Starting phenix.real_space_refine on Thu Aug 6 09:11:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yij_72992/08_2026/9yij_72992.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yij_72992/08_2026/9yij_72992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yij_72992/08_2026/9yij_72992.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yij_72992/08_2026/9yij_72992.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yij_72992/08_2026/9yij_72992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yij_72992/08_2026/9yij_72992.map" } resolution = 4.1 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= 0.009 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 8832 2.51 5 N 2370 2.21 5 O 2838 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14145 Number of models: 1 Model: "" Number of chains: 24 Chain: "G" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3447 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 413} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 938 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "F" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3447 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 413} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 938 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "E" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3447 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 413} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 938 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" 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: "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: "G" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.13, per 1000 atoms: 0.22 Number of scatterers: 14145 At special positions: 0 Unit cell: (123.968, 119.808, 115.648, 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 2838 8.00 N 2370 7.00 C 8832 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 433 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS C 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 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 E 54 " - pdb=" SG CYS E 74 " 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=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS A 605 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 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 ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA K 3 " - " MAN K 4 " " BMA O 3 " - " MAN O 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A 701 " - " ASN A 611 " " NAG B 701 " - " ASN B 611 " " NAG C 701 " - " ASN C 611 " " NAG D 1 " - " ASN G 262 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 156 " " NAG E 604 " - " ASN E 160 " " NAG E 605 " - " ASN E 197 " " NAG E 606 " - " ASN E 230 " " NAG E 607 " - " ASN E 234 " " NAG E 608 " - " ASN E 241 " " NAG E 609 " - " ASN E 276 " " NAG E 610 " - " ASN E 301 " " NAG E 611 " - " ASN E 344 " " NAG E 612 " - " ASN E 392 " " NAG E 613 " - " ASN E 448 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 133 " " NAG F 603 " - " ASN F 156 " " NAG F 604 " - " ASN F 160 " " NAG F 605 " - " ASN F 197 " " NAG F 606 " - " ASN F 230 " " NAG F 607 " - " ASN F 234 " " NAG F 608 " - " ASN F 241 " " NAG F 609 " - " ASN F 276 " " NAG F 610 " - " ASN F 301 " " NAG F 611 " - " ASN F 344 " " NAG F 612 " - " ASN F 392 " " NAG F 613 " - " ASN F 448 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 133 " " NAG G 603 " - " ASN G 156 " " NAG G 604 " - " ASN G 160 " " NAG G 605 " - " ASN G 197 " " NAG G 606 " - " ASN G 230 " " NAG G 607 " - " ASN G 234 " " NAG G 608 " - " ASN G 241 " " NAG G 609 " - " ASN G 276 " " NAG G 610 " - " ASN G 301 " " NAG G 611 " - " ASN G 344 " " NAG G 612 " - " ASN G 392 " " NAG G 613 " - " ASN G 448 " " NAG H 1 " - " ASN G 295 " " NAG I 1 " - " ASN G 332 " " NAG J 1 " - " ASN G 386 " " NAG K 1 " - " ASN F 262 " " NAG L 1 " - " ASN F 295 " " NAG M 1 " - " ASN F 332 " " NAG N 1 " - " ASN F 386 " " NAG O 1 " - " ASN E 262 " " NAG P 1 " - " ASN E 295 " " NAG Q 1 " - " ASN E 332 " " NAG R 1 " - " ASN E 386 " Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 560.4 milliseconds 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3126 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 24 sheets defined 27.4% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'G' and resid 99 through 117 Processing helix chain 'G' and resid 141 through 152 removed outlier: 3.640A pdb=" N GLY G 152 " --> pdb=" O ASP G 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 141 through 152' Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 335 through 353 Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 387 through 391 removed outlier: 3.584A pdb=" N PHE G 391 " --> pdb=" O SER G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 Processing helix chain 'G' and resid 474 through 483 removed outlier: 3.981A pdb=" N ASN G 478 " --> pdb=" O ASP G 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 537 through 544 removed outlier: 3.626A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 596 Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 651 removed outlier: 4.078A pdb=" N ASN C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 664 removed outlier: 4.099A pdb=" N ASP C 664 " --> pdb=" O LEU C 660 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 117 Processing helix chain 'F' and resid 141 through 152 removed outlier: 3.640A pdb=" N GLY F 152 " --> pdb=" O ASP F 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 141 through 152' Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 335 through 353 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 387 through 391 removed outlier: 3.584A pdb=" N PHE F 391 " --> pdb=" O SER F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 429 Processing helix chain 'F' and resid 474 through 483 removed outlier: 3.981A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 544 removed outlier: 3.626A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 651 removed outlier: 4.078A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 664 removed outlier: 4.098A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 141 through 152 removed outlier: 3.640A pdb=" N GLY E 152 " --> pdb=" O ASP E 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 141 through 152' Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 removed outlier: 3.584A pdb=" N PHE E 391 " --> pdb=" O SER E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 Processing helix chain 'E' and resid 474 through 483 removed outlier: 3.980A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 537 through 544 removed outlier: 3.626A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 596 Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 627 through 635 Processing helix chain 'A' and resid 638 through 651 removed outlier: 4.078A pdb=" N ASN A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 664 removed outlier: 4.098A pdb=" N ASP A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 495 through 499 removed outlier: 5.041A pdb=" N VAL C 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL G 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR C 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.780A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 91 through 93 Processing sheet with id=AA4, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AA5, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.181A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 271 through 273 removed outlier: 6.634A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 300 through 308 removed outlier: 6.747A pdb=" N ASN G 301 " --> pdb=" O ILE G 322 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE G 322 " --> pdb=" O ASN G 301 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N THR G 303 " --> pdb=" O GLY G 321 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 423 through 424 Processing sheet with id=AA9, first strand: chain 'F' and resid 495 through 499 removed outlier: 5.040A pdb=" N VAL B 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL F 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR B 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.779A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 91 through 93 Processing sheet with id=AB3, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AB4, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.181A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 271 through 273 removed outlier: 6.633A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE F 358 " --> pdb=" O GLU F 466 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N PHE F 468 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG F 360 " --> pdb=" O PHE F 468 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER F 393 " --> pdb=" O PHE F 361 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 300 through 308 removed outlier: 6.746A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 423 through 424 Processing sheet with id=AB8, first strand: chain 'E' and resid 495 through 499 removed outlier: 5.041A pdb=" N VAL A 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL E 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR A 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.779A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AC2, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC3, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.181A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.316A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.456A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.634A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.456A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.316A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 300 through 308 removed outlier: 6.746A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 423 through 424 510 hydrogen bonds defined for protein. 1386 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: 2.53 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4469 1.34 - 1.46: 2842 1.46 - 1.58: 6963 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 14412 Sorted by residual: bond pdb=" C2 BMA K 3 " pdb=" O2 BMA K 3 " ideal model delta sigma weight residual 1.402 1.434 -0.032 2.00e-02 2.50e+03 2.49e+00 bond pdb=" C3 NAG G 601 " pdb=" O3 NAG G 601 " ideal model delta sigma weight residual 1.403 1.434 -0.031 2.00e-02 2.50e+03 2.44e+00 bond pdb=" C2 BMA O 3 " pdb=" O2 BMA O 3 " ideal model delta sigma weight residual 1.402 1.433 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C2 BMA D 3 " pdb=" O2 BMA D 3 " ideal model delta sigma weight residual 1.402 1.433 -0.031 2.00e-02 2.50e+03 2.42e+00 bond pdb=" C3 NAG E 601 " pdb=" O3 NAG E 601 " ideal model delta sigma weight residual 1.403 1.434 -0.031 2.00e-02 2.50e+03 2.39e+00 ... (remaining 14407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 18999 1.74 - 3.48: 520 3.48 - 5.22: 39 5.22 - 6.96: 14 6.96 - 8.70: 3 Bond angle restraints: 19575 Sorted by residual: angle pdb=" C1 BMA O 3 " pdb=" O5 BMA O 3 " pdb=" C5 BMA O 3 " ideal model delta sigma weight residual 118.82 110.12 8.70 3.00e+00 1.11e-01 8.40e+00 angle pdb=" C1 BMA K 3 " pdb=" O5 BMA K 3 " pdb=" C5 BMA K 3 " ideal model delta sigma weight residual 118.82 110.16 8.66 3.00e+00 1.11e-01 8.34e+00 angle pdb=" C1 BMA D 3 " pdb=" O5 BMA D 3 " pdb=" C5 BMA D 3 " ideal model delta sigma weight residual 118.82 110.18 8.64 3.00e+00 1.11e-01 8.30e+00 angle pdb=" C SER A 599 " pdb=" CA SER A 599 " pdb=" CB SER A 599 " ideal model delta sigma weight residual 110.42 115.19 -4.77 1.99e+00 2.53e-01 5.74e+00 angle pdb=" C SER B 599 " pdb=" CA SER B 599 " pdb=" CB SER B 599 " ideal model delta sigma weight residual 110.42 115.18 -4.76 1.99e+00 2.53e-01 5.72e+00 ... (remaining 19570 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.53: 8984 24.53 - 49.05: 535 49.05 - 73.58: 41 73.58 - 98.11: 31 98.11 - 122.63: 48 Dihedral angle restraints: 9639 sinusoidal: 4821 harmonic: 4818 Sorted by residual: dihedral pdb=" CB CYS F 54 " pdb=" SG CYS F 54 " pdb=" SG CYS F 74 " pdb=" CB CYS F 74 " ideal model delta sinusoidal sigma weight residual 93.00 10.00 83.00 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual 93.00 10.02 82.98 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS G 54 " pdb=" SG CYS G 54 " pdb=" SG CYS G 74 " pdb=" CB CYS G 74 " ideal model delta sinusoidal sigma weight residual 93.00 10.03 82.97 1 1.00e+01 1.00e-02 8.43e+01 ... (remaining 9636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.017: 2412 1.017 - 2.035: 0 2.035 - 3.052: 0 3.052 - 4.070: 0 4.070 - 5.087: 9 Chirality restraints: 2421 Sorted by residual: chirality pdb=" C4 NAG E 604 " pdb=" C3 NAG E 604 " pdb=" C5 NAG E 604 " pdb=" O4 NAG E 604 " both_signs ideal model delta sigma weight residual False -2.53 2.56 -5.09 2.00e-01 2.50e+01 6.47e+02 chirality pdb=" C4 NAG G 604 " pdb=" C3 NAG G 604 " pdb=" C5 NAG G 604 " pdb=" O4 NAG G 604 " both_signs ideal model delta sigma weight residual False -2.53 2.55 -5.08 2.00e-01 2.50e+01 6.46e+02 chirality pdb=" C4 NAG F 604 " pdb=" C3 NAG F 604 " pdb=" C5 NAG F 604 " pdb=" O4 NAG F 604 " both_signs ideal model delta sigma weight residual False -2.53 2.55 -5.08 2.00e-01 2.50e+01 6.46e+02 ... (remaining 2418 not shown) Planarity restraints: 2463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 75 " -0.014 5.00e-02 4.00e+02 2.10e-02 7.03e-01 pdb=" N PRO F 76 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO F 76 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO F 76 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 75 " -0.014 5.00e-02 4.00e+02 2.08e-02 6.91e-01 pdb=" N PRO G 76 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO G 76 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO G 76 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 75 " -0.014 5.00e-02 4.00e+02 2.06e-02 6.78e-01 pdb=" N PRO E 76 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO E 76 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO E 76 " -0.011 5.00e-02 4.00e+02 ... (remaining 2460 not shown) Histogram of nonbonded interaction distances: 2.64 - 3.09: 10060 3.09 - 3.55: 14379 3.55 - 4.00: 22204 4.00 - 4.45: 26947 4.45 - 4.90: 40449 Nonbonded interactions: 114039 Sorted by model distance: nonbonded pdb=" N THR E 464 " pdb=" N THR E 465 " model vdw 2.643 2.560 nonbonded pdb=" N THR F 464 " pdb=" N THR F 465 " model vdw 2.643 2.560 nonbonded pdb=" N THR G 464 " pdb=" N THR G 465 " model vdw 2.644 2.560 nonbonded pdb=" N VAL F 127 " pdb=" O VAL F 127 " model vdw 2.649 2.496 nonbonded pdb=" N VAL E 127 " pdb=" O VAL E 127 " model vdw 2.650 2.496 ... (remaining 114034 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.340 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 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 : 0.005 0.032 14520 Z= 0.234 Angle : 0.688 12.431 19863 Z= 0.288 Chirality : 0.309 5.087 2421 Planarity : 0.002 0.021 2409 Dihedral : 17.426 122.634 6405 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.20 % Allowed : 5.86 % Favored : 93.94 % 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: -0.15 (0.22), residues: 1623 helix: 1.67 (0.28), residues: 399 sheet: -0.64 (0.26), residues: 396 loop : -0.66 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 273 TYR 0.005 0.001 TYR A 586 PHE 0.007 0.001 PHE F 53 TRP 0.004 0.001 TRP B 631 HIS 0.007 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.23 (14412) covalent geometry : angle 0.62146 / 0.27 (19575) SS BOND : bond 0.00184 / 0.13 ( 36) SS BOND : angle 0.92443 / 0.61 ( 72) hydrogen bonds : bond 0.11713 / 7.97 ( 495) hydrogen bonds : angle 6.26738 / 4.45 ( 1386) link_ALPHA1-3 : bond 0.00047 / 0.02 ( 3) link_ALPHA1-3 : angle 0.93110 / 0.62 ( 9) link_BETA1-4 : bond 0.01077 / 0.65 ( 15) link_BETA1-4 : angle 1.80714 / 1.35 ( 45) link_NAG-ASN : bond 0.00396 / 0.25 ( 54) link_NAG-ASN : angle 3.15865 / 2.30 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 562 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 166 ARG cc_start: 0.7492 (mmp80) cc_final: 0.7051 (mtp-110) REVERT: G 195 ASN cc_start: 0.7377 (p0) cc_final: 0.7165 (p0) REVERT: G 199 SER cc_start: 0.8526 (p) cc_final: 0.8271 (p) REVERT: G 207 LYS cc_start: 0.7990 (mmtm) cc_final: 0.7755 (tttp) REVERT: G 419 ARG cc_start: 0.8141 (mtm180) cc_final: 0.7920 (mtp85) REVERT: G 478 ASN cc_start: 0.8371 (m110) cc_final: 0.8150 (m-40) REVERT: C 584 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7394 (tm-30) REVERT: F 99 ASN cc_start: 0.7723 (p0) cc_final: 0.7448 (t0) REVERT: F 166 ARG cc_start: 0.7403 (mmp80) cc_final: 0.7149 (mtp-110) REVERT: F 207 LYS cc_start: 0.8114 (mmtm) cc_final: 0.7798 (tttp) REVERT: F 426 MET cc_start: 0.6503 (ptp) cc_final: 0.6135 (ptp) REVERT: F 484 TYR cc_start: 0.9001 (p90) cc_final: 0.8403 (p90) REVERT: B 577 GLN cc_start: 0.7960 (tt0) cc_final: 0.7731 (tm-30) REVERT: B 592 LEU cc_start: 0.8666 (mt) cc_final: 0.8445 (mt) REVERT: E 103 GLN cc_start: 0.7628 (mm110) cc_final: 0.7113 (tm-30) REVERT: E 195 ASN cc_start: 0.7405 (p0) cc_final: 0.7103 (p0) REVERT: E 199 SER cc_start: 0.8404 (p) cc_final: 0.8076 (p) REVERT: E 207 LYS cc_start: 0.8111 (mmtm) cc_final: 0.7718 (tttp) REVERT: E 426 MET cc_start: 0.6200 (ptp) cc_final: 0.5935 (ptp) REVERT: E 457 ASP cc_start: 0.8162 (m-30) cc_final: 0.7764 (m-30) REVERT: E 484 TYR cc_start: 0.8874 (p90) cc_final: 0.8322 (p90) outliers start: 3 outliers final: 0 residues processed: 565 average time/residue: 0.1055 time to fit residues: 89.0256 Evaluate side-chains 332 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.0270 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 85 HIS ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 HIS F 478 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN B 658 GLN E 85 HIS E 330 HIS A 591 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.142480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.123427 restraints weight = 22440.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.126611 restraints weight = 14019.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.128875 restraints weight = 10004.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.130445 restraints weight = 7758.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.131623 restraints weight = 6380.194| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 14520 Z= 0.234 Angle : 0.827 20.902 19863 Z= 0.367 Chirality : 0.049 0.350 2421 Planarity : 0.004 0.068 2409 Dihedral : 8.413 62.173 3261 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.34 % Allowed : 3.84 % Favored : 95.82 % 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: -0.33 (0.21), residues: 1623 helix: 1.45 (0.27), residues: 375 sheet: -0.26 (0.28), residues: 366 loop : -0.93 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 617 TYR 0.010 0.002 TYR G 191 PHE 0.018 0.003 PHE E 223 TRP 0.019 0.002 TRP F 35 HIS 0.004 0.001 HIS F 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.23 (14412) covalent geometry : angle 0.70483 / 0.34 (19575) SS BOND : bond 0.00334 / 0.23 ( 36) SS BOND : angle 1.52647 / 1.03 ( 72) hydrogen bonds : bond 0.03498 / 2.36 ( 495) hydrogen bonds : angle 5.26512 / 3.69 ( 1386) link_ALPHA1-3 : bond 0.00886 / 0.45 ( 3) link_ALPHA1-3 : angle 2.25910 / 1.58 ( 9) link_BETA1-4 : bond 0.00688 / 0.38 ( 15) link_BETA1-4 : angle 6.80178 / 5.24 ( 45) link_NAG-ASN : bond 0.00617 / 0.38 ( 54) link_NAG-ASN : angle 3.11354 / 2.25 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 384 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 103 GLN cc_start: 0.7967 (mm110) cc_final: 0.7237 (tm-30) REVERT: G 104 MET cc_start: 0.9240 (tpp) cc_final: 0.8404 (tpp) REVERT: G 166 ARG cc_start: 0.7770 (mmp80) cc_final: 0.7359 (mtp-110) REVERT: G 180 ASP cc_start: 0.8269 (m-30) cc_final: 0.8055 (m-30) REVERT: G 207 LYS cc_start: 0.8304 (mmtm) cc_final: 0.7854 (tttp) REVERT: G 208 VAL cc_start: 0.9202 (p) cc_final: 0.8939 (m) REVERT: G 258 GLN cc_start: 0.8831 (mt0) cc_final: 0.8614 (mt0) REVERT: G 419 ARG cc_start: 0.8279 (mtm180) cc_final: 0.7952 (mtp85) REVERT: G 423 ILE cc_start: 0.9636 (mm) cc_final: 0.9379 (mm) REVERT: G 428 GLN cc_start: 0.8316 (mp10) cc_final: 0.7968 (mp10) REVERT: G 468 PHE cc_start: 0.8849 (m-80) cc_final: 0.8300 (m-10) REVERT: G 478 ASN cc_start: 0.8618 (m110) cc_final: 0.8308 (m-40) REVERT: G 484 TYR cc_start: 0.8894 (p90) cc_final: 0.8676 (p90) REVERT: G 486 TYR cc_start: 0.9142 (m-80) cc_final: 0.8806 (m-10) REVERT: C 584 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7399 (tm-30) REVERT: C 621 GLU cc_start: 0.7874 (tm-30) cc_final: 0.6955 (mt-10) REVERT: C 647 GLU cc_start: 0.8023 (tt0) cc_final: 0.7773 (tt0) REVERT: F 166 ARG cc_start: 0.7721 (mmp80) cc_final: 0.7257 (mtp-110) REVERT: F 207 LYS cc_start: 0.8338 (mmtm) cc_final: 0.7933 (tttp) REVERT: F 213 ILE cc_start: 0.8859 (tp) cc_final: 0.8568 (pt) REVERT: F 258 GLN cc_start: 0.8576 (mt0) cc_final: 0.8278 (mt0) REVERT: F 457 ASP cc_start: 0.8418 (m-30) cc_final: 0.8185 (m-30) REVERT: F 484 TYR cc_start: 0.8850 (p90) cc_final: 0.8169 (p90) REVERT: B 577 GLN cc_start: 0.8416 (tt0) cc_final: 0.8044 (tm-30) REVERT: E 85 HIS cc_start: 0.8984 (t-90) cc_final: 0.8780 (t-90) REVERT: E 103 GLN cc_start: 0.7901 (mm110) cc_final: 0.7127 (tm-30) REVERT: E 180 ASP cc_start: 0.8432 (m-30) cc_final: 0.8069 (m-30) REVERT: E 207 LYS cc_start: 0.8287 (mmtm) cc_final: 0.7846 (tttp) REVERT: E 213 ILE cc_start: 0.8802 (tp) cc_final: 0.8546 (pt) REVERT: E 258 GLN cc_start: 0.8716 (mt0) cc_final: 0.8348 (mt0) REVERT: E 264 SER cc_start: 0.8855 (p) cc_final: 0.8532 (m) REVERT: E 423 ILE cc_start: 0.9559 (mm) cc_final: 0.9159 (mm) REVERT: E 457 ASP cc_start: 0.8327 (m-30) cc_final: 0.8120 (m-30) REVERT: E 484 TYR cc_start: 0.8777 (p90) cc_final: 0.8240 (p90) REVERT: A 577 GLN cc_start: 0.8741 (tp40) cc_final: 0.8189 (tm-30) REVERT: A 647 GLU cc_start: 0.7590 (tt0) cc_final: 0.6208 (tt0) outliers start: 5 outliers final: 0 residues processed: 387 average time/residue: 0.0938 time to fit residues: 56.7882 Evaluate side-chains 299 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 125 optimal weight: 3.9990 chunk 88 optimal weight: 0.0970 chunk 75 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 287 GLN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 GLN F 287 GLN F 330 HIS ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 GLN ** E 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 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 = 0.3605 r_free = 0.3605 target = 0.143175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.125051 restraints weight = 22447.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.128247 restraints weight = 13875.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.130452 restraints weight = 9756.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.132072 restraints weight = 7490.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.133275 restraints weight = 6066.965| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14520 Z= 0.154 Angle : 0.728 17.878 19863 Z= 0.325 Chirality : 0.046 0.322 2421 Planarity : 0.004 0.044 2409 Dihedral : 7.287 59.857 3261 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.07 % Allowed : 3.64 % Favored : 96.30 % 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: -0.53 (0.21), residues: 1623 helix: 1.04 (0.27), residues: 396 sheet: -0.23 (0.28), residues: 369 loop : -1.06 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 542 TYR 0.009 0.001 TYR C 586 PHE 0.015 0.002 PHE F 233 TRP 0.021 0.002 TRP F 35 HIS 0.004 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (14412) covalent geometry : angle 0.62055 / 0.30 (19575) SS BOND : bond 0.00296 / 0.18 ( 36) SS BOND : angle 1.42656 / 0.94 ( 72) hydrogen bonds : bond 0.03469 / 2.34 ( 495) hydrogen bonds : angle 5.11380 / 3.60 ( 1386) link_ALPHA1-3 : bond 0.01947 / 0.97 ( 3) link_ALPHA1-3 : angle 1.35892 / 0.91 ( 9) link_BETA1-4 : bond 0.00316 / 0.18 ( 15) link_BETA1-4 : angle 5.97727 / 4.63 ( 45) link_NAG-ASN : bond 0.00346 / 0.22 ( 54) link_NAG-ASN : angle 2.75672 / 1.99 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 363 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 92 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8193 (tp30) REVERT: G 95 MET cc_start: 0.9071 (ppp) cc_final: 0.8778 (ppp) REVERT: G 103 GLN cc_start: 0.8016 (mm110) cc_final: 0.7208 (tm-30) REVERT: G 166 ARG cc_start: 0.7747 (mmp80) cc_final: 0.7422 (mtp-110) REVERT: G 207 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7853 (tttp) REVERT: G 208 VAL cc_start: 0.9155 (p) cc_final: 0.8872 (m) REVERT: G 240 PRO cc_start: 0.8203 (Cg_endo) cc_final: 0.7862 (Cg_exo) REVERT: G 258 GLN cc_start: 0.8729 (mt0) cc_final: 0.8479 (mt0) REVERT: G 419 ARG cc_start: 0.8249 (mtm180) cc_final: 0.7888 (mtp85) REVERT: G 423 ILE cc_start: 0.9599 (mm) cc_final: 0.9370 (mm) REVERT: G 428 GLN cc_start: 0.8283 (mp10) cc_final: 0.7956 (mp10) REVERT: G 468 PHE cc_start: 0.8812 (m-80) cc_final: 0.8247 (m-10) REVERT: G 475 MET cc_start: 0.8910 (mmm) cc_final: 0.8710 (mmm) REVERT: G 478 ASN cc_start: 0.8559 (m110) cc_final: 0.8278 (m-40) REVERT: G 486 TYR cc_start: 0.9094 (m-80) cc_final: 0.8793 (m-10) REVERT: C 584 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7465 (tm-30) REVERT: C 621 GLU cc_start: 0.8095 (tm-30) cc_final: 0.6989 (mt-10) REVERT: C 628 TRP cc_start: 0.8914 (m100) cc_final: 0.8708 (m100) REVERT: F 85 HIS cc_start: 0.8891 (t70) cc_final: 0.8683 (t-90) REVERT: F 95 MET cc_start: 0.9208 (ppp) cc_final: 0.8888 (ppp) REVERT: F 104 MET cc_start: 0.9125 (tpp) cc_final: 0.8569 (tpp) REVERT: F 166 ARG cc_start: 0.7818 (mmp80) cc_final: 0.7379 (mtp-110) REVERT: F 180 ASP cc_start: 0.8287 (m-30) cc_final: 0.7887 (m-30) REVERT: F 207 LYS cc_start: 0.8281 (mmtm) cc_final: 0.7877 (tttp) REVERT: F 423 ILE cc_start: 0.9597 (mm) cc_final: 0.9303 (mm) REVERT: F 484 TYR cc_start: 0.8749 (p90) cc_final: 0.8540 (p90) REVERT: B 538 THR cc_start: 0.8169 (t) cc_final: 0.7625 (m) REVERT: B 577 GLN cc_start: 0.8388 (tt0) cc_final: 0.8004 (tm-30) REVERT: E 85 HIS cc_start: 0.8936 (t-90) cc_final: 0.8650 (t-90) REVERT: E 95 MET cc_start: 0.9095 (ppp) cc_final: 0.8816 (ppp) REVERT: E 103 GLN cc_start: 0.7993 (mm110) cc_final: 0.7133 (tm-30) REVERT: E 180 ASP cc_start: 0.8406 (m-30) cc_final: 0.8074 (m-30) REVERT: E 195 ASN cc_start: 0.7558 (p0) cc_final: 0.7256 (p0) REVERT: E 207 LYS cc_start: 0.8252 (mmtm) cc_final: 0.7806 (tttp) REVERT: E 258 GLN cc_start: 0.8639 (mt0) cc_final: 0.8273 (mt0) REVERT: E 423 ILE cc_start: 0.9516 (mm) cc_final: 0.9098 (mm) REVERT: E 484 TYR cc_start: 0.8791 (p90) cc_final: 0.8053 (p90) REVERT: A 577 GLN cc_start: 0.8724 (tp40) cc_final: 0.8085 (tm-30) outliers start: 1 outliers final: 0 residues processed: 364 average time/residue: 0.1018 time to fit residues: 58.3317 Evaluate side-chains 295 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 49 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 0.0870 chunk 84 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 48 optimal weight: 0.4980 chunk 105 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 352 HIS ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 GLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN E 330 HIS ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 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 = 0.3562 r_free = 0.3562 target = 0.140484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.125563 restraints weight = 21320.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.128198 restraints weight = 13349.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.130101 restraints weight = 9349.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.131412 restraints weight = 7075.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.132363 restraints weight = 5685.826| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14520 Z= 0.142 Angle : 0.630 10.260 19863 Z= 0.297 Chirality : 0.046 0.319 2421 Planarity : 0.004 0.055 2409 Dihedral : 6.686 52.148 3261 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.07 % Allowed : 2.42 % Favored : 97.51 % 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: -0.62 (0.21), residues: 1623 helix: 0.77 (0.27), residues: 417 sheet: -0.58 (0.26), residues: 405 loop : -0.89 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 542 TYR 0.010 0.001 TYR B 586 PHE 0.026 0.002 PHE F 223 TRP 0.022 0.001 TRP F 35 HIS 0.005 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (14412) covalent geometry : angle 0.56741 / 0.28 (19575) SS BOND : bond 0.00242 / 0.16 ( 36) SS BOND : angle 1.68649 / 1.12 ( 72) hydrogen bonds : bond 0.03241 / 2.21 ( 495) hydrogen bonds : angle 4.98923 / 3.50 ( 1386) link_ALPHA1-3 : bond 0.01542 / 0.78 ( 3) link_ALPHA1-3 : angle 1.29558 / 0.89 ( 9) link_BETA1-4 : bond 0.00406 / 0.24 ( 15) link_BETA1-4 : angle 2.23848 / 1.67 ( 45) link_NAG-ASN : bond 0.00384 / 0.25 ( 54) link_NAG-ASN : angle 2.64350 / 1.91 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 352 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9179 (ppp) cc_final: 0.8826 (ppp) REVERT: G 103 GLN cc_start: 0.7843 (mm110) cc_final: 0.7179 (tm-30) REVERT: G 104 MET cc_start: 0.9196 (tpp) cc_final: 0.8584 (tpp) REVERT: G 166 ARG cc_start: 0.7777 (mmp80) cc_final: 0.7458 (mtp-110) REVERT: G 207 LYS cc_start: 0.8186 (mmtm) cc_final: 0.7841 (tttp) REVERT: G 208 VAL cc_start: 0.9134 (p) cc_final: 0.8876 (m) REVERT: G 240 PRO cc_start: 0.8214 (Cg_endo) cc_final: 0.7887 (Cg_exo) REVERT: G 258 GLN cc_start: 0.8761 (mt0) cc_final: 0.8505 (mt0) REVERT: G 419 ARG cc_start: 0.8286 (mtm180) cc_final: 0.7838 (mtp85) REVERT: G 468 PHE cc_start: 0.8821 (m-80) cc_final: 0.8270 (m-10) REVERT: G 478 ASN cc_start: 0.8625 (m110) cc_final: 0.8360 (m-40) REVERT: C 538 THR cc_start: 0.8392 (p) cc_final: 0.8170 (p) REVERT: C 584 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7245 (tm-30) REVERT: C 628 TRP cc_start: 0.9077 (m100) cc_final: 0.8822 (m100) REVERT: F 85 HIS cc_start: 0.8888 (t70) cc_final: 0.8679 (t-90) REVERT: F 95 MET cc_start: 0.9190 (ppp) cc_final: 0.8896 (ppp) REVERT: F 104 MET cc_start: 0.9168 (tpp) cc_final: 0.8649 (tpp) REVERT: F 166 ARG cc_start: 0.7856 (mmp80) cc_final: 0.7399 (mtp-110) REVERT: F 180 ASP cc_start: 0.8286 (m-30) cc_final: 0.7942 (m-30) REVERT: F 207 LYS cc_start: 0.8237 (mmtm) cc_final: 0.7829 (tttp) REVERT: F 423 ILE cc_start: 0.9561 (mm) cc_final: 0.9292 (mm) REVERT: F 484 TYR cc_start: 0.8814 (p90) cc_final: 0.8574 (p90) REVERT: B 577 GLN cc_start: 0.8370 (tt0) cc_final: 0.8137 (tm-30) REVERT: B 621 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7055 (mt-10) REVERT: E 85 HIS cc_start: 0.8894 (t-90) cc_final: 0.8600 (t-90) REVERT: E 95 MET cc_start: 0.9166 (ppp) cc_final: 0.8883 (ppp) REVERT: E 180 ASP cc_start: 0.8323 (m-30) cc_final: 0.7960 (m-30) REVERT: E 207 LYS cc_start: 0.8241 (mmtm) cc_final: 0.7820 (tttp) REVERT: E 258 GLN cc_start: 0.8681 (mt0) cc_final: 0.8352 (mt0) REVERT: E 423 ILE cc_start: 0.9490 (mm) cc_final: 0.9079 (mm) REVERT: E 484 TYR cc_start: 0.8690 (p90) cc_final: 0.8147 (p90) REVERT: A 577 GLN cc_start: 0.8758 (tp40) cc_final: 0.8087 (tm-30) outliers start: 1 outliers final: 0 residues processed: 352 average time/residue: 0.1014 time to fit residues: 56.1160 Evaluate side-chains 281 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 127 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 57 optimal weight: 10.0000 chunk 4 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 287 GLN C 577 GLN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 GLN F 258 GLN F 287 GLN ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.142351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.123729 restraints weight = 22407.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.127090 restraints weight = 13812.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.129448 restraints weight = 9650.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.131017 restraints weight = 7331.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.132238 restraints weight = 5970.369| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14520 Z= 0.136 Angle : 0.615 9.694 19863 Z= 0.294 Chirality : 0.045 0.302 2421 Planarity : 0.004 0.062 2409 Dihedral : 6.054 52.152 3261 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.13 % Allowed : 1.75 % Favored : 98.11 % 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: -0.61 (0.21), residues: 1623 helix: 0.96 (0.27), residues: 396 sheet: -0.63 (0.27), residues: 408 loop : -0.92 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 542 TYR 0.019 0.001 TYR G 486 PHE 0.020 0.002 PHE F 383 TRP 0.021 0.001 TRP F 35 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (14412) covalent geometry : angle 0.55856 / 0.28 (19575) SS BOND : bond 0.00251 / 0.17 ( 36) SS BOND : angle 1.58133 / 1.04 ( 72) hydrogen bonds : bond 0.03163 / 2.14 ( 495) hydrogen bonds : angle 4.91306 / 3.44 ( 1386) link_ALPHA1-3 : bond 0.01153 / 0.57 ( 3) link_ALPHA1-3 : angle 1.63507 / 1.09 ( 9) link_BETA1-4 : bond 0.00286 / 0.17 ( 15) link_BETA1-4 : angle 2.07491 / 1.54 ( 45) link_NAG-ASN : bond 0.00320 / 0.20 ( 54) link_NAG-ASN : angle 2.50674 / 1.82 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 357 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9168 (ppp) cc_final: 0.8835 (ppp) REVERT: G 99 ASN cc_start: 0.7394 (t0) cc_final: 0.7152 (t0) REVERT: G 103 GLN cc_start: 0.7781 (mm110) cc_final: 0.7101 (tm-30) REVERT: G 104 MET cc_start: 0.9107 (ttm) cc_final: 0.8821 (tpp) REVERT: G 166 ARG cc_start: 0.7863 (mmp80) cc_final: 0.7570 (mtp-110) REVERT: G 207 LYS cc_start: 0.8175 (mmtm) cc_final: 0.7801 (tttp) REVERT: G 208 VAL cc_start: 0.9124 (p) cc_final: 0.8873 (m) REVERT: G 240 PRO cc_start: 0.8320 (Cg_endo) cc_final: 0.7984 (Cg_exo) REVERT: G 258 GLN cc_start: 0.8725 (mt0) cc_final: 0.8502 (mt0) REVERT: G 419 ARG cc_start: 0.8315 (mtm180) cc_final: 0.7918 (mtp85) REVERT: G 468 PHE cc_start: 0.8809 (m-80) cc_final: 0.8232 (m-10) REVERT: G 478 ASN cc_start: 0.8690 (m110) cc_final: 0.8377 (m-40) REVERT: C 574 LYS cc_start: 0.7987 (mmmm) cc_final: 0.7345 (mtmm) REVERT: F 85 HIS cc_start: 0.8873 (t70) cc_final: 0.8666 (t-90) REVERT: F 104 MET cc_start: 0.9171 (tpp) cc_final: 0.8960 (tpp) REVERT: F 166 ARG cc_start: 0.7874 (mmp80) cc_final: 0.7520 (mtp-110) REVERT: F 180 ASP cc_start: 0.8241 (m-30) cc_final: 0.7892 (m-30) REVERT: F 207 LYS cc_start: 0.8282 (mmtm) cc_final: 0.7825 (tttp) REVERT: F 423 ILE cc_start: 0.9573 (mm) cc_final: 0.9288 (mm) REVERT: B 577 GLN cc_start: 0.8431 (tt0) cc_final: 0.8122 (tm-30) REVERT: B 621 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7002 (mt-10) REVERT: E 85 HIS cc_start: 0.8853 (t-90) cc_final: 0.8542 (t-90) REVERT: E 95 MET cc_start: 0.9171 (ppp) cc_final: 0.8911 (ppp) REVERT: E 104 MET cc_start: 0.9250 (tpp) cc_final: 0.8964 (tpp) REVERT: E 180 ASP cc_start: 0.8260 (m-30) cc_final: 0.7866 (m-30) REVERT: E 207 LYS cc_start: 0.8272 (mmtm) cc_final: 0.7782 (tttp) REVERT: E 258 GLN cc_start: 0.8612 (mt0) cc_final: 0.8353 (mt0) REVERT: E 423 ILE cc_start: 0.9503 (mm) cc_final: 0.9069 (mm) REVERT: E 484 TYR cc_start: 0.8714 (p90) cc_final: 0.8039 (p90) REVERT: A 574 LYS cc_start: 0.8103 (mmmm) cc_final: 0.7518 (ptpp) REVERT: A 577 GLN cc_start: 0.8730 (tp40) cc_final: 0.8096 (tm-30) outliers start: 2 outliers final: 0 residues processed: 358 average time/residue: 0.1006 time to fit residues: 56.5062 Evaluate side-chains 287 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 158 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 183 GLN G 422 GLN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 ASN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 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 = 0.3428 r_free = 0.3428 target = 0.129530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.116326 restraints weight = 21301.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.118380 restraints weight = 14236.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.119990 restraints weight = 10494.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.121167 restraints weight = 8250.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.121943 restraints weight = 6749.943| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14520 Z= 0.230 Angle : 0.715 10.060 19863 Z= 0.346 Chirality : 0.047 0.297 2421 Planarity : 0.004 0.053 2409 Dihedral : 5.932 51.734 3261 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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: -0.96 (0.21), residues: 1623 helix: 0.55 (0.27), residues: 399 sheet: -0.89 (0.26), residues: 420 loop : -1.05 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 503 TYR 0.032 0.002 TYR G 486 PHE 0.017 0.003 PHE F 383 TRP 0.018 0.002 TRP B 596 HIS 0.009 0.001 HIS G 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.23 (14412) covalent geometry : angle 0.65981 / 0.33 (19575) SS BOND : bond 0.00446 / 0.30 ( 36) SS BOND : angle 1.75026 / 1.17 ( 72) hydrogen bonds : bond 0.03444 / 2.32 ( 495) hydrogen bonds : angle 5.12816 / 3.59 ( 1386) link_ALPHA1-3 : bond 0.01212 / 0.61 ( 3) link_ALPHA1-3 : angle 1.72935 / 1.16 ( 9) link_BETA1-4 : bond 0.00466 / 0.25 ( 15) link_BETA1-4 : angle 2.20459 / 1.63 ( 45) link_NAG-ASN : bond 0.00463 / 0.30 ( 54) link_NAG-ASN : angle 2.69133 / 1.89 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9120 (ppp) cc_final: 0.8884 (ppp) REVERT: G 166 ARG cc_start: 0.8190 (mmp80) cc_final: 0.7971 (mtp-110) REVERT: G 207 LYS cc_start: 0.8050 (mmtm) cc_final: 0.7835 (tttp) REVERT: G 240 PRO cc_start: 0.8295 (Cg_endo) cc_final: 0.8023 (Cg_exo) REVERT: G 419 ARG cc_start: 0.8344 (mtm180) cc_final: 0.8087 (mtp85) REVERT: G 475 MET cc_start: 0.8879 (mmm) cc_final: 0.8517 (mmm) REVERT: G 478 ASN cc_start: 0.8497 (m110) cc_final: 0.8248 (m110) REVERT: F 125 LEU cc_start: 0.8968 (tp) cc_final: 0.8742 (tp) REVERT: F 166 ARG cc_start: 0.8115 (mmp80) cc_final: 0.7908 (mtp-110) REVERT: F 180 ASP cc_start: 0.8055 (m-30) cc_final: 0.7664 (m-30) REVERT: F 188 ASN cc_start: 0.6535 (p0) cc_final: 0.6331 (p0) REVERT: F 207 LYS cc_start: 0.8168 (mmtm) cc_final: 0.7901 (tttp) REVERT: F 377 ASN cc_start: 0.8856 (t0) cc_final: 0.8426 (t0) REVERT: F 423 ILE cc_start: 0.9594 (mm) cc_final: 0.9122 (mm) REVERT: B 529 THR cc_start: 0.7837 (m) cc_final: 0.7613 (m) REVERT: B 542 ARG cc_start: 0.8739 (ttm110) cc_final: 0.8491 (ttm110) REVERT: B 577 GLN cc_start: 0.8624 (tt0) cc_final: 0.8346 (tm-30) REVERT: E 95 MET cc_start: 0.9222 (ppp) cc_final: 0.8980 (ppp) REVERT: E 132 THR cc_start: 0.8191 (p) cc_final: 0.7981 (t) REVERT: E 207 LYS cc_start: 0.8134 (mmtm) cc_final: 0.7864 (tttp) REVERT: E 258 GLN cc_start: 0.8682 (mt0) cc_final: 0.8477 (mt0) REVERT: E 484 TYR cc_start: 0.8757 (p90) cc_final: 0.8326 (p90) REVERT: A 577 GLN cc_start: 0.8822 (tp40) cc_final: 0.8310 (tm-30) REVERT: A 628 TRP cc_start: 0.9266 (m100) cc_final: 0.9041 (m100) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.1090 time to fit residues: 57.0926 Evaluate side-chains 267 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 71 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 183 GLN G 258 GLN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 GLN F 287 GLN ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 HIS ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.133495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.121065 restraints weight = 21234.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.123140 restraints weight = 14034.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.124549 restraints weight = 10204.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.125709 restraints weight = 8030.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.126434 restraints weight = 6553.056| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14520 Z= 0.198 Angle : 0.671 9.608 19863 Z= 0.325 Chirality : 0.047 0.278 2421 Planarity : 0.004 0.047 2409 Dihedral : 5.808 52.063 3261 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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: -0.95 (0.21), residues: 1623 helix: 0.48 (0.26), residues: 399 sheet: -0.89 (0.26), residues: 393 loop : -0.99 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 503 TYR 0.027 0.002 TYR G 486 PHE 0.016 0.002 PHE E 53 TRP 0.026 0.002 TRP A 596 HIS 0.007 0.001 HIS F 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (14412) covalent geometry : angle 0.61704 / 0.31 (19575) SS BOND : bond 0.00372 / 0.25 ( 36) SS BOND : angle 1.86695 / 1.23 ( 72) hydrogen bonds : bond 0.03381 / 2.27 ( 495) hydrogen bonds : angle 5.17778 / 3.62 ( 1386) link_ALPHA1-3 : bond 0.01011 / 0.51 ( 3) link_ALPHA1-3 : angle 1.73506 / 1.17 ( 9) link_BETA1-4 : bond 0.00385 / 0.21 ( 15) link_BETA1-4 : angle 1.97762 / 1.45 ( 45) link_NAG-ASN : bond 0.00388 / 0.25 ( 54) link_NAG-ASN : angle 2.51680 / 1.78 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 132 THR cc_start: 0.8212 (p) cc_final: 0.7915 (t) REVERT: G 240 PRO cc_start: 0.8345 (Cg_endo) cc_final: 0.8123 (Cg_exo) REVERT: G 382 PHE cc_start: 0.8841 (m-80) cc_final: 0.8460 (m-10) REVERT: G 419 ARG cc_start: 0.8301 (mtm180) cc_final: 0.8055 (mtp85) REVERT: G 486 TYR cc_start: 0.8686 (m-80) cc_final: 0.8120 (m-80) REVERT: C 658 GLN cc_start: 0.7614 (pp30) cc_final: 0.6772 (tt0) REVERT: F 125 LEU cc_start: 0.8948 (tp) cc_final: 0.8639 (tp) REVERT: F 180 ASP cc_start: 0.8022 (m-30) cc_final: 0.7723 (m-30) REVERT: F 188 ASN cc_start: 0.6814 (p0) cc_final: 0.6466 (p0) REVERT: F 207 LYS cc_start: 0.8110 (mmtm) cc_final: 0.7855 (tttp) REVERT: F 377 ASN cc_start: 0.8825 (t0) cc_final: 0.8438 (t0) REVERT: F 423 ILE cc_start: 0.9547 (mm) cc_final: 0.9155 (mm) REVERT: B 577 GLN cc_start: 0.8686 (tt0) cc_final: 0.8296 (tm-30) REVERT: E 132 THR cc_start: 0.8167 (p) cc_final: 0.7949 (t) REVERT: E 232 THR cc_start: 0.8149 (m) cc_final: 0.7808 (t) REVERT: E 484 TYR cc_start: 0.8768 (p90) cc_final: 0.8486 (p90) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.1007 time to fit residues: 51.4768 Evaluate side-chains 261 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 44 optimal weight: 0.2980 chunk 124 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 183 GLN ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 GLN F 478 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN E 377 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 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 = 0.3508 r_free = 0.3508 target = 0.136079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.123789 restraints weight = 20975.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.125980 restraints weight = 13743.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.127552 restraints weight = 9904.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.128687 restraints weight = 7605.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.129433 restraints weight = 6173.995| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14520 Z= 0.154 Angle : 0.651 9.520 19863 Z= 0.318 Chirality : 0.046 0.275 2421 Planarity : 0.004 0.059 2409 Dihedral : 5.463 52.523 3261 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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: -0.86 (0.21), residues: 1623 helix: 0.62 (0.26), residues: 396 sheet: -0.85 (0.26), residues: 405 loop : -0.95 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 166 TYR 0.015 0.001 TYR G 40 PHE 0.017 0.002 PHE E 53 TRP 0.027 0.002 TRP F 35 HIS 0.006 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (14412) covalent geometry : angle 0.60347 / 0.31 (19575) SS BOND : bond 0.00283 / 0.20 ( 36) SS BOND : angle 1.75353 / 1.15 ( 72) hydrogen bonds : bond 0.03469 / 2.32 ( 495) hydrogen bonds : angle 5.18498 / 3.60 ( 1386) link_ALPHA1-3 : bond 0.00932 / 0.47 ( 3) link_ALPHA1-3 : angle 1.60837 / 1.08 ( 9) link_BETA1-4 : bond 0.00287 / 0.17 ( 15) link_BETA1-4 : angle 1.78577 / 1.28 ( 45) link_NAG-ASN : bond 0.00330 / 0.20 ( 54) link_NAG-ASN : angle 2.35755 / 1.68 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 102 GLU cc_start: 0.8187 (mp0) cc_final: 0.7863 (mp0) REVERT: G 132 THR cc_start: 0.8160 (p) cc_final: 0.7898 (t) REVERT: G 240 PRO cc_start: 0.8325 (Cg_endo) cc_final: 0.8123 (Cg_exo) REVERT: G 382 PHE cc_start: 0.8703 (m-80) cc_final: 0.8247 (m-10) REVERT: G 419 ARG cc_start: 0.8223 (mtm180) cc_final: 0.8011 (mtp85) REVERT: G 486 TYR cc_start: 0.8597 (m-80) cc_final: 0.8192 (m-80) REVERT: C 628 TRP cc_start: 0.9201 (m100) cc_final: 0.8992 (m100) REVERT: C 655 LYS cc_start: 0.7428 (tppt) cc_final: 0.7204 (tptt) REVERT: C 658 GLN cc_start: 0.7627 (pp30) cc_final: 0.6681 (tt0) REVERT: F 96 TRP cc_start: 0.8915 (m100) cc_final: 0.8579 (m100) REVERT: F 180 ASP cc_start: 0.7919 (m-30) cc_final: 0.7661 (m-30) REVERT: F 207 LYS cc_start: 0.8065 (mmtm) cc_final: 0.7831 (tttp) REVERT: F 377 ASN cc_start: 0.8855 (t0) cc_final: 0.8512 (t0) REVERT: F 423 ILE cc_start: 0.9526 (mm) cc_final: 0.9169 (mm) REVERT: B 577 GLN cc_start: 0.8669 (tt0) cc_final: 0.8353 (tm-30) REVERT: B 630 GLN cc_start: 0.8283 (pm20) cc_final: 0.8013 (pm20) REVERT: B 658 GLN cc_start: 0.7684 (pp30) cc_final: 0.6901 (tt0) REVERT: E 132 THR cc_start: 0.8167 (p) cc_final: 0.7952 (t) REVERT: E 188 ASN cc_start: 0.7164 (p0) cc_final: 0.6957 (p0) REVERT: E 232 THR cc_start: 0.7974 (m) cc_final: 0.7722 (t) REVERT: E 258 GLN cc_start: 0.8840 (mt0) cc_final: 0.8608 (mt0) REVERT: E 382 PHE cc_start: 0.8825 (m-80) cc_final: 0.8460 (m-10) REVERT: E 423 ILE cc_start: 0.9509 (mm) cc_final: 0.9237 (mm) REVERT: E 484 TYR cc_start: 0.8810 (p90) cc_final: 0.8438 (p90) REVERT: A 647 GLU cc_start: 0.7131 (tp30) cc_final: 0.6918 (tp30) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.1026 time to fit residues: 53.6635 Evaluate side-chains 267 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 156 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 183 GLN G 258 GLN G 377 ASN ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 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 = 0.3461 r_free = 0.3461 target = 0.132297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.120189 restraints weight = 21237.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.122266 restraints weight = 13885.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.123855 restraints weight = 10013.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.124906 restraints weight = 7693.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.125780 restraints weight = 6257.334| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14520 Z= 0.207 Angle : 0.690 9.113 19863 Z= 0.338 Chirality : 0.047 0.271 2421 Planarity : 0.004 0.069 2409 Dihedral : 5.550 52.398 3261 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: -0.97 (0.20), residues: 1623 helix: 0.39 (0.26), residues: 399 sheet: -0.93 (0.26), residues: 399 loop : -0.94 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 166 TYR 0.015 0.002 TYR F 217 PHE 0.020 0.003 PHE E 210 TRP 0.026 0.002 TRP E 35 HIS 0.005 0.001 HIS B 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (14412) covalent geometry : angle 0.64223 / 0.33 (19575) SS BOND : bond 0.00462 / 0.30 ( 36) SS BOND : angle 1.85026 / 1.26 ( 72) hydrogen bonds : bond 0.03526 / 2.35 ( 495) hydrogen bonds : angle 5.28243 / 3.65 ( 1386) link_ALPHA1-3 : bond 0.00769 / 0.39 ( 3) link_ALPHA1-3 : angle 1.52999 / 1.07 ( 9) link_BETA1-4 : bond 0.00261 / 0.14 ( 15) link_BETA1-4 : angle 1.89001 / 1.37 ( 45) link_NAG-ASN : bond 0.00394 / 0.25 ( 54) link_NAG-ASN : angle 2.41330 / 1.71 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 188 ASN cc_start: 0.7340 (p0) cc_final: 0.7116 (p0) REVERT: G 240 PRO cc_start: 0.8383 (Cg_endo) cc_final: 0.8180 (Cg_exo) REVERT: G 382 PHE cc_start: 0.8761 (m-80) cc_final: 0.8330 (m-10) REVERT: G 419 ARG cc_start: 0.8273 (mtm180) cc_final: 0.8049 (mtp85) REVERT: G 486 TYR cc_start: 0.8743 (m-80) cc_final: 0.8494 (m-10) REVERT: C 630 GLN cc_start: 0.8339 (pm20) cc_final: 0.7861 (pm20) REVERT: C 658 GLN cc_start: 0.7670 (pp30) cc_final: 0.6746 (tt0) REVERT: F 104 MET cc_start: 0.8902 (tpp) cc_final: 0.8498 (tpp) REVERT: F 125 LEU cc_start: 0.8958 (tp) cc_final: 0.8744 (tp) REVERT: F 132 THR cc_start: 0.8044 (p) cc_final: 0.7775 (t) REVERT: F 180 ASP cc_start: 0.8044 (m-30) cc_final: 0.7620 (m-30) REVERT: F 207 LYS cc_start: 0.8091 (mmtm) cc_final: 0.7845 (tttp) REVERT: F 377 ASN cc_start: 0.8868 (t0) cc_final: 0.8489 (t0) REVERT: F 423 ILE cc_start: 0.9529 (mm) cc_final: 0.9188 (mm) REVERT: B 577 GLN cc_start: 0.8699 (tt0) cc_final: 0.8369 (tm-30) REVERT: B 658 GLN cc_start: 0.7659 (pp30) cc_final: 0.6930 (tt0) REVERT: E 132 THR cc_start: 0.8239 (p) cc_final: 0.8036 (t) REVERT: E 188 ASN cc_start: 0.7337 (p0) cc_final: 0.7105 (p0) REVERT: E 232 THR cc_start: 0.8222 (m) cc_final: 0.8014 (t) REVERT: E 258 GLN cc_start: 0.8789 (mt0) cc_final: 0.8498 (mt0) REVERT: E 434 MET cc_start: 0.8535 (ttt) cc_final: 0.8115 (ttt) REVERT: E 484 TYR cc_start: 0.8851 (p90) cc_final: 0.8641 (p90) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.0986 time to fit residues: 50.1718 Evaluate side-chains 251 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 161 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 377 ASN C 585 HIS C 616 ASN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 GLN F 348 GLN F 422 GLN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.133572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.121400 restraints weight = 20948.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.123457 restraints weight = 13746.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.125043 restraints weight = 9958.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.126093 restraints weight = 7685.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.126980 restraints weight = 6263.185| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14520 Z= 0.166 Angle : 0.656 8.823 19863 Z= 0.322 Chirality : 0.046 0.269 2421 Planarity : 0.004 0.088 2409 Dihedral : 5.388 52.702 3261 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.07 % Allowed : 0.54 % Favored : 99.39 % 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: -0.86 (0.20), residues: 1623 helix: 0.26 (0.26), residues: 417 sheet: -0.69 (0.27), residues: 369 loop : -0.87 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 542 TYR 0.018 0.001 TYR F 217 PHE 0.019 0.002 PHE E 210 TRP 0.036 0.002 TRP E 35 HIS 0.005 0.001 HIS B 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (14412) covalent geometry : angle 0.61010 / 0.31 (19575) SS BOND : bond 0.00334 / 0.22 ( 36) SS BOND : angle 1.76391 / 1.19 ( 72) hydrogen bonds : bond 0.03432 / 2.30 ( 495) hydrogen bonds : angle 5.28935 / 3.65 ( 1386) link_ALPHA1-3 : bond 0.00921 / 0.46 ( 3) link_ALPHA1-3 : angle 1.59452 / 1.07 ( 9) link_BETA1-4 : bond 0.00274 / 0.16 ( 15) link_BETA1-4 : angle 1.67031 / 1.19 ( 45) link_NAG-ASN : bond 0.00339 / 0.21 ( 54) link_NAG-ASN : angle 2.33172 / 1.66 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3246 Ramachandran restraints generated. 1623 Oldfield, 0 Emsley, 1623 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 320 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 161 MET cc_start: 0.8004 (tpp) cc_final: 0.7298 (ttm) REVERT: G 188 ASN cc_start: 0.7477 (p0) cc_final: 0.7206 (p0) REVERT: G 382 PHE cc_start: 0.8669 (m-80) cc_final: 0.8275 (m-10) REVERT: G 419 ARG cc_start: 0.8254 (mtm180) cc_final: 0.8006 (mtp85) REVERT: G 486 TYR cc_start: 0.8761 (m-80) cc_final: 0.8425 (m-10) REVERT: C 628 TRP cc_start: 0.9288 (m100) cc_final: 0.8984 (m100) REVERT: C 658 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.6744 (tt0) REVERT: F 125 LEU cc_start: 0.8967 (tp) cc_final: 0.8762 (tp) REVERT: F 132 THR cc_start: 0.8068 (p) cc_final: 0.7770 (t) REVERT: F 180 ASP cc_start: 0.8045 (m-30) cc_final: 0.7638 (m-30) REVERT: F 207 LYS cc_start: 0.8119 (mmtm) cc_final: 0.7830 (tttp) REVERT: F 377 ASN cc_start: 0.8900 (t0) cc_final: 0.8538 (t0) REVERT: F 423 ILE cc_start: 0.9521 (mm) cc_final: 0.9217 (mm) REVERT: B 577 GLN cc_start: 0.8631 (tt0) cc_final: 0.8328 (tm-30) REVERT: B 658 GLN cc_start: 0.7734 (pp30) cc_final: 0.6977 (tt0) REVERT: E 132 THR cc_start: 0.8253 (p) cc_final: 0.8038 (t) REVERT: E 188 ASN cc_start: 0.7423 (p0) cc_final: 0.7165 (p0) REVERT: E 232 THR cc_start: 0.8229 (m) cc_final: 0.8021 (t) REVERT: E 258 GLN cc_start: 0.8802 (mt0) cc_final: 0.8549 (mt0) REVERT: E 264 SER cc_start: 0.9041 (p) cc_final: 0.8836 (p) REVERT: E 434 MET cc_start: 0.8637 (ttt) cc_final: 0.8201 (ttt) REVERT: E 484 TYR cc_start: 0.8874 (p90) cc_final: 0.8652 (p90) REVERT: A 628 TRP cc_start: 0.9203 (m100) cc_final: 0.8947 (m100) outliers start: 1 outliers final: 0 residues processed: 320 average time/residue: 0.0952 time to fit residues: 49.0147 Evaluate side-chains 257 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 256 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 143 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 37 optimal weight: 0.0170 chunk 149 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN ** C 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.133173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.120975 restraints weight = 21078.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.123155 restraints weight = 13791.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.124628 restraints weight = 9926.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.125818 restraints weight = 7691.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.126563 restraints weight = 6232.850| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.5401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14520 Z= 0.169 Angle : 0.650 8.569 19863 Z= 0.318 Chirality : 0.046 0.267 2421 Planarity : 0.004 0.086 2409 Dihedral : 5.293 53.135 3261 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % 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: -0.78 (0.21), residues: 1623 helix: 0.29 (0.26), residues: 417 sheet: -0.56 (0.27), residues: 363 loop : -0.85 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 419 TYR 0.018 0.002 TYR F 217 PHE 0.019 0.002 PHE E 210 TRP 0.035 0.002 TRP E 35 HIS 0.008 0.001 HIS C 585 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (14412) covalent geometry : angle 0.60611 / 0.31 (19575) SS BOND : bond 0.00385 / 0.27 ( 36) SS BOND : angle 1.73010 / 1.17 ( 72) hydrogen bonds : bond 0.03420 / 2.31 ( 495) hydrogen bonds : angle 5.31111 / 3.67 ( 1386) link_ALPHA1-3 : bond 0.00755 / 0.38 ( 3) link_ALPHA1-3 : angle 1.49187 / 1.00 ( 9) link_BETA1-4 : bond 0.00255 / 0.14 ( 15) link_BETA1-4 : angle 1.62956 / 1.15 ( 45) link_NAG-ASN : bond 0.00328 / 0.21 ( 54) link_NAG-ASN : angle 2.28766 / 1.62 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2348.05 seconds wall clock time: 41 minutes 40.15 seconds (2500.15 seconds total)