Starting phenix.real_space_refine on Thu Jul 31 03:19:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nxd_12637/07_2025/7nxd_12637.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nxd_12637/07_2025/7nxd_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7nxd_12637/07_2025/7nxd_12637.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nxd_12637/07_2025/7nxd_12637.map" model { file = "/net/cci-nas-00/data/ceres_data/7nxd_12637/07_2025/7nxd_12637.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nxd_12637/07_2025/7nxd_12637.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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 dihedrals: 18 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 3 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: 7.71, per 1000 atoms: 0.60 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: 3.99 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.60 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: 4.24 Time building geometry restraints manager: 4.07 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 - 22.86: 8079 22.86 - 45.72: 266 45.72 - 68.58: 39 68.58 - 91.44: 45 91.44 - 114.31: 28 Dihedral angle restraints: 8457 sinusoidal: 3913 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 8454 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: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.750 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4646 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 : 14.128 114.306 5446 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (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 TRP 0.014 0.001 TRP A 121 HIS 0.003 0.000 HIS A 787 PHE 0.013 0.001 PHE A 876 TYR 0.010 0.001 TYR A 366 ARG 0.003 0.000 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.02075 ( 15) link_NAG-ASN : angle 6.21488 ( 45) link_ALPHA1-6 : bond 0.00142 ( 1) link_ALPHA1-6 : angle 0.89524 ( 3) link_BETA1-2 : bond 0.00239 ( 1) link_BETA1-2 : angle 2.15962 ( 3) link_BETA1-4 : bond 0.00324 ( 21) link_BETA1-4 : angle 1.92899 ( 63) link_ALPHA1-3 : bond 0.01246 ( 2) link_ALPHA1-3 : angle 5.02278 ( 6) hydrogen bonds : bond 0.29112 ( 322) hydrogen bonds : angle 10.47499 ( 879) SS BOND : bond 0.05867 ( 37) SS BOND : angle 1.69186 ( 74) covalent geometry : bond 0.01342 (13051) covalent geometry : angle 1.50906 (17678) *********************** 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 : 1.449 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: 0.6358 (p0) REVERT: B 335 SER cc_start: 0.6007 (p) cc_final: 0.4939 (p) REVERT: B 518 CYS cc_start: 0.7704 (OUTLIER) cc_final: 0.6920 (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: 0.3218 time to fit residues: 85.1025 Evaluate side-chains 100 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 GLN ** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 HIS A 587 HIS A 624 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 = 0.4182 r_free = 0.4182 target = 0.086890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.066649 restraints weight = 148463.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.067207 restraints weight = 135431.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.067207 restraints weight = 126165.431| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3895 r_free = 0.3895 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3867 r_free = 0.3867 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 229 | |-----------------------------------------------------------------------------| r_final: 0.3867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13128 Z= 0.225 Angle : 0.986 17.536 17872 Z= 0.460 Chirality : 0.058 0.685 2037 Planarity : 0.006 0.086 2295 Dihedral : 12.818 78.206 2532 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.20), residues: 1583 helix: 0.56 (0.39), residues: 149 sheet: -0.00 (0.23), residues: 489 loop : -0.90 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 947 HIS 0.016 0.001 HIS A 787 PHE 0.046 0.003 PHE B 160 TYR 0.019 0.002 TYR B 325 ARG 0.011 0.001 ARG A 742 Details of bonding type rmsd link_NAG-ASN : bond 0.00704 ( 15) link_NAG-ASN : angle 5.29361 ( 45) link_ALPHA1-6 : bond 0.00075 ( 1) link_ALPHA1-6 : angle 1.88230 ( 3) link_BETA1-2 : bond 0.00190 ( 1) link_BETA1-2 : angle 4.02757 ( 3) link_BETA1-4 : bond 0.00824 ( 21) link_BETA1-4 : angle 2.84423 ( 63) link_ALPHA1-3 : bond 0.01299 ( 2) link_ALPHA1-3 : angle 2.14832 ( 6) hydrogen bonds : bond 0.06146 ( 322) hydrogen bonds : angle 7.55557 ( 879) SS BOND : bond 0.00418 ( 37) SS BOND : angle 1.45000 ( 74) covalent geometry : bond 0.00491 (13051) covalent geometry : angle 0.93195 (17678) *********************** 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 115 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.376 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: 0.8820 (pp) cc_final: 0.8114 (pp) REVERT: A 188 TRP cc_start: 0.9407 (m-90) cc_final: 0.9100 (m-10) REVERT: A 303 LEU cc_start: 0.9688 (mp) cc_final: 0.9363 (tp) REVERT: A 313 THR cc_start: 0.9139 (p) cc_final: 0.8244 (p) REVERT: A 414 PHE cc_start: 0.8909 (m-10) cc_final: 0.8570 (m-80) REVERT: A 415 PHE cc_start: 0.8682 (t80) cc_final: 0.8222 (t80) REVERT: A 433 LEU cc_start: 0.7850 (tp) cc_final: 0.7589 (tp) REVERT: B 131 LEU cc_start: 0.8166 (mp) cc_final: 0.7881 (tp) REVERT: B 212 PHE cc_start: 0.9290 (t80) cc_final: 0.8820 (t80) REVERT: B 236 MET cc_start: 0.9424 (mmp) cc_final: 0.8972 (mmm) REVERT: B 256 PHE cc_start: 0.9110 (t80) cc_final: 0.8529 (t80) REVERT: B 315 PHE cc_start: 0.9115 (m-80) cc_final: 0.8899 (m-80) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.3719 time to fit residues: 61.6495 Evaluate side-chains 78 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.083119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.064849 restraints weight = 149684.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.065516 restraints weight = 135594.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.065815 restraints weight = 124211.873| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3765 r_free = 0.3765 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 229 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3764 r_free = 0.3764 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 250 | |-----------------------------------------------------------------------------| r_final: 0.3764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13128 Z= 0.141 Angle : 0.792 13.792 17872 Z= 0.366 Chirality : 0.051 0.491 2037 Planarity : 0.004 0.060 2295 Dihedral : 10.125 58.825 2532 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.07 % Allowed : 2.57 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.20), residues: 1583 helix: 0.72 (0.39), residues: 153 sheet: 0.25 (0.23), residues: 486 loop : -0.76 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 100 HIS 0.006 0.001 HIS A 787 PHE 0.022 0.002 PHE B 160 TYR 0.017 0.001 TYR A 920 ARG 0.011 0.001 ARG A 323 Details of bonding type rmsd link_NAG-ASN : bond 0.00445 ( 15) link_NAG-ASN : angle 4.55152 ( 45) link_ALPHA1-6 : bond 0.00281 ( 1) link_ALPHA1-6 : angle 1.48896 ( 3) link_BETA1-2 : bond 0.00496 ( 1) link_BETA1-2 : angle 3.27069 ( 3) link_BETA1-4 : bond 0.00737 ( 21) link_BETA1-4 : angle 2.56231 ( 63) link_ALPHA1-3 : bond 0.01427 ( 2) link_ALPHA1-3 : angle 1.05517 ( 6) hydrogen bonds : bond 0.04447 ( 322) hydrogen bonds : angle 6.65394 ( 879) SS BOND : bond 0.00243 ( 37) SS BOND : angle 1.21644 ( 74) covalent geometry : bond 0.00301 (13051) covalent geometry : angle 0.74096 (17678) *********************** 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 99 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 1.370 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: A 3 LEU cc_start: 0.8837 (pp) cc_final: 0.8223 (pp) REVERT: A 188 TRP cc_start: 0.9419 (m-90) cc_final: 0.9166 (m-10) REVERT: A 303 LEU cc_start: 0.9684 (mp) cc_final: 0.9379 (tp) REVERT: A 350 ARG cc_start: 0.9478 (mmm160) cc_final: 0.8938 (mmm160) REVERT: A 414 PHE cc_start: 0.9071 (m-10) cc_final: 0.8724 (m-80) REVERT: A 415 PHE cc_start: 0.8802 (t80) cc_final: 0.8293 (t80) REVERT: A 433 LEU cc_start: 0.7669 (tp) cc_final: 0.7445 (tp) REVERT: A 446 TYR cc_start: 0.8718 (m-10) cc_final: 0.8473 (m-10) REVERT: A 546 MET cc_start: 0.8881 (mpp) cc_final: 0.8592 (mpp) REVERT: A 567 LEU cc_start: 0.8962 (tp) cc_final: 0.8744 (tp) REVERT: B 131 LEU cc_start: 0.8277 (mp) cc_final: 0.7864 (tp) REVERT: B 236 MET cc_start: 0.9370 (mmp) cc_final: 0.8806 (mmm) REVERT: B 256 PHE cc_start: 0.9167 (t80) cc_final: 0.8606 (t80) REVERT: B 315 PHE cc_start: 0.9241 (m-80) cc_final: 0.9004 (m-80) outliers start: 1 outliers final: 0 residues processed: 98 average time/residue: 0.3236 time to fit residues: 44.7500 Evaluate side-chains 79 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 139 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 100 optimal weight: 0.5980 chunk 87 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 191 GLN ** 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 886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN ** B 458 HIS ** 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 = 0.4015 r_free = 0.4015 target = 0.074713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.056817 restraints weight = 155823.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.057370 restraints weight = 141842.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.057711 restraints weight = 130946.154| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 250 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 275 | |-----------------------------------------------------------------------------| r_final: 0.3711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 13128 Z= 0.234 Angle : 0.886 14.062 17872 Z= 0.424 Chirality : 0.053 0.615 2037 Planarity : 0.005 0.065 2295 Dihedral : 8.466 59.207 2532 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.20), residues: 1583 helix: 0.14 (0.40), residues: 152 sheet: -0.01 (0.22), residues: 520 loop : -0.85 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 157 HIS 0.012 0.002 HIS B 263 PHE 0.030 0.003 PHE A 285 TYR 0.027 0.002 TYR A 163 ARG 0.007 0.001 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00850 ( 15) link_NAG-ASN : angle 5.06794 ( 45) link_ALPHA1-6 : bond 0.00610 ( 1) link_ALPHA1-6 : angle 2.09929 ( 3) link_BETA1-2 : bond 0.00236 ( 1) link_BETA1-2 : angle 3.42262 ( 3) link_BETA1-4 : bond 0.00542 ( 21) link_BETA1-4 : angle 2.41370 ( 63) link_ALPHA1-3 : bond 0.01171 ( 2) link_ALPHA1-3 : angle 2.11718 ( 6) hydrogen bonds : bond 0.04542 ( 322) hydrogen bonds : angle 6.66625 ( 879) SS BOND : bond 0.00428 ( 37) SS BOND : angle 1.30949 ( 74) covalent geometry : bond 0.00505 (13051) covalent geometry : angle 0.83431 (17678) *********************** 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 83 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.560 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: A 3 LEU cc_start: 0.8827 (pp) cc_final: 0.8107 (pp) REVERT: A 303 LEU cc_start: 0.9630 (mp) cc_final: 0.9365 (tp) REVERT: A 414 PHE cc_start: 0.9186 (m-10) cc_final: 0.8842 (m-80) REVERT: A 415 PHE cc_start: 0.8994 (t80) cc_final: 0.8482 (t80) REVERT: A 446 TYR cc_start: 0.8911 (m-10) cc_final: 0.8452 (m-10) REVERT: A 458 LEU cc_start: 0.8413 (tp) cc_final: 0.8134 (tp) REVERT: B 135 MET cc_start: 0.8061 (mtt) cc_final: 0.7799 (mmm) REVERT: B 212 PHE cc_start: 0.9323 (t80) cc_final: 0.8856 (t80) REVERT: B 236 MET cc_start: 0.9426 (mmp) cc_final: 0.8956 (mmm) REVERT: B 254 LEU cc_start: 0.9046 (mt) cc_final: 0.8845 (mt) REVERT: B 256 PHE cc_start: 0.9259 (t80) cc_final: 0.8865 (t80) REVERT: B 315 PHE cc_start: 0.9311 (m-80) cc_final: 0.9004 (m-80) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.3222 time to fit residues: 38.0835 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 : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 46 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 57 optimal weight: 20.0000 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 165 GLN A 191 GLN A 787 HIS ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 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 = 0.4037 r_free = 0.4037 target = 0.075770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.058157 restraints weight = 155048.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.058700 restraints weight = 139296.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.059126 restraints weight = 127103.645| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 275 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 272 | |-----------------------------------------------------------------------------| r_final: 0.3618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13128 Z= 0.140 Angle : 0.750 13.035 17872 Z= 0.348 Chirality : 0.049 0.592 2037 Planarity : 0.004 0.055 2295 Dihedral : 8.110 57.788 2532 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1583 helix: 0.50 (0.41), residues: 152 sheet: 0.21 (0.22), residues: 499 loop : -0.82 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 703 HIS 0.005 0.001 HIS B 301 PHE 0.012 0.002 PHE B 160 TYR 0.020 0.002 TYR A 284 ARG 0.006 0.000 ARG A 323 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 15) link_NAG-ASN : angle 4.64395 ( 45) link_ALPHA1-6 : bond 0.00034 ( 1) link_ALPHA1-6 : angle 1.55201 ( 3) link_BETA1-2 : bond 0.00229 ( 1) link_BETA1-2 : angle 3.02486 ( 3) link_BETA1-4 : bond 0.00608 ( 21) link_BETA1-4 : angle 2.32702 ( 63) link_ALPHA1-3 : bond 0.01326 ( 2) link_ALPHA1-3 : angle 1.66512 ( 6) hydrogen bonds : bond 0.03585 ( 322) hydrogen bonds : angle 6.26749 ( 879) SS BOND : bond 0.00195 ( 37) SS BOND : angle 0.98469 ( 74) covalent geometry : bond 0.00299 (13051) covalent geometry : angle 0.69834 (17678) *********************** 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 79 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.578 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: 0.8812 (pp) cc_final: 0.8129 (pp) REVERT: A 414 PHE cc_start: 0.9301 (m-10) cc_final: 0.8973 (m-80) REVERT: A 415 PHE cc_start: 0.9113 (t80) cc_final: 0.8646 (t80) REVERT: A 446 TYR cc_start: 0.8869 (m-10) cc_final: 0.8316 (m-10) REVERT: B 38 MET cc_start: 0.9313 (mmp) cc_final: 0.9044 (mmm) REVERT: B 135 MET cc_start: 0.8068 (mtt) cc_final: 0.7826 (mmm) REVERT: B 212 PHE cc_start: 0.9353 (t80) cc_final: 0.8827 (t80) REVERT: B 236 MET cc_start: 0.9448 (mmp) cc_final: 0.8941 (mmm) REVERT: B 256 PHE cc_start: 0.9251 (t80) cc_final: 0.8778 (t80) REVERT: B 315 PHE cc_start: 0.9343 (m-80) cc_final: 0.9061 (m-80) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.3055 time to fit residues: 35.2804 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 : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 37 optimal weight: 20.0000 chunk 151 optimal weight: 30.0000 chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 58 optimal weight: 0.0970 chunk 40 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 overall best weight: 3.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 564 HIS ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.073906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.056308 restraints weight = 159231.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.056808 restraints weight = 141909.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.057257 restraints weight = 130357.342| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 272 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3577 r_free = 0.3577 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 273 | |-----------------------------------------------------------------------------| r_final: 0.3577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13128 Z= 0.151 Angle : 0.742 12.408 17872 Z= 0.348 Chirality : 0.048 0.476 2037 Planarity : 0.004 0.054 2295 Dihedral : 8.127 60.125 2532 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.21), residues: 1583 helix: 0.21 (0.40), residues: 159 sheet: 0.21 (0.22), residues: 505 loop : -0.79 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 100 HIS 0.010 0.001 HIS A 787 PHE 0.017 0.002 PHE B 164 TYR 0.019 0.002 TYR A 163 ARG 0.009 0.000 ARG B 426 Details of bonding type rmsd link_NAG-ASN : bond 0.00397 ( 15) link_NAG-ASN : angle 4.17731 ( 45) link_ALPHA1-6 : bond 0.00222 ( 1) link_ALPHA1-6 : angle 1.83747 ( 3) link_BETA1-2 : bond 0.00025 ( 1) link_BETA1-2 : angle 2.97319 ( 3) link_BETA1-4 : bond 0.00608 ( 21) link_BETA1-4 : angle 2.26058 ( 63) link_ALPHA1-3 : bond 0.01061 ( 2) link_ALPHA1-3 : angle 1.69101 ( 6) hydrogen bonds : bond 0.03626 ( 322) hydrogen bonds : angle 6.30081 ( 879) SS BOND : bond 0.00284 ( 37) SS BOND : angle 0.91024 ( 74) covalent geometry : bond 0.00330 (13051) covalent geometry : angle 0.69771 (17678) *********************** 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 74 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LEU cc_start: 0.8736 (pp) cc_final: 0.8049 (pp) REVERT: A 228 ASP cc_start: 0.8742 (m-30) cc_final: 0.8498 (m-30) REVERT: A 414 PHE cc_start: 0.9327 (m-10) cc_final: 0.9013 (m-80) REVERT: A 415 PHE cc_start: 0.9235 (t80) cc_final: 0.8825 (t80) REVERT: A 446 TYR cc_start: 0.8944 (m-10) cc_final: 0.8372 (m-10) REVERT: A 529 LEU cc_start: 0.9349 (tt) cc_final: 0.8961 (mm) REVERT: B 38 MET cc_start: 0.9352 (mmp) cc_final: 0.9103 (mmm) REVERT: B 212 PHE cc_start: 0.9420 (t80) cc_final: 0.8916 (t80) REVERT: B 236 MET cc_start: 0.9484 (mmp) cc_final: 0.9013 (mmm) REVERT: B 256 PHE cc_start: 0.9324 (t80) cc_final: 0.8937 (t80) REVERT: B 315 PHE cc_start: 0.9320 (m-80) cc_final: 0.9101 (m-80) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.3642 time to fit residues: 39.9601 Evaluate side-chains 57 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 89 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 chunk 87 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 HIS ** A 712 HIS ** 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 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS B 93 GLN ** B 277 ASN ** 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 = 0.3889 r_free = 0.3889 target = 0.068187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.051020 restraints weight = 163801.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.051441 restraints weight = 148423.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.051822 restraints weight = 137428.651| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 273 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 272 | |-----------------------------------------------------------------------------| r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.7198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 13128 Z= 0.228 Angle : 0.847 12.922 17872 Z= 0.413 Chirality : 0.049 0.454 2037 Planarity : 0.005 0.054 2295 Dihedral : 8.519 67.412 2532 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 27.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.20), residues: 1583 helix: -0.37 (0.38), residues: 159 sheet: 0.06 (0.22), residues: 504 loop : -0.93 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 703 HIS 0.007 0.002 HIS B 263 PHE 0.025 0.003 PHE B 164 TYR 0.026 0.002 TYR A 327 ARG 0.007 0.001 ARG A 593 Details of bonding type rmsd link_NAG-ASN : bond 0.00620 ( 15) link_NAG-ASN : angle 4.12111 ( 45) link_ALPHA1-6 : bond 0.00309 ( 1) link_ALPHA1-6 : angle 2.32210 ( 3) link_BETA1-2 : bond 0.00299 ( 1) link_BETA1-2 : angle 3.24292 ( 3) link_BETA1-4 : bond 0.00566 ( 21) link_BETA1-4 : angle 2.30570 ( 63) link_ALPHA1-3 : bond 0.00850 ( 2) link_ALPHA1-3 : angle 1.86888 ( 6) hydrogen bonds : bond 0.04342 ( 322) hydrogen bonds : angle 7.17951 ( 879) SS BOND : bond 0.00747 ( 37) SS BOND : angle 1.39576 ( 74) covalent geometry : bond 0.00479 (13051) covalent geometry : angle 0.80707 (17678) *********************** 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 71 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.413 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: 0.8929 (pp) cc_final: 0.8142 (pp) REVERT: A 415 PHE cc_start: 0.9575 (t80) cc_final: 0.9234 (t80) REVERT: A 446 TYR cc_start: 0.9212 (m-10) cc_final: 0.8662 (m-10) REVERT: A 925 MET cc_start: 0.1411 (pmm) cc_final: 0.0961 (pmm) REVERT: B 127 TYR cc_start: 0.9203 (t80) cc_final: 0.8682 (t80) REVERT: B 128 LEU cc_start: 0.9816 (mt) cc_final: 0.9610 (mt) REVERT: B 236 MET cc_start: 0.9710 (mmp) cc_final: 0.9347 (mmm) REVERT: B 256 PHE cc_start: 0.9688 (t80) cc_final: 0.9263 (t80) REVERT: B 315 PHE cc_start: 0.9534 (m-80) cc_final: 0.9239 (m-80) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2911 time to fit residues: 29.9973 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 : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 51 optimal weight: 8.9990 chunk 145 optimal weight: 0.8980 chunk 129 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 30 optimal weight: 20.0000 chunk 116 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN ** A 381 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3940 r_free = 0.3940 target = 0.070615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.053375 restraints weight = 161373.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.053908 restraints weight = 143484.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.054352 restraints weight = 130456.646| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 272 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 273 | |-----------------------------------------------------------------------------| r_final: 0.3471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.7264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13128 Z= 0.136 Angle : 0.731 12.145 17872 Z= 0.343 Chirality : 0.048 0.429 2037 Planarity : 0.004 0.055 2295 Dihedral : 8.420 72.806 2532 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.21), residues: 1583 helix: -0.33 (0.39), residues: 159 sheet: 0.10 (0.22), residues: 511 loop : -0.90 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 703 HIS 0.003 0.001 HIS A 712 PHE 0.011 0.002 PHE B 160 TYR 0.016 0.002 TYR A 26 ARG 0.004 0.001 ARG A 449 Details of bonding type rmsd link_NAG-ASN : bond 0.00374 ( 15) link_NAG-ASN : angle 3.85983 ( 45) link_ALPHA1-6 : bond 0.00255 ( 1) link_ALPHA1-6 : angle 1.68073 ( 3) link_BETA1-2 : bond 0.00154 ( 1) link_BETA1-2 : angle 3.03092 ( 3) link_BETA1-4 : bond 0.00639 ( 21) link_BETA1-4 : angle 2.25945 ( 63) link_ALPHA1-3 : bond 0.01094 ( 2) link_ALPHA1-3 : angle 1.59502 ( 6) hydrogen bonds : bond 0.03474 ( 322) hydrogen bonds : angle 6.73344 ( 879) SS BOND : bond 0.00217 ( 37) SS BOND : angle 1.10830 ( 74) covalent geometry : bond 0.00289 (13051) covalent geometry : angle 0.68952 (17678) *********************** 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 67 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.414 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: 0.8821 (pp) cc_final: 0.8033 (pp) REVERT: A 414 PHE cc_start: 0.9845 (m-80) cc_final: 0.9598 (m-80) REVERT: A 415 PHE cc_start: 0.9604 (t80) cc_final: 0.9292 (t80) REVERT: A 446 TYR cc_start: 0.9202 (m-10) cc_final: 0.8674 (m-10) REVERT: A 529 LEU cc_start: 0.9173 (tt) cc_final: 0.8799 (mm) REVERT: A 652 LEU cc_start: 0.9188 (tp) cc_final: 0.8107 (pp) REVERT: B 127 TYR cc_start: 0.9229 (t80) cc_final: 0.8751 (t80) REVERT: B 236 MET cc_start: 0.9522 (mmp) cc_final: 0.9206 (mmm) REVERT: B 256 PHE cc_start: 0.9678 (t80) cc_final: 0.9220 (t80) REVERT: B 315 PHE cc_start: 0.9542 (m-80) cc_final: 0.9259 (m-80) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2806 time to fit residues: 27.6483 Evaluate side-chains 56 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 19 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 107 optimal weight: 9.9990 chunk 142 optimal weight: 20.0000 chunk 123 optimal weight: 30.0000 chunk 64 optimal weight: 10.0000 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN ** A 381 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 HIS ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 ASN B 628 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.063279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.042941 restraints weight = 133080.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.042863 restraints weight = 126064.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.043191 restraints weight = 118615.031| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 273 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 275 | |-----------------------------------------------------------------------------| r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.7818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13128 Z= 0.166 Angle : 0.759 12.049 17872 Z= 0.356 Chirality : 0.048 0.420 2037 Planarity : 0.004 0.054 2295 Dihedral : 8.511 77.989 2532 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.21), residues: 1583 helix: -0.40 (0.38), residues: 158 sheet: 0.08 (0.23), residues: 496 loop : -0.92 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 703 HIS 0.007 0.001 HIS B 263 PHE 0.014 0.002 PHE B 605 TYR 0.018 0.002 TYR A 163 ARG 0.006 0.001 ARG A 593 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 15) link_NAG-ASN : angle 4.03541 ( 45) link_ALPHA1-6 : bond 0.00078 ( 1) link_ALPHA1-6 : angle 2.08023 ( 3) link_BETA1-2 : bond 0.00119 ( 1) link_BETA1-2 : angle 3.15319 ( 3) link_BETA1-4 : bond 0.00682 ( 21) link_BETA1-4 : angle 2.25368 ( 63) link_ALPHA1-3 : bond 0.00778 ( 2) link_ALPHA1-3 : angle 1.61245 ( 6) hydrogen bonds : bond 0.03629 ( 322) hydrogen bonds : angle 6.89712 ( 879) SS BOND : bond 0.00277 ( 37) SS BOND : angle 1.20236 ( 74) covalent geometry : bond 0.00351 (13051) covalent geometry : angle 0.71699 (17678) *********************** 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 68 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.330 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: 0.8605 (pp) cc_final: 0.7860 (pp) REVERT: A 415 PHE cc_start: 0.9612 (t80) cc_final: 0.9345 (t80) REVERT: A 446 TYR cc_start: 0.9233 (m-10) cc_final: 0.8744 (m-10) REVERT: B 127 TYR cc_start: 0.9227 (t80) cc_final: 0.8851 (t80) REVERT: B 256 PHE cc_start: 0.9645 (t80) cc_final: 0.9345 (t80) REVERT: B 315 PHE cc_start: 0.9529 (m-80) cc_final: 0.9256 (m-80) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2824 time to fit residues: 28.4785 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 : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 113 optimal weight: 0.0030 chunk 102 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 60 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN ** A 668 HIS ** 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 816 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.065374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.044233 restraints weight = 132936.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.044233 restraints weight = 125582.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.044233 restraints weight = 125582.653| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 275 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 275 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.7804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13128 Z= 0.117 Angle : 0.708 12.283 17872 Z= 0.328 Chirality : 0.048 0.415 2037 Planarity : 0.004 0.052 2295 Dihedral : 8.433 81.087 2532 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.21), residues: 1583 helix: -0.22 (0.38), residues: 159 sheet: 0.11 (0.23), residues: 498 loop : -0.88 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 703 HIS 0.003 0.001 HIS B 263 PHE 0.013 0.001 PHE B 538 TYR 0.010 0.001 TYR A 920 ARG 0.007 0.000 ARG A 312 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 15) link_NAG-ASN : angle 3.80439 ( 45) link_ALPHA1-6 : bond 0.00472 ( 1) link_ALPHA1-6 : angle 1.51611 ( 3) link_BETA1-2 : bond 0.00217 ( 1) link_BETA1-2 : angle 2.99865 ( 3) link_BETA1-4 : bond 0.00685 ( 21) link_BETA1-4 : angle 2.22807 ( 63) link_ALPHA1-3 : bond 0.00818 ( 2) link_ALPHA1-3 : angle 1.42583 ( 6) hydrogen bonds : bond 0.03182 ( 322) hydrogen bonds : angle 6.46417 ( 879) SS BOND : bond 0.00304 ( 37) SS BOND : angle 1.06614 ( 74) covalent geometry : bond 0.00253 (13051) covalent geometry : angle 0.66717 (17678) ********************** 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 70 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 LEU cc_start: 0.8475 (pp) cc_final: 0.7780 (pp) REVERT: A 228 ASP cc_start: 0.9468 (m-30) cc_final: 0.9220 (m-30) REVERT: A 446 TYR cc_start: 0.9214 (m-10) cc_final: 0.8783 (m-10) REVERT: A 546 MET cc_start: 0.9269 (mpp) cc_final: 0.8804 (mpp) REVERT: A 652 LEU cc_start: 0.9277 (tp) cc_final: 0.8229 (pp) REVERT: B 127 TYR cc_start: 0.9276 (t80) cc_final: 0.8920 (t80) REVERT: B 236 MET cc_start: 0.9463 (mmp) cc_final: 0.9252 (mmm) REVERT: B 256 PHE cc_start: 0.9656 (t80) cc_final: 0.9375 (t80) REVERT: B 315 PHE cc_start: 0.9525 (m-80) cc_final: 0.9263 (m-80) REVERT: B 334 LYS cc_start: 0.6578 (mmmt) cc_final: 0.4990 (ptpt) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.3891 time to fit residues: 40.0172 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 : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 113 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 668 HIS ** 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 816 GLN ** 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 = 0.3937 r_free = 0.3937 target = 0.069918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.053884 restraints weight = 160482.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.053799 restraints weight = 145348.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.054074 restraints weight = 132350.394| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 275 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 274 | |-----------------------------------------------------------------------------| r_final: 0.3453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.7966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13128 Z= 0.116 Angle : 0.696 12.050 17872 Z= 0.323 Chirality : 0.047 0.392 2037 Planarity : 0.004 0.052 2295 Dihedral : 8.447 86.990 2532 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.20), residues: 1583 helix: -0.06 (0.39), residues: 159 sheet: 0.12 (0.23), residues: 484 loop : -0.87 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 100 HIS 0.003 0.001 HIS B 263 PHE 0.015 0.001 PHE B 538 TYR 0.013 0.001 TYR B 528 ARG 0.008 0.000 ARG B 521 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 15) link_NAG-ASN : angle 3.52318 ( 45) link_ALPHA1-6 : bond 0.00348 ( 1) link_ALPHA1-6 : angle 1.67313 ( 3) link_BETA1-2 : bond 0.00100 ( 1) link_BETA1-2 : angle 2.97895 ( 3) link_BETA1-4 : bond 0.00644 ( 21) link_BETA1-4 : angle 2.21741 ( 63) link_ALPHA1-3 : bond 0.00758 ( 2) link_ALPHA1-3 : angle 1.43673 ( 6) hydrogen bonds : bond 0.03121 ( 322) hydrogen bonds : angle 6.31358 ( 879) SS BOND : bond 0.00188 ( 37) SS BOND : angle 1.08066 ( 74) covalent geometry : bond 0.00254 (13051) covalent geometry : angle 0.65819 (17678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5945.92 seconds wall clock time: 108 minutes 39.47 seconds (6519.47 seconds total)