Starting phenix.real_space_refine on Fri Jul 3 08:13:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nxd_12637/07_2026/7nxd_12637.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nxd_12637/07_2026/7nxd_12637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nxd_12637/07_2026/7nxd_12637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nxd_12637/07_2026/7nxd_12637.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7nxd_12637/07_2026/7nxd_12637.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nxd_12637/07_2026/7nxd_12637.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nxd_12637/07_2026/7nxd_12637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nxd_12637/07_2026/7nxd_12637.map" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 7 9.91 5 Mg 1 5.21 5 S 94 5.16 5 C 7948 2.51 5 N 2142 2.21 5 O 2613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12805 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 6953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 6953 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 58, 'TRANS': 846} Chain breaks: 2 Chain: "B" Number of atoms: 5314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5314 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 25, 'TRANS': 664} Chain breaks: 2 Chain: "C" 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 chiralities: 3 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "E" 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 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 chiralities: 2 Chain: "G" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "H" 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 chiralities: 2 Chain: "I" 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 chiralities: 2 Chain: "J" 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 chiralities: 2 Chain: "K" 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 chiralities: 2 Chain: "L" 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 chiralities: 2 Chain: "M" 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 chiralities: 3 Chain: "N" 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 chiralities: 2 Chain: "O" 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 chiralities: 3 Chain: "P" 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 chiralities: 3 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 19 Unusual residues: {' CA': 5, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 28 residue: pdb=" N ALA A 784 " occ=0.66 ... (3 atoms not shown) pdb=" CB ALA A 784 " occ=0.66 residue: pdb=" N TYR A 789 " occ=0.66 ... (10 atoms not shown) pdb=" OH TYR A 789 " occ=0.66 residue: pdb=" N GLU A 790 " occ=0.66 ... (7 atoms not shown) pdb=" OE2 GLU A 790 " occ=0.66 residue: pdb=" N LEU A 882 " occ=0.66 ... (6 atoms not shown) pdb=" CD2 LEU A 882 " occ=0.66 residue: pdb=" N TRP A 900 " occ=0.66 ... (12 atoms not shown) pdb=" CH2 TRP A 900 " occ=0.66 residue: pdb=" N PRO A 926 " occ=0.66 ... (5 atoms not shown) pdb=" CD PRO A 926 " occ=0.66 residue: pdb=" N TYR A 927 " occ=0.66 ... (10 atoms not shown) pdb=" OH TYR A 927 " occ=0.66 residue: pdb=" N GLY B 618 " occ=0.75 ... (2 atoms not shown) pdb=" O GLY B 618 " occ=0.75 residue: pdb=" N CYS B 620 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS B 620 " occ=0.75 residue: pdb=" N LYS B 624 " occ=0.75 ... (7 atoms not shown) pdb=" NZ LYS B 624 " occ=0.75 residue: pdb=" N GLU B 625 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU B 625 " occ=0.75 residue: pdb=" N CYS B 626 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS B 626 " occ=0.75 ... (remaining 16 not shown) Time building chain proxies: 2.92, per 1000 atoms: 0.23 Number of scatterers: 12805 At special positions: 0 Unit cell: (104.55, 136, 168.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 7 19.99 S 94 16.00 Mg 1 11.99 O 2613 8.00 N 2142 7.00 C 7948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 472 " - pdb=" SG CYS A 481 " distance=2.03 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 543 " distance=2.03 Simple disulfide: pdb=" SG CYS A 604 " - pdb=" SG CYS A 610 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 690 " distance=2.03 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 916 " distance=2.03 Simple disulfide: pdb=" SG CYS A 828 " - pdb=" SG CYS A 880 " distance=2.03 Simple disulfide: pdb=" SG CYS A 870 " - pdb=" SG CYS A 875 " distance=2.03 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 25 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 444 " distance=2.04 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 44 " distance=2.03 Simple disulfide: pdb=" SG CYS B 187 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 281 " distance=1.83 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 395 " distance=2.30 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 442 " distance=1.92 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 457 " - pdb=" SG CYS B 469 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 480 " distance=2.03 Simple disulfide: pdb=" SG CYS B 482 " - pdb=" SG CYS B 513 " distance=2.02 Simple disulfide: pdb=" SG CYS B 496 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 505 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 518 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 556 " distance=2.03 Simple disulfide: pdb=" SG CYS B 540 " - pdb=" SG CYS B 554 " distance=2.03 Simple disulfide: pdb=" SG CYS B 548 " - pdb=" SG CYS B 559 " distance=2.03 Simple disulfide: pdb=" SG CYS B 561 " - pdb=" SG CYS B 570 " distance=2.03 Simple disulfide: pdb=" SG CYS B 572 " - pdb=" SG CYS B 595 " distance=2.03 Simple disulfide: pdb=" SG CYS B 579 " - pdb=" SG CYS B 593 " distance=2.02 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 598 " distance=2.04 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 610 " distance=2.04 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 616 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 626 " - pdb=" SG CYS B 645 " distance=2.04 Simple disulfide: pdb=" SG CYS B 629 " - pdb=" SG CYS B 641 " distance=2.04 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 703 " 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 ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA G 3 " - " MAN G 6 " ALPHA1-6 " BMA G 3 " - " MAN G 4 " BETA1-2 " MAN G 4 " - " NAG G 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " NAG-ASN " NAG A1106 " - " ASN A 483 " " NAG C 1 " - " ASN A 43 " " NAG D 1 " - " ASN A 141 " " NAG E 1 " - " ASN A 256 " " NAG F 1 " - " ASN A 266 " " NAG G 1 " - " ASN A 275 " " NAG H 1 " - " ASN A 568 " " NAG I 1 " - " ASN A 489 " " NAG J 1 " - " ASN B 192 " " NAG K 1 " - " ASN B 249 " " NAG L 1 " - " ASN B 343 " " NAG M 1 " - " ASN B 386 " " NAG N 1 " - " ASN B 397 " " NAG O 1 " - " ASN B 461 " " NAG P 1 " - " ASN B 30 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 512.9 milliseconds 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2900 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 29 sheets defined 12.9% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 80 through 87 Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 509 through 512 Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 900 through 907 removed outlier: 3.731A pdb=" N ARG A 907 " --> pdb=" O THR A 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 3.702A pdb=" N CYS B 18 " --> pdb=" O SER B 14 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 19 " --> pdb=" O CYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 42 Processing helix chain 'B' and resid 47 through 54 removed outlier: 3.590A pdb=" N GLY B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 135 through 157 removed outlier: 3.509A pdb=" N ASN B 141 " --> pdb=" O ASP B 137 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N THR B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG B 155 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 removed outlier: 3.813A pdb=" N ASN B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 219 removed outlier: 4.040A pdb=" N PHE B 212 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 removed outlier: 3.705A pdb=" N ALA B 234 " --> pdb=" O GLY B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 321 through 332 removed outlier: 3.834A pdb=" N ASN B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 361 Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'B' and resid 444 through 450 Processing helix chain 'B' and resid 503 through 507 Processing helix chain 'B' and resid 546 through 551 removed outlier: 3.503A pdb=" N GLY B 549 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.728A pdb=" N SER A 437 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 418 " --> pdb=" O GLY A 436 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 removed outlier: 4.025A pdb=" N TYR A 26 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER A 34 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL A 55 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 removed outlier: 4.093A pdb=" N SER A 120 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 108 removed outlier: 4.061A pdb=" N THR A 139 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG A 144 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.580A pdb=" N SER A 169 " --> pdb=" O GLY A 181 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 217 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 234 through 238 removed outlier: 4.106A pdb=" N SER A 234 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A 274 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN A 266 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N SER A 272 " --> pdb=" O ASN A 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 288 through 292 removed outlier: 3.578A pdb=" N ALA A 288 " --> pdb=" O GLY A 305 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 326 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU A 340 " --> pdb=" O VAL A 326 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 312 removed outlier: 3.637A pdb=" N GLN A 319 " --> pdb=" O ASP A 311 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 355 through 357 removed outlier: 3.780A pdb=" N VAL A 369 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 384 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 402 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 386 " --> pdb=" O GLN A 400 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 519 through 521 removed outlier: 3.510A pdb=" N LEU A 488 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 544 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE A 486 " --> pdb=" O ARG A 544 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER A 485 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 459 " --> pdb=" O SER A 485 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN A 489 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 491 " --> pdb=" O SER A 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 498 through 499 Processing sheet with id=AB3, first strand: chain 'A' and resid 529 through 532 Processing sheet with id=AB4, first strand: chain 'A' and resid 529 through 532 Processing sheet with id=AB5, first strand: chain 'A' and resid 614 through 621 removed outlier: 3.555A pdb=" N GLU A 621 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN A 634 " --> pdb=" O GLU A 621 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 664 " --> pdb=" O ARG A 707 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N THR A 709 " --> pdb=" O TYR A 662 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR A 662 " --> pdb=" O THR A 709 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 677 through 680 removed outlier: 3.743A pdb=" N LEU A 687 " --> pdb=" O PHE A 680 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 688 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ALA A 650 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 725 " --> pdb=" O ARG A 653 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A 723 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 751 through 757 removed outlier: 6.304A pdb=" N GLN A 894 " --> pdb=" O VAL A 823 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A 823 " --> pdb=" O GLN A 894 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N HIS A 896 " --> pdb=" O THR A 821 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 828 through 830 removed outlier: 3.655A pdb=" N LEU A 804 " --> pdb=" O CYS A 880 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N GLN A 801 " --> pdb=" O LEU A 923 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 923 " --> pdb=" O GLN A 801 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN A 866 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLN A 915 " --> pdb=" O GLN A 866 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU A 868 " --> pdb=" O GLN A 915 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N GLU A 917 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 828 through 830 removed outlier: 3.655A pdb=" N LEU A 804 " --> pdb=" O CYS A 880 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N GLN A 801 " --> pdb=" O LEU A 923 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 923 " --> pdb=" O GLN A 801 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 25 through 27 Processing sheet with id=AC2, first strand: chain 'B' and resid 67 through 68 removed outlier: 6.060A pdb=" N LEU B 99 " --> pdb=" O ILE B 437 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 423 " --> pdb=" O VAL B 436 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 109 through 111 removed outlier: 3.654A pdb=" N GLN B 109 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 109 through 111 removed outlier: 3.654A pdb=" N GLN B 109 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 199 through 201 removed outlier: 7.062A pdb=" N ILE B 123 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N GLY B 163 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B 125 " --> pdb=" O GLY B 163 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLY B 165 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYR B 127 " --> pdb=" O GLY B 165 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N PHE B 167 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N MET B 129 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP B 124 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL B 255 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR B 126 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N SER B 257 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU B 128 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 258 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 317 " --> pdb=" O GLY B 338 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 362 through 363 Processing sheet with id=AC7, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AC8, first strand: chain 'B' and resid 509 through 512 removed outlier: 3.514A pdb=" N VAL B 517 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 512 " --> pdb=" O GLN B 515 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 553 through 555 Processing sheet with id=AD1, first strand: chain 'B' and resid 592 through 594 removed outlier: 3.898A pdb=" N GLU B 594 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 671 through 674 removed outlier: 3.590A pdb=" N PHE B 683 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B 673 " --> pdb=" O PHE B 681 " (cutoff:3.500A) 342 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2648 1.33 - 1.45: 3073 1.45 - 1.58: 7218 1.58 - 1.70: 0 1.70 - 1.82: 112 Bond restraints: 13051 Sorted by residual: bond pdb=" N CYS B 415 " pdb=" CA CYS B 415 " ideal model delta sigma weight residual 1.457 1.492 -0.035 9.10e-03 1.21e+04 1.51e+01 bond pdb=" N GLU A 126 " pdb=" CA GLU A 126 " ideal model delta sigma weight residual 1.453 1.488 -0.035 9.20e-03 1.18e+04 1.44e+01 bond pdb=" N LYS B 87 " pdb=" CA LYS B 87 " ideal model delta sigma weight residual 1.456 1.488 -0.033 8.70e-03 1.32e+04 1.40e+01 bond pdb=" N VAL B 476 " pdb=" CA VAL B 476 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.17e-02 7.31e+03 1.30e+01 bond pdb=" N VAL A 756 " pdb=" CA VAL A 756 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.11e-02 8.12e+03 1.29e+01 ... (remaining 13046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 13231 1.74 - 3.47: 4029 3.47 - 5.21: 376 5.21 - 6.94: 33 6.94 - 8.68: 9 Bond angle restraints: 17678 Sorted by residual: angle pdb=" CA GLY B 607 " pdb=" C GLY B 607 " pdb=" O GLY B 607 " ideal model delta sigma weight residual 122.37 118.05 4.32 7.30e-01 1.88e+00 3.51e+01 angle pdb=" C ARG A 350 " pdb=" N PHE A 351 " pdb=" CA PHE A 351 " ideal model delta sigma weight residual 120.75 129.43 -8.68 1.51e+00 4.39e-01 3.30e+01 angle pdb=" CA GLY B 530 " pdb=" C GLY B 530 " pdb=" O GLY B 530 " ideal model delta sigma weight residual 122.23 118.56 3.67 6.90e-01 2.10e+00 2.83e+01 angle pdb=" C LEU A 79 " pdb=" N LEU A 80 " pdb=" CA LEU A 80 " ideal model delta sigma weight residual 122.30 115.21 7.09 1.35e+00 5.49e-01 2.76e+01 angle pdb=" CA GLY B 81 " pdb=" C GLY B 81 " pdb=" O GLY B 81 " ideal model delta sigma weight residual 122.23 118.66 3.57 6.90e-01 2.10e+00 2.68e+01 ... (remaining 17673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7247 17.99 - 35.99: 313 35.99 - 53.98: 55 53.98 - 71.97: 15 71.97 - 89.97: 7 Dihedral angle restraints: 7637 sinusoidal: 3093 harmonic: 4544 Sorted by residual: dihedral pdb=" CB CYS B 457 " pdb=" SG CYS B 457 " pdb=" SG CYS B 469 " pdb=" CB CYS B 469 " ideal model delta sinusoidal sigma weight residual -86.00 -175.97 89.97 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" CB CYS A 472 " pdb=" SG CYS A 472 " pdb=" SG CYS A 481 " pdb=" CB CYS A 481 " ideal model delta sinusoidal sigma weight residual -86.00 -170.83 84.83 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 444 " pdb=" CB CYS B 444 " ideal model delta sinusoidal sigma weight residual -86.00 -165.52 79.52 1 1.00e+01 1.00e-02 7.85e+01 ... (remaining 7634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 1817 0.169 - 0.337: 213 0.337 - 0.506: 6 0.506 - 0.674: 0 0.674 - 0.843: 1 Chirality restraints: 2037 Sorted by residual: chirality pdb=" C1 MAN D 4 " pdb=" O3 BMA D 3 " pdb=" C2 MAN D 4 " pdb=" O5 MAN D 4 " both_signs ideal model delta sigma weight residual False 2.40 1.56 0.84 2.00e-02 2.50e+03 1.78e+03 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.48e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.66e+02 ... (remaining 2034 not shown) Planarity restraints: 2310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " -0.360 2.00e-02 2.50e+03 3.10e-01 1.20e+03 pdb=" C7 NAG O 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " 0.551 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.351 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C7 NAG G 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.099 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.540 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.352 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C7 NAG E 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.540 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " -0.150 2.00e-02 2.50e+03 ... (remaining 2307 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 101 2.44 - 3.06: 9052 3.06 - 3.67: 18096 3.67 - 4.29: 26307 4.29 - 4.90: 43308 Nonbonded interactions: 96864 Sorted by model distance: nonbonded pdb=" O SER B 134 " pdb="CA CA B1002 " model vdw 1.831 2.510 nonbonded pdb=" OD1 ASP A 243 " pdb="CA CA A1101 " model vdw 1.885 2.510 nonbonded pdb=" OG SER A 241 " pdb="CA CA A1101 " model vdw 1.904 2.510 nonbonded pdb=" OD1 ASN A 428 " pdb="CA CA A1104 " model vdw 1.914 2.510 nonbonded pdb=" OD2 ASP B 226 " pdb="CA CA B1003 " model vdw 2.011 2.510 ... (remaining 96859 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' selection = chain 'E' selection = chain 'M' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.980 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4448 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 : 0.014 0.272 13128 Z= 1.021 Angle : 1.544 27.188 17872 Z= 1.120 Chirality : 0.108 0.843 2037 Planarity : 0.029 0.310 2295 Dihedral : 9.251 74.975 4626 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 64.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.96 % Rotamer: Outliers : 1.03 % Allowed : 8.30 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.20), residues: 1583 helix: 1.10 (0.49), residues: 132 sheet: -0.17 (0.24), residues: 460 loop : -1.21 (0.18), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 78 TYR 0.010 0.001 TYR A 366 PHE 0.013 0.001 PHE A 876 TRP 0.014 0.001 TRP A 121 HIS 0.003 0.000 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.01342 / 1.01 (13051) covalent geometry : angle 1.50906 / 1.12 (17678) SS BOND : bond 0.05867 / 4.58 ( 37) SS BOND : angle 1.69186 / 0.94 ( 74) hydrogen bonds : bond 0.29112 / 20.44 ( 322) hydrogen bonds : angle 10.47499 / 7.46 ( 879) link_ALPHA1-3 : bond 0.01246 / 0.66 ( 2) link_ALPHA1-3 : angle 5.02278 / 3.24 ( 6) link_ALPHA1-6 : bond 0.00142 / 0.07 ( 1) link_ALPHA1-6 : angle 0.89524 / 0.80 ( 3) link_BETA1-2 : bond 0.00239 / 0.13 ( 1) link_BETA1-2 : angle 2.15962 / 1.22 ( 3) link_BETA1-4 : bond 0.00324 / 0.18 ( 21) link_BETA1-4 : angle 1.92899 / 1.28 ( 63) link_NAG-ASN : bond 0.02075 / 0.96 ( 15) link_NAG-ASN : angle 6.21488 / 3.82 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.6769 (m-30) cc_final: 0.6341 (p0) REVERT: B 335 SER cc_start: 0.6006 (p) cc_final: 0.4947 (p) REVERT: B 518 CYS cc_start: 0.7704 (OUTLIER) cc_final: 0.6919 (m) REVERT: B 659 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5746 (mp) outliers start: 14 outliers final: 5 residues processed: 193 average time/residue: 0.1234 time to fit residues: 33.0048 Evaluate side-chains 98 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 GLN A 161 GLN A 165 GLN A 564 HIS A 587 HIS A 787 HIS A 801 GLN ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 GLN B 74 ASN B 77 ASN B 93 GLN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 GLN ** B 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN B 623 HIS B 628 GLN B 670 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.088323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.068118 restraints weight = 147593.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.068820 restraints weight = 134121.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.069252 restraints weight = 122975.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.069671 restraints weight = 114630.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.069863 restraints weight = 109139.745| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 189 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 11 (15 function evaluations) r_final: 0.3821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13128 Z= 0.200 Angle : 0.965 15.885 17872 Z= 0.447 Chirality : 0.057 0.660 2037 Planarity : 0.005 0.083 2295 Dihedral : 4.354 17.148 1712 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.20), residues: 1583 helix: 0.55 (0.39), residues: 149 sheet: 0.07 (0.23), residues: 481 loop : -0.87 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 742 TYR 0.016 0.002 TYR B 175 PHE 0.039 0.003 PHE B 160 TRP 0.016 0.002 TRP A 947 HIS 0.015 0.001 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 (13051) covalent geometry : angle 0.91621 / 0.44 (17678) SS BOND : bond 0.00307 / 0.18 ( 37) SS BOND : angle 1.49537 / 1.12 ( 74) hydrogen bonds : bond 0.06168 / 4.55 ( 322) hydrogen bonds : angle 7.57325 / 5.26 ( 879) link_ALPHA1-3 : bond 0.01861 / 0.98 ( 2) link_ALPHA1-3 : angle 1.77960 / 1.14 ( 6) link_ALPHA1-6 : bond 0.00564 / 0.30 ( 1) link_ALPHA1-6 : angle 1.33191 / 1.19 ( 3) link_BETA1-2 : bond 0.00305 / 0.16 ( 1) link_BETA1-2 : angle 3.14980 / 1.92 ( 3) link_BETA1-4 : bond 0.00714 / 0.39 ( 21) link_BETA1-4 : angle 2.52275 / 1.74 ( 63) link_NAG-ASN : bond 0.00715 / 0.40 ( 15) link_NAG-ASN : angle 5.11020 / 3.31 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.390 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 3 LEU cc_start: 0.8755 (pp) cc_final: 0.8209 (pp) REVERT: A 303 LEU cc_start: 0.9685 (mp) cc_final: 0.9373 (tp) REVERT: A 414 PHE cc_start: 0.8854 (m-10) cc_final: 0.8535 (m-80) REVERT: A 415 PHE cc_start: 0.8630 (t80) cc_final: 0.8166 (t80) REVERT: A 433 LEU cc_start: 0.7667 (tp) cc_final: 0.7433 (tp) REVERT: A 619 PHE cc_start: 0.8332 (t80) cc_final: 0.7912 (t80) REVERT: B 131 LEU cc_start: 0.8099 (mp) cc_final: 0.7798 (tp) REVERT: B 164 PHE cc_start: 0.9258 (t80) cc_final: 0.8159 (t80) REVERT: B 236 MET cc_start: 0.9380 (mmp) cc_final: 0.8915 (mmm) REVERT: B 256 PHE cc_start: 0.9066 (t80) cc_final: 0.8509 (t80) REVERT: B 315 PHE cc_start: 0.9118 (m-80) cc_final: 0.8902 (m-80) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.1169 time to fit residues: 19.3636 Evaluate side-chains 82 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 147 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 149 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 GLN A 624 HIS ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 GLN B 349 GLN ** B 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.077974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.060025 restraints weight = 154746.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.060384 restraints weight = 138723.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.060829 restraints weight = 128225.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.061226 restraints weight = 121697.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.061361 restraints weight = 115008.525| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3669 r_free = 0.3669 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 189 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3669 r_free = 0.3669 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 220 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.3669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 13128 Z= 0.216 Angle : 0.847 14.218 17872 Z= 0.408 Chirality : 0.051 0.456 2037 Planarity : 0.005 0.060 2295 Dihedral : 4.699 23.749 1712 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.07 % Allowed : 3.30 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.20), residues: 1583 helix: 0.28 (0.39), residues: 152 sheet: -0.01 (0.22), residues: 499 loop : -0.90 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 323 TYR 0.031 0.002 TYR A 163 PHE 0.024 0.003 PHE A 722 TRP 0.019 0.003 TRP A 188 HIS 0.007 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.22 (13051) covalent geometry : angle 0.80920 / 0.40 (17678) SS BOND : bond 0.00649 / 0.31 ( 37) SS BOND : angle 1.30108 / 0.93 ( 74) hydrogen bonds : bond 0.04760 / 3.37 ( 322) hydrogen bonds : angle 6.80638 / 4.72 ( 879) link_ALPHA1-3 : bond 0.01253 / 0.66 ( 2) link_ALPHA1-3 : angle 1.30268 / 0.82 ( 6) link_ALPHA1-6 : bond 0.00397 / 0.21 ( 1) link_ALPHA1-6 : angle 1.28157 / 0.82 ( 3) link_BETA1-2 : bond 0.00117 / 0.06 ( 1) link_BETA1-2 : angle 2.43411 / 1.52 ( 3) link_BETA1-4 : bond 0.00590 / 0.30 ( 21) link_BETA1-4 : angle 2.20475 / 1.50 ( 63) link_NAG-ASN : bond 0.00489 / 0.26 ( 15) link_NAG-ASN : angle 4.12951 / 2.67 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.399 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 3 LEU cc_start: 0.8815 (pp) cc_final: 0.8164 (pp) REVERT: A 303 LEU cc_start: 0.9645 (mp) cc_final: 0.9419 (tp) REVERT: A 414 PHE cc_start: 0.9093 (m-10) cc_final: 0.8776 (m-80) REVERT: A 415 PHE cc_start: 0.8878 (t80) cc_final: 0.8342 (t80) REVERT: A 433 LEU cc_start: 0.7553 (tp) cc_final: 0.7260 (tp) REVERT: A 446 TYR cc_start: 0.8835 (m-10) cc_final: 0.8461 (m-10) REVERT: A 567 LEU cc_start: 0.9246 (tp) cc_final: 0.8808 (tp) REVERT: A 897 PHE cc_start: 0.6576 (p90) cc_final: 0.5977 (p90) REVERT: B 129 MET cc_start: 0.8686 (ttp) cc_final: 0.8472 (tpp) REVERT: B 135 MET cc_start: 0.8529 (mtp) cc_final: 0.7642 (mmm) REVERT: B 212 PHE cc_start: 0.9291 (t80) cc_final: 0.8819 (t80) REVERT: B 236 MET cc_start: 0.9366 (mmp) cc_final: 0.8848 (mmm) REVERT: B 256 PHE cc_start: 0.9172 (t80) cc_final: 0.8823 (t80) REVERT: B 315 PHE cc_start: 0.9262 (m-80) cc_final: 0.9030 (m-80) outliers start: 1 outliers final: 0 residues processed: 87 average time/residue: 0.1200 time to fit residues: 14.8037 Evaluate side-chains 64 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 59 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 61 optimal weight: 20.0000 chunk 154 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 GLN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 GLN ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 894 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN ** B 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.076147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.058539 restraints weight = 155140.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.059028 restraints weight = 139002.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.059412 restraints weight = 127317.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.059710 restraints weight = 119315.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.059893 restraints weight = 113802.742| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 220 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 230 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13128 Z= 0.164 Angle : 0.771 13.766 17872 Z= 0.362 Chirality : 0.050 0.498 2037 Planarity : 0.004 0.056 2295 Dihedral : 4.619 20.195 1712 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.07 % Allowed : 2.94 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.20), residues: 1583 helix: 0.66 (0.41), residues: 152 sheet: 0.03 (0.22), residues: 511 loop : -0.76 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 426 TYR 0.023 0.002 TYR A 920 PHE 0.019 0.002 PHE A 876 TRP 0.016 0.002 TRP A 703 HIS 0.006 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (13051) covalent geometry : angle 0.73012 / 0.35 (17678) SS BOND : bond 0.00311 / 0.18 ( 37) SS BOND : angle 1.11983 / 0.80 ( 74) hydrogen bonds : bond 0.03879 / 2.88 ( 322) hydrogen bonds : angle 6.33198 / 4.39 ( 879) link_ALPHA1-3 : bond 0.00801 / 0.42 ( 2) link_ALPHA1-3 : angle 1.32492 / 0.95 ( 6) link_ALPHA1-6 : bond 0.00423 / 0.22 ( 1) link_ALPHA1-6 : angle 1.34043 / 1.06 ( 3) link_BETA1-2 : bond 0.00106 / 0.06 ( 1) link_BETA1-2 : angle 2.77272 / 1.72 ( 3) link_BETA1-4 : bond 0.00625 / 0.31 ( 21) link_BETA1-4 : angle 2.11734 / 1.45 ( 63) link_NAG-ASN : bond 0.00554 / 0.27 ( 15) link_NAG-ASN : angle 4.21014 / 2.60 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.516 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 3 LEU cc_start: 0.8782 (pp) cc_final: 0.8097 (pp) REVERT: A 303 LEU cc_start: 0.9649 (mp) cc_final: 0.9374 (tp) REVERT: A 414 PHE cc_start: 0.9190 (m-10) cc_final: 0.8884 (m-80) REVERT: A 415 PHE cc_start: 0.9016 (t80) cc_final: 0.8510 (t80) REVERT: A 446 TYR cc_start: 0.8752 (m-10) cc_final: 0.8268 (m-10) REVERT: B 130 ASP cc_start: 0.8307 (t0) cc_final: 0.7657 (t0) REVERT: B 135 MET cc_start: 0.8597 (mtp) cc_final: 0.7727 (mmm) REVERT: B 212 PHE cc_start: 0.9321 (t80) cc_final: 0.8824 (t80) REVERT: B 236 MET cc_start: 0.9361 (mmp) cc_final: 0.8821 (mmm) REVERT: B 256 PHE cc_start: 0.9246 (t80) cc_final: 0.8688 (t80) REVERT: B 315 PHE cc_start: 0.9308 (m-80) cc_final: 0.9050 (m-80) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.1384 time to fit residues: 15.9969 Evaluate side-chains 62 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 45 optimal weight: 30.0000 chunk 157 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 133 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 117 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 GLN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS A 894 GLN B 92 HIS B 93 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.068599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.051310 restraints weight = 164734.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.051740 restraints weight = 148750.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.052002 restraints weight = 138536.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.052180 restraints weight = 128495.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.052600 restraints weight = 124074.298| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3445 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 230 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 219 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (14 function evaluations) r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.6842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 13128 Z= 0.255 Angle : 0.913 13.687 17872 Z= 0.451 Chirality : 0.052 0.431 2037 Planarity : 0.006 0.056 2295 Dihedral : 5.499 28.633 1712 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 30.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.15 % Allowed : 2.72 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.20), residues: 1583 helix: -0.53 (0.39), residues: 159 sheet: -0.12 (0.22), residues: 507 loop : -1.02 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 542 TYR 0.034 0.003 TYR A 230 PHE 0.030 0.003 PHE B 164 TRP 0.023 0.003 TRP A 157 HIS 0.011 0.002 HIS A 787 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.25 (13051) covalent geometry : angle 0.88126 / 0.44 (17678) SS BOND : bond 0.00427 / 0.29 ( 37) SS BOND : angle 1.60443 / 1.10 ( 74) hydrogen bonds : bond 0.04971 / 3.51 ( 322) hydrogen bonds : angle 7.31277 / 5.24 ( 879) link_ALPHA1-3 : bond 0.00631 / 0.33 ( 2) link_ALPHA1-3 : angle 1.45153 / 1.01 ( 6) link_ALPHA1-6 : bond 0.00063 / 0.03 ( 1) link_ALPHA1-6 : angle 1.24183 / 0.95 ( 3) link_BETA1-2 : bond 0.00400 / 0.21 ( 1) link_BETA1-2 : angle 2.85336 / 1.80 ( 3) link_BETA1-4 : bond 0.00582 / 0.28 ( 21) link_BETA1-4 : angle 2.14332 / 1.41 ( 63) link_NAG-ASN : bond 0.00644 / 0.32 ( 15) link_NAG-ASN : angle 3.79280 / 2.39 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.537 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 3 LEU cc_start: 0.8914 (pp) cc_final: 0.8100 (pp) REVERT: A 414 PHE cc_start: 0.9671 (m-10) cc_final: 0.9419 (m-80) REVERT: A 415 PHE cc_start: 0.9457 (t80) cc_final: 0.9136 (t80) REVERT: A 446 TYR cc_start: 0.9117 (m-10) cc_final: 0.8519 (m-10) REVERT: B 127 TYR cc_start: 0.8923 (t80) cc_final: 0.8677 (t80) REVERT: B 128 LEU cc_start: 0.9708 (mt) cc_final: 0.9386 (mt) REVERT: B 129 MET cc_start: 0.8592 (tpt) cc_final: 0.7890 (tpt) REVERT: B 135 MET cc_start: 0.8788 (mtp) cc_final: 0.8508 (mmm) REVERT: B 149 LEU cc_start: 0.9530 (tp) cc_final: 0.9300 (pp) REVERT: B 236 MET cc_start: 0.9627 (mmp) cc_final: 0.9075 (mmm) REVERT: B 256 PHE cc_start: 0.9654 (t80) cc_final: 0.8786 (t80) REVERT: B 315 PHE cc_start: 0.9512 (m-80) cc_final: 0.9221 (m-80) outliers start: 2 outliers final: 0 residues processed: 72 average time/residue: 0.1252 time to fit residues: 12.8996 Evaluate side-chains 55 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 5 optimal weight: 6.9990 chunk 98 optimal weight: 0.0870 chunk 74 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 146 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 92 optimal weight: 20.0000 overall best weight: 1.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS A 787 HIS ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.072012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.055688 restraints weight = 159730.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.055877 restraints weight = 144067.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.056294 restraints weight = 130361.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.056381 restraints weight = 119344.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.056774 restraints weight = 116327.221| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 219 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 218 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (11 function evaluations) r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.6834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 13128 Z= 0.137 Angle : 0.736 12.687 17872 Z= 0.348 Chirality : 0.048 0.449 2037 Planarity : 0.004 0.053 2295 Dihedral : 4.993 26.123 1712 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.21), residues: 1583 helix: -0.06 (0.40), residues: 159 sheet: 0.08 (0.22), residues: 516 loop : -0.90 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 312 TYR 0.014 0.002 TYR A 261 PHE 0.013 0.002 PHE B 160 TRP 0.021 0.002 TRP A 703 HIS 0.004 0.001 HIS A 896 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (13051) covalent geometry : angle 0.70228 / 0.34 (17678) SS BOND : bond 0.00235 / 0.14 ( 37) SS BOND : angle 1.06559 / 0.75 ( 74) hydrogen bonds : bond 0.03712 / 2.70 ( 322) hydrogen bonds : angle 6.70230 / 4.72 ( 879) link_ALPHA1-3 : bond 0.00868 / 0.46 ( 2) link_ALPHA1-3 : angle 1.27491 / 0.93 ( 6) link_ALPHA1-6 : bond 0.00672 / 0.35 ( 1) link_ALPHA1-6 : angle 1.09588 / 0.88 ( 3) link_BETA1-2 : bond 0.00259 / 0.14 ( 1) link_BETA1-2 : angle 2.99147 / 1.78 ( 3) link_BETA1-4 : bond 0.00605 / 0.30 ( 21) link_BETA1-4 : angle 2.02096 / 1.36 ( 63) link_NAG-ASN : bond 0.00406 / 0.20 ( 15) link_NAG-ASN : angle 3.55272 / 2.24 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.321 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 3 LEU cc_start: 0.8675 (pp) cc_final: 0.7904 (pp) REVERT: A 165 GLN cc_start: 0.9543 (tt0) cc_final: 0.9333 (tm-30) REVERT: A 414 PHE cc_start: 0.9389 (m-10) cc_final: 0.9146 (m-80) REVERT: A 415 PHE cc_start: 0.9331 (t80) cc_final: 0.9033 (t80) REVERT: A 446 TYR cc_start: 0.8905 (m-10) cc_final: 0.8307 (m-10) REVERT: B 38 MET cc_start: 0.9407 (mmp) cc_final: 0.9137 (mmm) REVERT: B 130 ASP cc_start: 0.8210 (t0) cc_final: 0.7811 (t0) REVERT: B 135 MET cc_start: 0.8644 (mtp) cc_final: 0.8251 (mmm) REVERT: B 212 PHE cc_start: 0.9411 (t80) cc_final: 0.8966 (t80) REVERT: B 236 MET cc_start: 0.9335 (mmp) cc_final: 0.8872 (mmm) REVERT: B 256 PHE cc_start: 0.9392 (t80) cc_final: 0.8803 (t80) REVERT: B 315 PHE cc_start: 0.9383 (m-80) cc_final: 0.9090 (m-80) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1192 time to fit residues: 12.6394 Evaluate side-chains 54 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 123 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 69 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 86 optimal weight: 40.0000 chunk 3 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 149 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 46 GLN ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN B 628 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.067527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.050261 restraints weight = 165492.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.050661 restraints weight = 149146.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.050790 restraints weight = 138553.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.051101 restraints weight = 133282.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.051352 restraints weight = 126386.753| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3400 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 218 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3400 r_free = 0.3400 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 218 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3400 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.7683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 13128 Z= 0.215 Angle : 0.818 12.854 17872 Z= 0.398 Chirality : 0.049 0.418 2037 Planarity : 0.005 0.106 2295 Dihedral : 5.414 29.906 1712 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 27.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.21), residues: 1583 helix: -0.52 (0.38), residues: 151 sheet: -0.05 (0.22), residues: 517 loop : -1.03 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 593 TYR 0.025 0.002 TYR A 327 PHE 0.021 0.002 PHE B 164 TRP 0.020 0.002 TRP A 703 HIS 0.010 0.002 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.21 (13051) covalent geometry : angle 0.78643 / 0.39 (17678) SS BOND : bond 0.00368 / 0.23 ( 37) SS BOND : angle 1.47107 / 1.00 ( 74) hydrogen bonds : bond 0.04246 / 3.03 ( 322) hydrogen bonds : angle 7.30233 / 5.22 ( 879) link_ALPHA1-3 : bond 0.00562 / 0.29 ( 2) link_ALPHA1-3 : angle 1.55141 / 1.11 ( 6) link_ALPHA1-6 : bond 0.00030 / 0.02 ( 1) link_ALPHA1-6 : angle 0.96742 / 0.84 ( 3) link_BETA1-2 : bond 0.00277 / 0.15 ( 1) link_BETA1-2 : angle 3.01845 / 1.87 ( 3) link_BETA1-4 : bond 0.00543 / 0.27 ( 21) link_BETA1-4 : angle 2.06518 / 1.37 ( 63) link_NAG-ASN : bond 0.00541 / 0.26 ( 15) link_NAG-ASN : angle 3.49337 / 2.22 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.512 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 3 LEU cc_start: 0.8815 (pp) cc_final: 0.8015 (pp) REVERT: A 165 GLN cc_start: 0.9681 (tt0) cc_final: 0.9387 (tm-30) REVERT: A 414 PHE cc_start: 0.9676 (m-10) cc_final: 0.9435 (m-80) REVERT: A 415 PHE cc_start: 0.9542 (t80) cc_final: 0.9277 (t80) REVERT: A 446 TYR cc_start: 0.9088 (m-10) cc_final: 0.8410 (m-10) REVERT: B 127 TYR cc_start: 0.8931 (t80) cc_final: 0.8701 (t80) REVERT: B 129 MET cc_start: 0.8478 (tpt) cc_final: 0.7739 (tpt) REVERT: B 130 ASP cc_start: 0.8668 (t0) cc_final: 0.8300 (t0) REVERT: B 135 MET cc_start: 0.8799 (mtp) cc_final: 0.8567 (mmm) REVERT: B 236 MET cc_start: 0.9477 (mmp) cc_final: 0.9073 (mmm) REVERT: B 256 PHE cc_start: 0.9614 (t80) cc_final: 0.9008 (t80) REVERT: B 315 PHE cc_start: 0.9501 (m-80) cc_final: 0.9184 (m-80) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.1300 time to fit residues: 11.9938 Evaluate side-chains 51 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 32 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 152 optimal weight: 50.0000 chunk 128 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 2 ASN A 624 HIS ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 GLN ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.060443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.040501 restraints weight = 134768.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.040824 restraints weight = 125120.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.040823 restraints weight = 117512.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.040823 restraints weight = 117517.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.040823 restraints weight = 117517.637| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 218 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 212 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 10 (15 function evaluations) r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.8487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 13128 Z= 0.216 Angle : 0.840 12.911 17872 Z= 0.410 Chirality : 0.051 0.447 2037 Planarity : 0.006 0.160 2295 Dihedral : 5.797 32.565 1712 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 27.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.07 % Allowed : 1.40 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.20), residues: 1583 helix: -1.04 (0.37), residues: 164 sheet: -0.34 (0.23), residues: 495 loop : -1.20 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 447 TYR 0.021 0.002 TYR B 380 PHE 0.026 0.003 PHE A 348 TRP 0.029 0.002 TRP A 703 HIS 0.010 0.002 HIS A 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.22 (13051) covalent geometry : angle 0.80739 / 0.40 (17678) SS BOND : bond 0.00358 / 0.24 ( 37) SS BOND : angle 1.33806 / 0.90 ( 74) hydrogen bonds : bond 0.04470 / 3.22 ( 322) hydrogen bonds : angle 7.65851 / 5.45 ( 879) link_ALPHA1-3 : bond 0.00675 / 0.35 ( 2) link_ALPHA1-3 : angle 1.63541 / 1.21 ( 6) link_ALPHA1-6 : bond 0.00401 / 0.21 ( 1) link_ALPHA1-6 : angle 1.12481 / 1.04 ( 3) link_BETA1-2 : bond 0.00299 / 0.16 ( 1) link_BETA1-2 : angle 3.14102 / 2.05 ( 3) link_BETA1-4 : bond 0.00530 / 0.24 ( 21) link_BETA1-4 : angle 2.19506 / 1.52 ( 63) link_NAG-ASN : bond 0.00632 / 0.30 ( 15) link_NAG-ASN : angle 3.68491 / 2.30 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LEU cc_start: 0.8669 (pp) cc_final: 0.8007 (pp) REVERT: A 165 GLN cc_start: 0.9731 (tt0) cc_final: 0.9492 (tm-30) REVERT: A 310 MET cc_start: 0.9468 (tmm) cc_final: 0.9256 (tmm) REVERT: A 415 PHE cc_start: 0.9654 (t80) cc_final: 0.9430 (t80) REVERT: A 446 TYR cc_start: 0.9143 (m-10) cc_final: 0.8653 (m-10) REVERT: A 654 VAL cc_start: 0.8423 (t) cc_final: 0.8208 (m) REVERT: B 256 PHE cc_start: 0.9641 (t80) cc_final: 0.9126 (t80) REVERT: B 315 PHE cc_start: 0.9601 (m-80) cc_final: 0.9268 (m-80) outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.1278 time to fit residues: 11.5307 Evaluate side-chains 49 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 5 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 147 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 128 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.068885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.052586 restraints weight = 161337.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.052669 restraints weight = 143435.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.052931 restraints weight = 131059.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.053335 restraints weight = 122186.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.053675 restraints weight = 115245.316| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3449 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 212 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 212 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.8396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13128 Z= 0.130 Angle : 0.747 12.036 17872 Z= 0.353 Chirality : 0.050 0.515 2037 Planarity : 0.004 0.053 2295 Dihedral : 5.264 30.341 1712 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.21), residues: 1583 helix: -0.55 (0.39), residues: 154 sheet: -0.09 (0.23), residues: 488 loop : -1.02 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 742 TYR 0.019 0.002 TYR A 284 PHE 0.020 0.002 PHE A 637 TRP 0.024 0.002 TRP A 703 HIS 0.004 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (13051) covalent geometry : angle 0.71600 / 0.35 (17678) SS BOND : bond 0.00312 / 0.15 ( 37) SS BOND : angle 1.11052 / 0.83 ( 74) hydrogen bonds : bond 0.03546 / 2.62 ( 322) hydrogen bonds : angle 6.99519 / 4.92 ( 879) link_ALPHA1-3 : bond 0.00877 / 0.46 ( 2) link_ALPHA1-3 : angle 1.33206 / 0.99 ( 6) link_ALPHA1-6 : bond 0.00831 / 0.44 ( 1) link_ALPHA1-6 : angle 0.99622 / 0.90 ( 3) link_BETA1-2 : bond 0.00246 / 0.13 ( 1) link_BETA1-2 : angle 3.13754 / 1.86 ( 3) link_BETA1-4 : bond 0.00553 / 0.28 ( 21) link_BETA1-4 : angle 2.10620 / 1.41 ( 63) link_NAG-ASN : bond 0.00427 / 0.22 ( 15) link_NAG-ASN : angle 3.35900 / 2.15 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LEU cc_start: 0.8652 (pp) cc_final: 0.7974 (pp) REVERT: A 25 PHE cc_start: 0.8162 (m-80) cc_final: 0.7923 (m-80) REVERT: A 165 GLN cc_start: 0.9681 (tt0) cc_final: 0.9467 (tm-30) REVERT: A 414 PHE cc_start: 0.9839 (m-80) cc_final: 0.9589 (m-80) REVERT: A 415 PHE cc_start: 0.9617 (t80) cc_final: 0.9365 (t80) REVERT: A 446 TYR cc_start: 0.8933 (m-10) cc_final: 0.8353 (m-10) REVERT: A 546 MET cc_start: 0.9375 (mmp) cc_final: 0.8895 (mpp) REVERT: A 652 LEU cc_start: 0.9039 (tp) cc_final: 0.7920 (pp) REVERT: B 38 MET cc_start: 0.9472 (mmp) cc_final: 0.9260 (mmm) REVERT: B 236 MET cc_start: 0.9486 (mmp) cc_final: 0.9229 (mmm) REVERT: B 256 PHE cc_start: 0.9682 (t80) cc_final: 0.9129 (t80) REVERT: B 315 PHE cc_start: 0.9621 (m-80) cc_final: 0.9277 (m-80) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1189 time to fit residues: 11.5186 Evaluate side-chains 52 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 32 optimal weight: 0.0470 chunk 148 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 overall best weight: 3.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 HIS ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.067202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.050153 restraints weight = 164805.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.050666 restraints weight = 146654.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.050934 restraints weight = 133893.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.051061 restraints weight = 125922.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.051420 restraints weight = 121387.779| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 212 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 213 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.8627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13128 Z= 0.149 Angle : 0.746 13.963 17872 Z= 0.351 Chirality : 0.049 0.469 2037 Planarity : 0.004 0.053 2295 Dihedral : 5.171 31.482 1712 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.21), residues: 1583 helix: -0.91 (0.38), residues: 164 sheet: -0.10 (0.23), residues: 487 loop : -1.04 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 593 TYR 0.016 0.002 TYR A 327 PHE 0.012 0.002 PHE B 605 TRP 0.021 0.002 TRP A 703 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (13051) covalent geometry : angle 0.71283 / 0.34 (17678) SS BOND : bond 0.00267 / 0.16 ( 37) SS BOND : angle 1.25948 / 0.97 ( 74) hydrogen bonds : bond 0.03605 / 2.68 ( 322) hydrogen bonds : angle 7.03215 / 4.95 ( 879) link_ALPHA1-3 : bond 0.00671 / 0.35 ( 2) link_ALPHA1-3 : angle 1.50162 / 1.11 ( 6) link_ALPHA1-6 : bond 0.00663 / 0.35 ( 1) link_ALPHA1-6 : angle 1.07748 / 0.99 ( 3) link_BETA1-2 : bond 0.00030 / 0.02 ( 1) link_BETA1-2 : angle 3.01541 / 1.87 ( 3) link_BETA1-4 : bond 0.00566 / 0.29 ( 21) link_BETA1-4 : angle 2.15598 / 1.42 ( 63) link_NAG-ASN : bond 0.00420 / 0.20 ( 15) link_NAG-ASN : angle 3.37499 / 2.23 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.506 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 3 LEU cc_start: 0.8583 (pp) cc_final: 0.7871 (pp) REVERT: A 25 PHE cc_start: 0.8061 (m-80) cc_final: 0.7827 (m-80) REVERT: A 165 GLN cc_start: 0.9737 (tt0) cc_final: 0.9473 (tm-30) REVERT: A 414 PHE cc_start: 0.9850 (m-80) cc_final: 0.9628 (m-80) REVERT: A 415 PHE cc_start: 0.9635 (t80) cc_final: 0.9398 (t80) REVERT: A 446 TYR cc_start: 0.8996 (m-10) cc_final: 0.8441 (m-10) REVERT: A 529 LEU cc_start: 0.9354 (tt) cc_final: 0.9024 (mm) REVERT: A 652 LEU cc_start: 0.9131 (tp) cc_final: 0.8004 (pp) REVERT: A 654 VAL cc_start: 0.8296 (t) cc_final: 0.8009 (m) REVERT: B 127 TYR cc_start: 0.8726 (t80) cc_final: 0.8483 (t80) REVERT: B 256 PHE cc_start: 0.9698 (t80) cc_final: 0.9194 (t80) REVERT: B 315 PHE cc_start: 0.9642 (m-80) cc_final: 0.9284 (m-80) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1178 time to fit residues: 10.9466 Evaluate side-chains 55 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 144 optimal weight: 40.0000 chunk 49 optimal weight: 20.0000 chunk 145 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 52 optimal weight: 0.0470 chunk 112 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 22 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 2.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 GLN A 891 GLN A 940 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.067839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.050626 restraints weight = 162526.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.051138 restraints weight = 145516.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.051378 restraints weight = 132564.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 14)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.051756 restraints weight = 125666.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.052092 restraints weight = 114224.311| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 213 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 213 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.8800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13128 Z= 0.128 Angle : 0.710 13.138 17872 Z= 0.333 Chirality : 0.048 0.467 2037 Planarity : 0.004 0.052 2295 Dihedral : 4.984 32.126 1712 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.21), residues: 1583 helix: -0.87 (0.37), residues: 170 sheet: -0.02 (0.23), residues: 482 loop : -1.06 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 939 TYR 0.014 0.002 TYR A 26 PHE 0.020 0.002 PHE A 897 TRP 0.023 0.002 TRP A 703 HIS 0.007 0.001 HIS B 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (13051) covalent geometry : angle 0.67815 / 0.33 (17678) SS BOND : bond 0.00205 / 0.13 ( 37) SS BOND : angle 1.13388 / 0.86 ( 74) hydrogen bonds : bond 0.03275 / 2.43 ( 322) hydrogen bonds : angle 6.80818 / 4.77 ( 879) link_ALPHA1-3 : bond 0.00736 / 0.38 ( 2) link_ALPHA1-3 : angle 1.41357 / 1.06 ( 6) link_ALPHA1-6 : bond 0.00783 / 0.41 ( 1) link_ALPHA1-6 : angle 1.01706 / 0.94 ( 3) link_BETA1-2 : bond 0.00124 / 0.07 ( 1) link_BETA1-2 : angle 2.99971 / 1.83 ( 3) link_BETA1-4 : bond 0.00537 / 0.27 ( 21) link_BETA1-4 : angle 2.09340 / 1.38 ( 63) link_NAG-ASN : bond 0.00350 / 0.18 ( 15) link_NAG-ASN : angle 3.19110 / 2.05 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2772.90 seconds wall clock time: 48 minutes 34.19 seconds (2914.19 seconds total)