Starting phenix.real_space_refine on Wed Mar 4 21:20:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l8t_23236/03_2026/7l8t_23236.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8t_23236/03_2026/7l8t_23236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l8t_23236/03_2026/7l8t_23236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8t_23236/03_2026/7l8t_23236.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l8t_23236/03_2026/7l8t_23236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8t_23236/03_2026/7l8t_23236.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 10171 2.51 5 N 2771 2.21 5 O 3290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16337 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3521 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 2 Chain: "B" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1198 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 2, 'TRANS': 149} Chain: "C" Number of atoms: 3516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3516 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 2 Chain: "D" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1147 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Chain: "E" Number of atoms: 3516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3516 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 2 Chain: "F" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1147 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Chain: "H" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 580 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'TRANS': 115} Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 116 Planarities with less than four sites: {'UNK:plan-1': 116} Unresolved non-hydrogen planarities: 116 Chain: "L" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 510 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'TRANS': 101} Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'UNK:plan-1': 102} Unresolved non-hydrogen planarities: 102 Chain: "G" 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} 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: "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: "M" 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: "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: 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: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" 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: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 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 Time building chain proxies: 3.44, per 1000 atoms: 0.21 Number of scatterers: 16337 At special positions: 0 Unit cell: (126.69, 135.96, 131.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 3290 8.00 N 2771 7.00 C 10171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.09 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.02 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.05 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS D 561 " distance=2.01 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.06 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.02 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.05 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.02 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.10 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " 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 ALPHA1-2 " MAN I 4 " - " MAN I 5 " ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA P 3 " - " MAN P 4 " " BMA S 3 " - " MAN S 4 " ALPHA1-6 " BMA I 3 " - " MAN I 6 " " BMA P 3 " - " MAN P 5 " " BMA S 3 " - " MAN S 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 241 " " NAG A 604 " - " ASN A 276 " " NAG A 605 " - " ASN A 392 " " NAG A 606 " - " ASN A 339 " " NAG A 607 " - " ASN A 295 " " NAG A 608 " - " ASN A 448 " " NAG A 609 " - " ASN A 301 " " NAG A 610 " - " ASN A 160 " " NAG A 611 " - " ASN A 197 " " NAG A 612 " - " ASN A 133 " " NAG A 613 " - " ASN A 355 " " NAG A 614 " - " ASN A 289 " " NAG A 615 " - " ASN A 137 " " NAG A 616 " - " ASN A 363 " " NAG B 701 " - " ASN B 618 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 241 " " NAG C 604 " - " ASN C 276 " " NAG C 605 " - " ASN C 386 " " NAG C 606 " - " ASN C 339 " " NAG C 607 " - " ASN C 295 " " NAG C 608 " - " ASN C 448 " " NAG C 609 " - " ASN C 301 " " NAG C 610 " - " ASN C 160 " " NAG C 611 " - " ASN C 197 " " NAG C 612 " - " ASN C 133 " " NAG C 613 " - " ASN C 355 " " NAG C 614 " - " ASN C 289 " " NAG C 615 " - " ASN C 363 " " NAG D 701 " - " ASN D 618 " " NAG D 702 " - " ASN D 637 " " NAG D 703 " - " ASN D 611 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 241 " " NAG E 604 " - " ASN E 276 " " NAG E 605 " - " ASN E 392 " " NAG E 606 " - " ASN E 339 " " NAG E 607 " - " ASN E 332 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 448 " " NAG E 610 " - " ASN E 301 " " NAG E 611 " - " ASN E 160 " " NAG E 612 " - " ASN E 197 " " NAG E 613 " - " ASN E 133 " " NAG E 614 " - " ASN E 355 " " NAG E 615 " - " ASN E 289 " " NAG E 616 " - " ASN E 363 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 611 " " NAG G 1 " - " ASN A 386 " " NAG I 1 " - " ASN A 262 " " NAG J 1 " - " ASN A 156 " " NAG K 1 " - " ASN A 332 " " NAG M 1 " - " ASN B 611 " " NAG N 1 " - " ASN C 392 " " NAG O 1 " - " ASN C 332 " " NAG P 1 " - " ASN C 262 " " NAG Q 1 " - " ASN C 156 " " NAG R 1 " - " ASN E 386 " " NAG S 1 " - " ASN E 262 " " NAG T 1 " - " ASN E 156 " Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 877.5 milliseconds 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3762 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 34 sheets defined 32.7% alpha, 35.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 57 through 61 removed outlier: 4.051A pdb=" N TYR A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 114 removed outlier: 3.871A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.521A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.356A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 537 Processing helix chain 'B' and resid 538 through 554 removed outlier: 3.831A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 557 No H-bonds generated for 'chain 'B' and resid 555 through 557' Processing helix chain 'B' and resid 558 through 566 Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 627 through 635 removed outlier: 4.702A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 663 Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.649A pdb=" N HIS C 72 " --> pdb=" O VAL C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.964A pdb=" N ASN C 98 " --> pdb=" O MET C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 116 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 480 removed outlier: 3.514A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 484 removed outlier: 5.060A pdb=" N TYR C 484 " --> pdb=" O SER C 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 481 through 484' Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.394A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.515A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 554 removed outlier: 3.841A pdb=" N LEU D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE D 548 " --> pdb=" O LEU D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 557 No H-bonds generated for 'chain 'D' and resid 555 through 557' Processing helix chain 'D' and resid 558 through 565 removed outlier: 4.022A pdb=" N GLN D 562 " --> pdb=" O ALA D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 596 Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'E' and resid 58 through 62 Processing helix chain 'E' and resid 67 through 72 Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.012A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 334 through 354 removed outlier: 3.520A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 460 through 463 removed outlier: 3.940A pdb=" N SER E 463 " --> pdb=" O SER E 460 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 460 through 463' Processing helix chain 'E' and resid 475 through 484 removed outlier: 4.093A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.197A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 554 removed outlier: 3.751A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILE F 548 " --> pdb=" O LEU F 544 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 566 removed outlier: 4.060A pdb=" N GLN F 562 " --> pdb=" O ALA F 558 " (cutoff:3.500A) Processing helix chain 'F' and resid 568 through 596 Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 661 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.319A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.426A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.553A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.558A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.500A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.558A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.500A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.425A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 393 through 395 removed outlier: 3.873A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.606A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.587A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AB5, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AB6, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.624A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.556A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.152A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.120A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.719A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.704A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.522A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.860A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.522A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.704A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.719A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.120A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.152A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.883A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.168A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC5, first strand: chain 'E' and resid 91 through 92 Processing sheet with id=AC6, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC7, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.422A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 393 through 395 removed outlier: 10.312A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 11.070A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.044A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.457A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.794A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.491A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.408A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 259 through 261 Processing sheet with id=AD1, first strand: chain 'E' and resid 271 through 273 Processing sheet with id=AD2, first strand: chain 'E' and resid 315 through 323A removed outlier: 6.559A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY E 321 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD4, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.899A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 7 through 9 removed outlier: 4.164A pdb=" N UNK L 23 " --> pdb=" O UNK L 9 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AD7, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.697A pdb=" N UNK L 36 " --> pdb=" O UNK L 48 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N UNK L 86 " --> pdb=" O UNK L 39 " (cutoff:3.500A) 655 hydrogen bonds defined for protein. 1731 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 3135 1.31 - 1.45: 5419 1.45 - 1.60: 7898 1.60 - 1.74: 34 1.74 - 1.88: 129 Bond restraints: 16615 Sorted by residual: bond pdb=" NE ARG E 503 " pdb=" CZ ARG E 503 " ideal model delta sigma weight residual 1.326 1.422 -0.096 1.10e-02 8.26e+03 7.56e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.380 0.117 1.40e-02 5.10e+03 6.93e+01 bond pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 1.497 1.397 0.100 1.40e-02 5.10e+03 5.07e+01 bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.398 -0.072 1.10e-02 8.26e+03 4.26e+01 bond pdb=" CB ILE A 396 " pdb=" CG1 ILE A 396 " ideal model delta sigma weight residual 1.530 1.657 -0.127 2.00e-02 2.50e+03 4.04e+01 ... (remaining 16610 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 21139 3.27 - 6.54: 1380 6.54 - 9.81: 75 9.81 - 13.09: 3 13.09 - 16.36: 1 Bond angle restraints: 22598 Sorted by residual: angle pdb=" N HIS A 66 " pdb=" CA HIS A 66 " pdb=" C HIS A 66 " ideal model delta sigma weight residual 108.63 92.27 16.36 1.60e+00 3.91e-01 1.05e+02 angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 129.13 -9.57 1.02e+00 9.61e-01 8.81e+01 angle pdb=" C GLU E 492 " pdb=" N PRO E 493 " pdb=" CA PRO E 493 " ideal model delta sigma weight residual 119.56 128.97 -9.41 1.02e+00 9.61e-01 8.51e+01 angle pdb=" N GLY A 458 " pdb=" CA GLY A 458 " pdb=" C GLY A 458 " ideal model delta sigma weight residual 111.95 103.91 8.04 9.50e-01 1.11e+00 7.16e+01 angle pdb=" C CYS A 205 " pdb=" N PRO A 206 " pdb=" CA PRO A 206 " ideal model delta sigma weight residual 119.56 127.89 -8.33 1.02e+00 9.61e-01 6.68e+01 ... (remaining 22593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.23: 10794 21.23 - 42.47: 260 42.47 - 63.70: 78 63.70 - 84.93: 25 84.93 - 106.17: 16 Dihedral angle restraints: 11173 sinusoidal: 5386 harmonic: 5787 Sorted by residual: dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -154.12 68.12 1 1.00e+01 1.00e-02 6.02e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 156.76 -63.76 1 1.00e+01 1.00e-02 5.35e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 155.66 -62.66 1 1.00e+01 1.00e-02 5.19e+01 ... (remaining 11170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1867 0.100 - 0.200: 603 0.200 - 0.300: 229 0.300 - 0.400: 115 0.400 - 0.500: 48 Chirality restraints: 2862 Sorted by residual: chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.55e+02 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.45e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.20e+02 ... (remaining 2859 not shown) Planarity restraints: 2850 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 603 " 0.340 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG A 603 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A 603 " 0.084 2.00e-02 2.50e+03 pdb=" N2 NAG A 603 " -0.522 2.00e-02 2.50e+03 pdb=" O7 NAG A 603 " 0.178 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " -0.328 2.00e-02 2.50e+03 2.80e-01 9.80e+02 pdb=" C7 NAG K 2 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " -0.174 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " 0.492 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 601 " 0.294 2.00e-02 2.50e+03 2.54e-01 8.05e+02 pdb=" C7 NAG A 601 " -0.067 2.00e-02 2.50e+03 pdb=" C8 NAG A 601 " 0.007 2.00e-02 2.50e+03 pdb=" N2 NAG A 601 " -0.436 2.00e-02 2.50e+03 pdb=" O7 NAG A 601 " 0.202 2.00e-02 2.50e+03 ... (remaining 2847 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4578 2.83 - 3.35: 14863 3.35 - 3.86: 25871 3.86 - 4.38: 30273 4.38 - 4.90: 49027 Nonbonded interactions: 124612 Sorted by model distance: nonbonded pdb=" O3 NAG A 615 " pdb=" O7 NAG A 615 " model vdw 2.311 3.040 nonbonded pdb=" O3 NAG K 2 " pdb=" O7 NAG K 2 " model vdw 2.316 3.040 nonbonded pdb=" N UNK H 96 " pdb=" O UNK H 96 " model vdw 2.385 2.496 nonbonded pdb=" N ILE E 213 " pdb=" O ILE E 213 " model vdw 2.391 2.496 nonbonded pdb=" N ILE A 213 " pdb=" O ILE A 213 " model vdw 2.407 2.496 ... (remaining 124607 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 'A' and resid 32 through 615) selection = chain 'C' selection = (chain 'E' and resid 32 through 615) } ncs_group { reference = (chain 'B' and resid 521 through 702) selection = (chain 'D' and (resid 521 through 663 or resid 702 through 703)) selection = (chain 'F' and (resid 521 through 663 or resid 701 through 702)) } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' } ncs_group { reference = (chain 'H' and resid 16 through 117) selection = chain 'L' } ncs_group { reference = chain 'P' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.220 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 : 0.023 0.127 16739 Z= 1.228 Angle : 1.734 16.357 22934 Z= 1.104 Chirality : 0.139 0.500 2862 Planarity : 0.014 0.294 2784 Dihedral : 11.186 106.168 7303 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.19), residues: 1752 helix: 0.04 (0.21), residues: 478 sheet: 0.95 (0.23), residues: 446 loop : 0.98 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 557 TYR 0.043 0.007 TYR C 40 PHE 0.035 0.006 PHE A 383 TRP 0.053 0.010 TRP F 623 HIS 0.012 0.003 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.02242 (16615) covalent geometry : angle 1.70483 (22598) SS BOND : bond 0.01849 ( 36) SS BOND : angle 3.23086 ( 72) hydrogen bonds : bond 0.17839 ( 641) hydrogen bonds : angle 7.23975 ( 1731) link_ALPHA1-2 : bond 0.08203 ( 1) link_ALPHA1-2 : angle 3.80235 ( 3) link_ALPHA1-3 : bond 0.07921 ( 3) link_ALPHA1-3 : angle 3.87447 ( 9) link_ALPHA1-6 : bond 0.05812 ( 3) link_ALPHA1-6 : angle 3.95308 ( 9) link_BETA1-4 : bond 0.06682 ( 15) link_BETA1-4 : angle 4.57127 ( 45) link_NAG-ASN : bond 0.07358 ( 66) link_NAG-ASN : angle 2.55920 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.9175 (m-80) cc_final: 0.8960 (m-10) REVERT: B 552 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8404 (mm110) REVERT: B 575 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8385 (mm110) REVERT: B 626 MET cc_start: 0.8932 (mmm) cc_final: 0.8643 (mmm) REVERT: B 638 TYR cc_start: 0.8869 (m-80) cc_final: 0.8389 (m-10) REVERT: C 99 ASN cc_start: 0.8873 (t0) cc_final: 0.8607 (t0) REVERT: C 102 GLU cc_start: 0.8457 (tp30) cc_final: 0.8086 (tp30) REVERT: C 199 SER cc_start: 0.9500 (p) cc_final: 0.9132 (t) REVERT: C 381 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7291 (mt-10) REVERT: D 536 THR cc_start: 0.8824 (p) cc_final: 0.8526 (p) REVERT: E 65 LYS cc_start: 0.8759 (mttt) cc_final: 0.8545 (UNCLASSIFIED) REVERT: E 91 GLU cc_start: 0.6740 (tp30) cc_final: 0.6400 (tt0) REVERT: E 150 MET cc_start: 0.8446 (mtp) cc_final: 0.8022 (mtt) REVERT: F 530 MET cc_start: 0.7984 (mtp) cc_final: 0.7557 (mtp) REVERT: F 542 ARG cc_start: 0.8334 (mtp180) cc_final: 0.7975 (ttp-170) REVERT: F 560 GLU cc_start: 0.8429 (pm20) cc_final: 0.8225 (pm20) REVERT: F 599 SER cc_start: 0.9214 (t) cc_final: 0.9005 (p) REVERT: F 647 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7184 (mt-10) outliers start: 0 outliers final: 0 residues processed: 428 average time/residue: 0.1360 time to fit residues: 84.1799 Evaluate side-chains 217 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 562 GLN C 85 HIS C 188 ASN C 203 GLN C 280 ASN C 352 HIS C 478 ASN D 543 ASN D 550 GLN D 551 GLN D 562 GLN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN E 249 HIS E 462 ASN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.120803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.101205 restraints weight = 27963.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.103962 restraints weight = 17308.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.105807 restraints weight = 12571.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.107078 restraints weight = 10175.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.107926 restraints weight = 8732.397| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16739 Z= 0.187 Angle : 0.817 15.457 22934 Z= 0.397 Chirality : 0.049 0.284 2862 Planarity : 0.004 0.030 2784 Dihedral : 8.492 80.939 3931 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.73 % Allowed : 8.76 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.20), residues: 1752 helix: 1.19 (0.24), residues: 487 sheet: 0.92 (0.24), residues: 417 loop : 0.56 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 542 TYR 0.037 0.002 TYR E 61 PHE 0.032 0.002 PHE E 53 TRP 0.020 0.002 TRP D 623 HIS 0.012 0.002 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00410 (16615) covalent geometry : angle 0.74472 (22598) SS BOND : bond 0.00396 ( 36) SS BOND : angle 1.75176 ( 72) hydrogen bonds : bond 0.06433 ( 641) hydrogen bonds : angle 5.56826 ( 1731) link_ALPHA1-2 : bond 0.00572 ( 1) link_ALPHA1-2 : angle 1.74122 ( 3) link_ALPHA1-3 : bond 0.01237 ( 3) link_ALPHA1-3 : angle 2.22141 ( 9) link_ALPHA1-6 : bond 0.00772 ( 3) link_ALPHA1-6 : angle 1.59139 ( 9) link_BETA1-4 : bond 0.00650 ( 15) link_BETA1-4 : angle 2.52061 ( 45) link_NAG-ASN : bond 0.00429 ( 66) link_NAG-ASN : angle 3.33063 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 273 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7528 (mm-30) REVERT: B 552 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8409 (mm-40) REVERT: B 575 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8071 (mm-40) REVERT: B 659 ASP cc_start: 0.7907 (m-30) cc_final: 0.7669 (m-30) REVERT: C 49 GLU cc_start: 0.7419 (tt0) cc_final: 0.7069 (tt0) REVERT: C 72 HIS cc_start: 0.7721 (m-70) cc_final: 0.7353 (m90) REVERT: C 102 GLU cc_start: 0.7948 (tp30) cc_final: 0.7656 (tp30) REVERT: C 199 SER cc_start: 0.9350 (p) cc_final: 0.8878 (t) REVERT: C 381 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6853 (mt-10) REVERT: D 542 ARG cc_start: 0.8094 (mtp85) cc_final: 0.7762 (tpp80) REVERT: E 91 GLU cc_start: 0.6671 (tp30) cc_final: 0.6311 (tp30) REVERT: E 111 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8622 (mp) REVERT: E 150 MET cc_start: 0.7954 (mtp) cc_final: 0.7706 (mtt) REVERT: F 530 MET cc_start: 0.7873 (mtp) cc_final: 0.7665 (mtp) REVERT: F 545 LEU cc_start: 0.8753 (mt) cc_final: 0.8220 (mt) REVERT: F 599 SER cc_start: 0.9243 (t) cc_final: 0.9040 (p) REVERT: F 616 ASN cc_start: 0.7246 (t0) cc_final: 0.7011 (p0) REVERT: F 622 ILE cc_start: 0.8287 (mt) cc_final: 0.7941 (mt) REVERT: F 633 LYS cc_start: 0.8643 (mmtm) cc_final: 0.8440 (mmtm) REVERT: F 647 GLU cc_start: 0.7759 (mt-10) cc_final: 0.6963 (mt-10) outliers start: 43 outliers final: 27 residues processed: 303 average time/residue: 0.1335 time to fit residues: 59.3153 Evaluate side-chains 232 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 462 ASN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 602 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS E 85 HIS ** E 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 GLN ** F 552 GLN ** 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 = 0.3450 r_free = 0.3450 target = 0.118947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.099292 restraints weight = 28075.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.102000 restraints weight = 17391.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.103823 restraints weight = 12705.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.104926 restraints weight = 10295.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.105815 restraints weight = 8971.719| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 16739 Z= 0.213 Angle : 0.731 11.578 22934 Z= 0.357 Chirality : 0.047 0.277 2862 Planarity : 0.004 0.032 2784 Dihedral : 7.836 74.320 3931 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.24 % Allowed : 11.61 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.20), residues: 1752 helix: 1.33 (0.25), residues: 480 sheet: 0.68 (0.22), residues: 467 loop : 0.40 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 617 TYR 0.030 0.002 TYR E 61 PHE 0.024 0.002 PHE E 53 TRP 0.018 0.002 TRP E 35 HIS 0.010 0.002 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00493 (16615) covalent geometry : angle 0.67633 (22598) SS BOND : bond 0.00486 ( 36) SS BOND : angle 1.70858 ( 72) hydrogen bonds : bond 0.05516 ( 641) hydrogen bonds : angle 5.19449 ( 1731) link_ALPHA1-2 : bond 0.00889 ( 1) link_ALPHA1-2 : angle 1.48365 ( 3) link_ALPHA1-3 : bond 0.01233 ( 3) link_ALPHA1-3 : angle 1.62203 ( 9) link_ALPHA1-6 : bond 0.00972 ( 3) link_ALPHA1-6 : angle 1.30462 ( 9) link_BETA1-4 : bond 0.00523 ( 15) link_BETA1-4 : angle 2.03759 ( 45) link_NAG-ASN : bond 0.00587 ( 66) link_NAG-ASN : angle 2.72274 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 225 time to evaluate : 0.532 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 87 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7860 (pm20) REVERT: A 268 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7497 (mm-30) REVERT: B 552 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8292 (mm110) REVERT: B 575 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8178 (mm-40) REVERT: B 659 ASP cc_start: 0.7897 (m-30) cc_final: 0.7569 (m-30) REVERT: C 99 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8173 (t0) REVERT: C 199 SER cc_start: 0.9352 (p) cc_final: 0.8877 (t) REVERT: C 381 GLU cc_start: 0.7279 (mt-10) cc_final: 0.6963 (mt-10) REVERT: D 551 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.6830 (mp-120) REVERT: D 617 ARG cc_start: 0.8050 (mtt90) cc_final: 0.7823 (ttm170) REVERT: E 91 GLU cc_start: 0.6772 (tp30) cc_final: 0.6370 (tp30) REVERT: E 96 TRP cc_start: 0.8681 (m100) cc_final: 0.8200 (m100) REVERT: E 150 MET cc_start: 0.7967 (mtp) cc_final: 0.7749 (mtt) REVERT: F 530 MET cc_start: 0.7972 (mtp) cc_final: 0.7732 (mtp) REVERT: F 545 LEU cc_start: 0.8707 (mt) cc_final: 0.8220 (mt) REVERT: F 616 ASN cc_start: 0.7193 (t0) cc_final: 0.6845 (p0) REVERT: F 622 ILE cc_start: 0.8239 (mt) cc_final: 0.7794 (mp) REVERT: F 647 GLU cc_start: 0.7765 (mt-10) cc_final: 0.6769 (mt-10) outliers start: 51 outliers final: 38 residues processed: 265 average time/residue: 0.1265 time to fit residues: 49.4299 Evaluate side-chains 244 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 203 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 656 ASN Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 551 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 602 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 154 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 187 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 562 GLN ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.115315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.095596 restraints weight = 28375.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.098174 restraints weight = 17892.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.099895 restraints weight = 13263.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.101041 restraints weight = 10853.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.101815 restraints weight = 9473.312| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 16739 Z= 0.251 Angle : 0.750 11.560 22934 Z= 0.365 Chirality : 0.048 0.268 2862 Planarity : 0.004 0.034 2784 Dihedral : 7.643 66.172 3931 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.06 % Allowed : 11.80 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.20), residues: 1752 helix: 1.53 (0.25), residues: 449 sheet: 0.59 (0.23), residues: 436 loop : 0.08 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 557 TYR 0.025 0.002 TYR E 61 PHE 0.021 0.003 PHE E 53 TRP 0.016 0.002 TRP E 35 HIS 0.009 0.002 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00593 (16615) covalent geometry : angle 0.70387 (22598) SS BOND : bond 0.00494 ( 36) SS BOND : angle 1.64669 ( 72) hydrogen bonds : bond 0.05364 ( 641) hydrogen bonds : angle 5.13232 ( 1731) link_ALPHA1-2 : bond 0.00714 ( 1) link_ALPHA1-2 : angle 1.41266 ( 3) link_ALPHA1-3 : bond 0.01162 ( 3) link_ALPHA1-3 : angle 2.05718 ( 9) link_ALPHA1-6 : bond 0.00830 ( 3) link_ALPHA1-6 : angle 1.32449 ( 9) link_BETA1-4 : bond 0.00406 ( 15) link_BETA1-4 : angle 1.75769 ( 45) link_NAG-ASN : bond 0.00467 ( 66) link_NAG-ASN : angle 2.57761 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 209 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9185 (m100) cc_final: 0.8296 (m100) REVERT: A 59 LYS cc_start: 0.8176 (tppt) cc_final: 0.7744 (tmtt) REVERT: A 87 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7725 (pp20) REVERT: A 161 MET cc_start: 0.8053 (tpp) cc_final: 0.7851 (tpp) REVERT: A 268 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7495 (mm-30) REVERT: B 552 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8373 (mm110) REVERT: B 553 SER cc_start: 0.8709 (m) cc_final: 0.8438 (t) REVERT: B 575 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8285 (mm-40) REVERT: C 99 ASN cc_start: 0.7852 (OUTLIER) cc_final: 0.7224 (t0) REVERT: C 199 SER cc_start: 0.9376 (p) cc_final: 0.8757 (t) REVERT: C 381 GLU cc_start: 0.7285 (mt-10) cc_final: 0.7071 (mt-10) REVERT: D 542 ARG cc_start: 0.7907 (tpp80) cc_final: 0.7675 (tpp80) REVERT: D 551 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.6854 (mp-120) REVERT: D 617 ARG cc_start: 0.8018 (mtt90) cc_final: 0.6658 (ttm-80) REVERT: E 96 TRP cc_start: 0.8651 (m100) cc_final: 0.8149 (m100) REVERT: E 111 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8811 (mp) REVERT: E 150 MET cc_start: 0.7990 (mtp) cc_final: 0.7758 (mtt) REVERT: F 530 MET cc_start: 0.8066 (mtp) cc_final: 0.7768 (mtp) REVERT: F 545 LEU cc_start: 0.8743 (mt) cc_final: 0.8252 (mt) REVERT: F 551 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7812 (pt0) REVERT: F 616 ASN cc_start: 0.7220 (t0) cc_final: 0.6878 (p0) REVERT: F 622 ILE cc_start: 0.8337 (mt) cc_final: 0.8027 (mp) REVERT: F 647 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6972 (mt-10) outliers start: 64 outliers final: 45 residues processed: 256 average time/residue: 0.1262 time to fit residues: 48.1289 Evaluate side-chains 246 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 196 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 551 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 551 GLN Chi-restraints excluded: chain F residue 602 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 83 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 174 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 146 optimal weight: 0.0570 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 562 GLN ** D 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.117645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.098226 restraints weight = 27860.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.100830 restraints weight = 17438.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.102584 restraints weight = 12849.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.103620 restraints weight = 10467.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.104508 restraints weight = 9168.761| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 16739 Z= 0.161 Angle : 0.653 10.145 22934 Z= 0.317 Chirality : 0.045 0.248 2862 Planarity : 0.003 0.036 2784 Dihedral : 7.150 60.774 3931 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.55 % Allowed : 12.63 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.20), residues: 1752 helix: 1.72 (0.25), residues: 454 sheet: 0.64 (0.24), residues: 431 loop : -0.02 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 617 TYR 0.023 0.001 TYR E 61 PHE 0.019 0.002 PHE E 53 TRP 0.010 0.001 TRP F 631 HIS 0.008 0.001 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00372 (16615) covalent geometry : angle 0.60848 (22598) SS BOND : bond 0.00380 ( 36) SS BOND : angle 1.33776 ( 72) hydrogen bonds : bond 0.04760 ( 641) hydrogen bonds : angle 4.91118 ( 1731) link_ALPHA1-2 : bond 0.00747 ( 1) link_ALPHA1-2 : angle 1.37823 ( 3) link_ALPHA1-3 : bond 0.01274 ( 3) link_ALPHA1-3 : angle 1.66067 ( 9) link_ALPHA1-6 : bond 0.00780 ( 3) link_ALPHA1-6 : angle 1.45043 ( 9) link_BETA1-4 : bond 0.00407 ( 15) link_BETA1-4 : angle 1.57902 ( 45) link_NAG-ASN : bond 0.00395 ( 66) link_NAG-ASN : angle 2.37013 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 222 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9147 (m100) cc_final: 0.8306 (m100) REVERT: A 87 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7886 (pm20) REVERT: A 268 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7521 (mm-30) REVERT: B 552 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8341 (mm110) REVERT: B 553 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8409 (t) REVERT: B 575 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8270 (mm-40) REVERT: C 199 SER cc_start: 0.9390 (p) cc_final: 0.8770 (t) REVERT: C 236 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8466 (p) REVERT: C 381 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6978 (mt-10) REVERT: D 542 ARG cc_start: 0.7951 (tpp80) cc_final: 0.7659 (tpp80) REVERT: D 551 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.6868 (mp-120) REVERT: E 91 GLU cc_start: 0.6651 (tp30) cc_final: 0.6069 (tp30) REVERT: E 96 TRP cc_start: 0.8618 (m100) cc_final: 0.8263 (m100) REVERT: E 111 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8790 (mp) REVERT: E 376 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7645 (t80) REVERT: F 530 MET cc_start: 0.8044 (mtp) cc_final: 0.7768 (mtp) REVERT: F 545 LEU cc_start: 0.8777 (mt) cc_final: 0.8281 (mt) REVERT: F 616 ASN cc_start: 0.7242 (t0) cc_final: 0.6917 (p0) REVERT: F 622 ILE cc_start: 0.8323 (mt) cc_final: 0.8040 (mp) REVERT: F 633 LYS cc_start: 0.8730 (mmtm) cc_final: 0.8470 (mmtm) REVERT: F 647 GLU cc_start: 0.7458 (mt-10) cc_final: 0.6627 (mt-10) outliers start: 56 outliers final: 41 residues processed: 263 average time/residue: 0.1271 time to fit residues: 49.7887 Evaluate side-chains 251 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 204 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 551 GLN Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 556 LEU Chi-restraints excluded: chain F residue 602 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 75 optimal weight: 1.9990 chunk 8 optimal weight: 0.0770 chunk 166 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 181 optimal weight: 9.9990 overall best weight: 1.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 562 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 562 GLN E 72 HIS E 246 GLN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.097483 restraints weight = 28001.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.100183 restraints weight = 17173.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.101999 restraints weight = 12520.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.103229 restraints weight = 10120.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.104011 restraints weight = 8749.606| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 16739 Z= 0.172 Angle : 0.650 9.738 22934 Z= 0.317 Chirality : 0.045 0.249 2862 Planarity : 0.004 0.052 2784 Dihedral : 6.919 55.731 3931 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.19 % Allowed : 13.07 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.20), residues: 1752 helix: 1.62 (0.25), residues: 466 sheet: 0.55 (0.24), residues: 424 loop : -0.10 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 557 TYR 0.022 0.001 TYR E 61 PHE 0.018 0.002 PHE E 53 TRP 0.011 0.001 TRP F 631 HIS 0.009 0.002 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00402 (16615) covalent geometry : angle 0.60925 (22598) SS BOND : bond 0.00469 ( 36) SS BOND : angle 1.53061 ( 72) hydrogen bonds : bond 0.04572 ( 641) hydrogen bonds : angle 4.83887 ( 1731) link_ALPHA1-2 : bond 0.00679 ( 1) link_ALPHA1-2 : angle 1.39462 ( 3) link_ALPHA1-3 : bond 0.01234 ( 3) link_ALPHA1-3 : angle 1.64495 ( 9) link_ALPHA1-6 : bond 0.00776 ( 3) link_ALPHA1-6 : angle 1.47720 ( 9) link_BETA1-4 : bond 0.00384 ( 15) link_BETA1-4 : angle 1.52069 ( 45) link_NAG-ASN : bond 0.00406 ( 66) link_NAG-ASN : angle 2.23523 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 207 time to evaluate : 0.584 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 35 TRP cc_start: 0.9209 (m100) cc_final: 0.8360 (m100) REVERT: A 59 LYS cc_start: 0.8196 (tppt) cc_final: 0.7772 (tptm) REVERT: A 87 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7919 (pm20) REVERT: A 268 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7478 (mm-30) REVERT: B 548 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8760 (mt) REVERT: B 552 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8325 (mm110) REVERT: B 553 SER cc_start: 0.8641 (m) cc_final: 0.8380 (t) REVERT: B 575 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8278 (mm-40) REVERT: B 584 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8172 (mp0) REVERT: C 199 SER cc_start: 0.9384 (p) cc_final: 0.8781 (t) REVERT: C 236 THR cc_start: 0.8847 (OUTLIER) cc_final: 0.8496 (p) REVERT: D 551 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.6847 (mp-120) REVERT: D 648 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7586 (mm-30) REVERT: E 91 GLU cc_start: 0.6697 (tp30) cc_final: 0.6063 (tp30) REVERT: E 96 TRP cc_start: 0.8531 (m100) cc_final: 0.8250 (m100) REVERT: E 111 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8798 (mp) REVERT: E 376 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.7733 (t80) REVERT: F 530 MET cc_start: 0.8082 (mtp) cc_final: 0.7822 (mtp) REVERT: F 545 LEU cc_start: 0.8713 (mt) cc_final: 0.8275 (mt) REVERT: F 551 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7651 (pt0) REVERT: F 616 ASN cc_start: 0.7240 (t0) cc_final: 0.6947 (p0) REVERT: F 622 ILE cc_start: 0.8331 (mt) cc_final: 0.8089 (mp) REVERT: F 633 LYS cc_start: 0.8713 (mmtm) cc_final: 0.8347 (mmtm) REVERT: F 647 GLU cc_start: 0.7482 (mt-10) cc_final: 0.6993 (mt-10) outliers start: 66 outliers final: 49 residues processed: 254 average time/residue: 0.1225 time to fit residues: 46.6617 Evaluate side-chains 260 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 352 HIS Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 551 GLN Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 551 GLN Chi-restraints excluded: chain F residue 556 LEU Chi-restraints excluded: chain F residue 602 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 102 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 184 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 175 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 188 optimal weight: 10.0000 chunk 164 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 562 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS E 246 GLN ** F 552 GLN ** 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 = 0.3396 r_free = 0.3396 target = 0.115073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.095483 restraints weight = 28240.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.098043 restraints weight = 17866.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.099748 restraints weight = 13271.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.100899 restraints weight = 10884.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.101573 restraints weight = 9507.281| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 16739 Z= 0.229 Angle : 0.698 11.207 22934 Z= 0.339 Chirality : 0.047 0.252 2862 Planarity : 0.004 0.046 2784 Dihedral : 7.086 55.707 3931 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.25 % Allowed : 13.45 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.20), residues: 1752 helix: 1.63 (0.25), residues: 458 sheet: 0.46 (0.24), residues: 424 loop : -0.17 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 579 TYR 0.022 0.002 TYR E 61 PHE 0.017 0.002 PHE E 53 TRP 0.012 0.001 TRP F 631 HIS 0.009 0.002 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00544 (16615) covalent geometry : angle 0.66035 (22598) SS BOND : bond 0.00466 ( 36) SS BOND : angle 1.50940 ( 72) hydrogen bonds : bond 0.04859 ( 641) hydrogen bonds : angle 4.97137 ( 1731) link_ALPHA1-2 : bond 0.00707 ( 1) link_ALPHA1-2 : angle 1.44460 ( 3) link_ALPHA1-3 : bond 0.01204 ( 3) link_ALPHA1-3 : angle 1.67275 ( 9) link_ALPHA1-6 : bond 0.00767 ( 3) link_ALPHA1-6 : angle 1.43411 ( 9) link_BETA1-4 : bond 0.00354 ( 15) link_BETA1-4 : angle 1.52692 ( 45) link_NAG-ASN : bond 0.00485 ( 66) link_NAG-ASN : angle 2.24506 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 202 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9226 (m100) cc_final: 0.8371 (m100) REVERT: A 87 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7970 (pm20) REVERT: A 268 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7489 (mm-30) REVERT: B 548 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8871 (mt) REVERT: B 553 SER cc_start: 0.8649 (m) cc_final: 0.8392 (t) REVERT: B 575 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8336 (mm-40) REVERT: C 199 SER cc_start: 0.9400 (p) cc_final: 0.8815 (t) REVERT: C 236 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8470 (p) REVERT: D 551 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.6857 (mp-120) REVERT: D 648 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7662 (mm-30) REVERT: E 91 GLU cc_start: 0.6725 (tp30) cc_final: 0.6112 (tp30) REVERT: E 96 TRP cc_start: 0.8543 (m100) cc_final: 0.8248 (m100) REVERT: E 111 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8718 (mp) REVERT: E 376 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.7818 (t80) REVERT: F 530 MET cc_start: 0.8133 (mtp) cc_final: 0.7841 (mtp) REVERT: F 545 LEU cc_start: 0.8758 (mt) cc_final: 0.8291 (mt) REVERT: F 616 ASN cc_start: 0.7254 (t0) cc_final: 0.7019 (p0) REVERT: F 622 ILE cc_start: 0.8346 (mt) cc_final: 0.8048 (mp) outliers start: 67 outliers final: 52 residues processed: 251 average time/residue: 0.1286 time to fit residues: 48.0851 Evaluate side-chains 253 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 195 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 551 GLN Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 602 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 24 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 chunk 164 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 185 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 562 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.115043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.095476 restraints weight = 28325.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.098027 restraints weight = 17947.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.099736 restraints weight = 13328.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.100868 restraints weight = 10921.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.101653 restraints weight = 9553.562| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 16739 Z= 0.213 Angle : 0.688 11.104 22934 Z= 0.334 Chirality : 0.046 0.252 2862 Planarity : 0.004 0.041 2784 Dihedral : 7.119 55.827 3931 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.37 % Favored : 96.58 % Rotamer: Outliers : 4.12 % Allowed : 14.09 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.20), residues: 1752 helix: 1.65 (0.25), residues: 458 sheet: 0.36 (0.24), residues: 424 loop : -0.28 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 579 TYR 0.022 0.001 TYR E 61 PHE 0.016 0.002 PHE E 53 TRP 0.012 0.001 TRP F 631 HIS 0.006 0.002 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00507 (16615) covalent geometry : angle 0.64718 (22598) SS BOND : bond 0.00474 ( 36) SS BOND : angle 1.90341 ( 72) hydrogen bonds : bond 0.04811 ( 641) hydrogen bonds : angle 4.96554 ( 1731) link_ALPHA1-2 : bond 0.00733 ( 1) link_ALPHA1-2 : angle 1.42558 ( 3) link_ALPHA1-3 : bond 0.01226 ( 3) link_ALPHA1-3 : angle 1.61954 ( 9) link_ALPHA1-6 : bond 0.00762 ( 3) link_ALPHA1-6 : angle 1.43906 ( 9) link_BETA1-4 : bond 0.00350 ( 15) link_BETA1-4 : angle 1.50077 ( 45) link_NAG-ASN : bond 0.00428 ( 66) link_NAG-ASN : angle 2.21650 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 201 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9223 (m100) cc_final: 0.8365 (m100) REVERT: A 59 LYS cc_start: 0.8367 (tppt) cc_final: 0.7677 (tmtt) REVERT: A 87 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: B 548 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8873 (mt) REVERT: B 553 SER cc_start: 0.8661 (OUTLIER) cc_final: 0.8392 (t) REVERT: B 584 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8251 (mp0) REVERT: C 199 SER cc_start: 0.9401 (p) cc_final: 0.8838 (t) REVERT: C 236 THR cc_start: 0.8878 (OUTLIER) cc_final: 0.8514 (p) REVERT: D 551 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.6826 (mp-120) REVERT: D 648 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7630 (mm-30) REVERT: E 91 GLU cc_start: 0.6725 (tp30) cc_final: 0.6113 (tp30) REVERT: E 96 TRP cc_start: 0.8527 (m100) cc_final: 0.8272 (m100) REVERT: E 111 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8728 (mp) REVERT: E 376 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.7840 (t80) REVERT: F 530 MET cc_start: 0.8119 (mtp) cc_final: 0.7832 (mtp) REVERT: F 545 LEU cc_start: 0.8772 (mt) cc_final: 0.8254 (mt) REVERT: F 622 ILE cc_start: 0.8356 (mt) cc_final: 0.8063 (mp) REVERT: F 633 LYS cc_start: 0.8604 (mmtm) cc_final: 0.8325 (mmtm) outliers start: 65 outliers final: 55 residues processed: 246 average time/residue: 0.1340 time to fit residues: 48.6411 Evaluate side-chains 255 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 193 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 352 HIS Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 551 GLN Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 556 LEU Chi-restraints excluded: chain F residue 602 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 16 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 183 optimal weight: 10.0000 chunk 154 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN B 552 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS E 85 HIS ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.116890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.097345 restraints weight = 28119.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.099949 restraints weight = 17615.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.101689 restraints weight = 13007.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.102872 restraints weight = 10613.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.103570 restraints weight = 9229.102| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 16739 Z= 0.141 Angle : 0.630 10.787 22934 Z= 0.307 Chirality : 0.044 0.251 2862 Planarity : 0.003 0.036 2784 Dihedral : 6.769 55.702 3931 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.20 % Favored : 96.75 % Rotamer: Outliers : 3.43 % Allowed : 15.23 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.52 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.20), residues: 1752 helix: 1.78 (0.26), residues: 460 sheet: 0.47 (0.24), residues: 431 loop : -0.24 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 579 TYR 0.021 0.001 TYR E 61 PHE 0.017 0.002 PHE E 53 TRP 0.011 0.001 TRP E 338 HIS 0.006 0.001 HIS B 564 Details of bonding type rmsd covalent geometry : bond 0.00325 (16615) covalent geometry : angle 0.58996 (22598) SS BOND : bond 0.00494 ( 36) SS BOND : angle 1.61216 ( 72) hydrogen bonds : bond 0.04345 ( 641) hydrogen bonds : angle 4.79047 ( 1731) link_ALPHA1-2 : bond 0.00710 ( 1) link_ALPHA1-2 : angle 1.36317 ( 3) link_ALPHA1-3 : bond 0.01231 ( 3) link_ALPHA1-3 : angle 1.40959 ( 9) link_ALPHA1-6 : bond 0.00766 ( 3) link_ALPHA1-6 : angle 1.50097 ( 9) link_BETA1-4 : bond 0.00364 ( 15) link_BETA1-4 : angle 1.44350 ( 45) link_NAG-ASN : bond 0.00374 ( 66) link_NAG-ASN : angle 2.13275 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 208 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9229 (m100) cc_final: 0.8420 (m100) REVERT: A 59 LYS cc_start: 0.8315 (tppt) cc_final: 0.7714 (tmtt) REVERT: A 87 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8011 (pm20) REVERT: A 425 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8298 (t0) REVERT: A 475 MET cc_start: 0.8186 (mmm) cc_final: 0.7741 (mmm) REVERT: B 575 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8349 (mm-40) REVERT: B 617 ARG cc_start: 0.8075 (mtt-85) cc_final: 0.7677 (mtp85) REVERT: B 656 ASN cc_start: 0.8461 (m110) cc_final: 0.8236 (m-40) REVERT: C 99 ASN cc_start: 0.7948 (t0) cc_final: 0.7728 (t0) REVERT: C 199 SER cc_start: 0.9412 (p) cc_final: 0.8860 (t) REVERT: C 236 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8498 (p) REVERT: D 551 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.6730 (mp-120) REVERT: D 648 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7665 (mm-30) REVERT: E 91 GLU cc_start: 0.6695 (tp30) cc_final: 0.6094 (tp30) REVERT: E 96 TRP cc_start: 0.8500 (m100) cc_final: 0.8222 (m100) REVERT: E 111 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8675 (mp) REVERT: E 376 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7710 (t80) REVERT: F 530 MET cc_start: 0.8134 (mtp) cc_final: 0.7861 (mtp) REVERT: F 545 LEU cc_start: 0.8754 (mt) cc_final: 0.8286 (mt) REVERT: F 622 ILE cc_start: 0.8308 (mt) cc_final: 0.8077 (mt) REVERT: F 633 LYS cc_start: 0.8629 (mmtm) cc_final: 0.8373 (mmtm) outliers start: 54 outliers final: 45 residues processed: 240 average time/residue: 0.1262 time to fit residues: 45.2849 Evaluate side-chains 250 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 199 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 352 HIS Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 551 GLN Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 556 LEU Chi-restraints excluded: chain F residue 602 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 140 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 550 GLN E 72 HIS E 85 HIS ** F 552 GLN ** 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 = 0.3440 r_free = 0.3440 target = 0.118451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.098466 restraints weight = 28086.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.101208 restraints weight = 17271.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.103048 restraints weight = 12613.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.104292 restraints weight = 10215.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.105071 restraints weight = 8819.579| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16739 Z= 0.132 Angle : 0.623 10.653 22934 Z= 0.306 Chirality : 0.044 0.250 2862 Planarity : 0.003 0.034 2784 Dihedral : 6.552 55.271 3931 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.08 % Favored : 96.86 % Rotamer: Outliers : 3.55 % Allowed : 15.42 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.20), residues: 1752 helix: 1.75 (0.26), residues: 467 sheet: 0.44 (0.24), residues: 433 loop : -0.26 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 557 TYR 0.020 0.001 TYR E 61 PHE 0.021 0.002 PHE F 522 TRP 0.012 0.001 TRP F 614 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00303 (16615) covalent geometry : angle 0.58490 (22598) SS BOND : bond 0.00405 ( 36) SS BOND : angle 1.50266 ( 72) hydrogen bonds : bond 0.04126 ( 641) hydrogen bonds : angle 4.70223 ( 1731) link_ALPHA1-2 : bond 0.00661 ( 1) link_ALPHA1-2 : angle 1.38897 ( 3) link_ALPHA1-3 : bond 0.01205 ( 3) link_ALPHA1-3 : angle 1.33722 ( 9) link_ALPHA1-6 : bond 0.00759 ( 3) link_ALPHA1-6 : angle 1.53492 ( 9) link_BETA1-4 : bond 0.00376 ( 15) link_BETA1-4 : angle 1.43648 ( 45) link_NAG-ASN : bond 0.00399 ( 66) link_NAG-ASN : angle 2.08828 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 206 time to evaluate : 0.583 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 35 TRP cc_start: 0.9230 (m100) cc_final: 0.8449 (m100) REVERT: A 59 LYS cc_start: 0.8272 (tppt) cc_final: 0.7665 (tmtt) REVERT: A 87 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8028 (pm20) REVERT: A 475 MET cc_start: 0.8134 (mmm) cc_final: 0.7699 (mmm) REVERT: B 575 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8313 (mm-40) REVERT: B 626 MET cc_start: 0.8095 (mmm) cc_final: 0.7863 (mtt) REVERT: B 656 ASN cc_start: 0.8436 (m110) cc_final: 0.8221 (m-40) REVERT: C 99 ASN cc_start: 0.7896 (t0) cc_final: 0.7678 (t0) REVERT: C 199 SER cc_start: 0.9398 (p) cc_final: 0.8840 (t) REVERT: C 236 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8519 (p) REVERT: C 492 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7609 (mt-10) REVERT: D 551 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.6837 (mp-120) REVERT: D 648 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7585 (mm-30) REVERT: E 91 GLU cc_start: 0.6678 (tp30) cc_final: 0.6079 (tp30) REVERT: E 96 TRP cc_start: 0.8425 (m100) cc_final: 0.8175 (m100) REVERT: E 111 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8673 (mp) REVERT: E 376 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7649 (t80) REVERT: F 530 MET cc_start: 0.8120 (mtp) cc_final: 0.7845 (mtp) REVERT: F 545 LEU cc_start: 0.8707 (mt) cc_final: 0.8235 (mt) REVERT: F 622 ILE cc_start: 0.8328 (mt) cc_final: 0.8118 (mt) REVERT: F 633 LYS cc_start: 0.8659 (mmtm) cc_final: 0.8373 (mmtm) outliers start: 56 outliers final: 44 residues processed: 238 average time/residue: 0.1329 time to fit residues: 47.2353 Evaluate side-chains 250 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 553 SER Chi-restraints excluded: chain B residue 561 CYS Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 352 HIS Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 551 GLN Chi-restraints excluded: chain D residue 564 HIS Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 268 GLU Chi-restraints excluded: chain E residue 272 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 376 PHE Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 529 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 556 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 602 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 49 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 192 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 182 optimal weight: 20.0000 chunk 115 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 550 GLN E 72 HIS E 85 HIS ** F 552 GLN ** 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 = 0.3399 r_free = 0.3399 target = 0.115558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.096010 restraints weight = 28347.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.098540 restraints weight = 18029.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.100223 restraints weight = 13417.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.101356 restraints weight = 11014.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.102143 restraints weight = 9620.848| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 16739 Z= 0.233 Angle : 0.712 11.646 22934 Z= 0.346 Chirality : 0.047 0.253 2862 Planarity : 0.004 0.037 2784 Dihedral : 6.958 55.328 3931 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.60 % Favored : 96.35 % Rotamer: Outliers : 3.49 % Allowed : 15.61 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.20), residues: 1752 helix: 1.66 (0.25), residues: 462 sheet: 0.26 (0.24), residues: 427 loop : -0.36 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 557 TYR 0.020 0.002 TYR E 61 PHE 0.018 0.002 PHE F 522 TRP 0.015 0.001 TRP F 614 HIS 0.007 0.002 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00555 (16615) covalent geometry : angle 0.67711 (22598) SS BOND : bond 0.00461 ( 36) SS BOND : angle 1.64459 ( 72) hydrogen bonds : bond 0.04739 ( 641) hydrogen bonds : angle 4.90017 ( 1731) link_ALPHA1-2 : bond 0.00661 ( 1) link_ALPHA1-2 : angle 1.53961 ( 3) link_ALPHA1-3 : bond 0.01159 ( 3) link_ALPHA1-3 : angle 1.54903 ( 9) link_ALPHA1-6 : bond 0.00745 ( 3) link_ALPHA1-6 : angle 1.44554 ( 9) link_BETA1-4 : bond 0.00334 ( 15) link_BETA1-4 : angle 1.49242 ( 45) link_NAG-ASN : bond 0.00470 ( 66) link_NAG-ASN : angle 2.16887 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2357.73 seconds wall clock time: 41 minutes 34.04 seconds (2494.04 seconds total)