp) cc_final: 0.9207 (mt) REVERT: A 120 GLU cc_start: 0.9768 (tt0) cc_final: 0.9212 (mt-10) REVERT: A 137 LEU cc_start: 0.9498 (mp) cc_final: 0.9154 (tt) REVERT: A 294 MET cc_start: 0.8562 (ppp) cc_final: 0.8239 (ppp) REVERT: A 340 LEU cc_start: 0.9775 (tt) cc_final: 0.9322 (mp) REVERT: A 434 LEU cc_start: 0.9398 (mt) cc_final: 0.9098 (mt) REVERT: A 504 MET cc_start: 0.9624 (mmp) cc_final: 0.9248 (mmp) REVERT: A 553 MET cc_start: 0.9648 (tpt) cc_final: 0.9329 (tpp) REVERT: B 120 GLU cc_start: 0.9674 (tt0) cc_final: 0.9178 (mt-10) REVERT: B 294 MET cc_start: 0.9567 (ppp) cc_final: 0.9016 (ppp) REVERT: B 376 LEU cc_start: 0.9564 (mt) cc_final: 0.9088 (tt) REVERT: B 442 MET cc_start: 0.9818 (ttt) cc_final: 0.9398 (tmm) REVERT: B 455 ASN cc_start: 0.9481 (m110) cc_final: 0.9202 (m110) REVERT: M 703 LYS cc_start: 0.9561 (tptm) cc_final: 0.9044 (tptt) REVERT: M 706 GLU cc_start: 0.9595 (mm-30) cc_final: 0.9252 (mt-10) REVERT: M 710 HIS cc_start: 0.9651 (m90) cc_final: 0.9289 (m-70) REVERT: L 15 LEU cc_start: 0.9750 (mm) cc_final: 0.9522 (pp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2090 time to fit residues: 28.5890 Evaluate side-chains 72 residues out of total 1286 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 23 optimal weight: 0.0050 chunk 126 optimal weight: 0.0670 chunk 130 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 overall best weight: 1.8138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 HIS B 276 GLN ** B 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.032437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.021438 restraints weight = 125566.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.022234 restraints weight = 85852.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.022799 restraints weight = 65513.936| |-----------------------------------------------------------------------------| r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12045 Z= 0.129 Angle : 0.680 11.121 16380 Z= 0.327 Chirality : 0.046 0.262 1862 Planarity : 0.004 0.061 2050 Dihedral : 6.793 49.174 2130 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.23), residues: 1372 helix: -1.14 (0.34), residues: 200 sheet: -0.66 (0.33), residues: 219 loop : -1.67 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 493 HIS 0.007 0.001 HIS B 100 PHE 0.036 0.002 PHE P 714 TYR 0.032 0.002 TYR M 708 ARG 0.004 0.000 ARG B 386 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 12) link_NAG-ASN : angle 3.49600 ( 36) link_BETA1-4 : bond 0.00388 ( 10) link_BETA1-4 : angle 2.15650 ( 30) hydrogen bonds : bond 0.03411 ( 230) hydrogen bonds : angle 6.18460 ( 591) link_BETA1-6 : bond 0.00357 ( 6) link_BETA1-6 : angle 1.47524 ( 18) SS BOND : bond 0.00239 ( 31) SS BOND : angle 0.78945 ( 62) covalent geometry : bond 0.00278 (11986) covalent geometry : angle 0.65310 (16234) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3812.41 seconds wall clock time: 67 minutes 7.53 seconds (4027.53 seconds total)