Starting phenix.real_space_refine on Wed Aug 5 20:30:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wh7_37532/08_2026/8wh7_37532.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wh7_37532/08_2026/8wh7_37532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wh7_37532/08_2026/8wh7_37532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wh7_37532/08_2026/8wh7_37532.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wh7_37532/08_2026/8wh7_37532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wh7_37532/08_2026/8wh7_37532.map" } resolution = 2.65 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= -0.002 sd= 0.306 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 54 5.16 5 C 7194 2.51 5 N 1926 2.21 5 O 2349 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: 11523 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3685 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3685 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3685 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" 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: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} 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 Time building chain proxies: 2.74, per 1000 atoms: 0.24 Number of scatterers: 11523 At special positions: 0 Unit cell: (93.74, 98.04, 145.34, 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 54 16.00 O 2349 8.00 N 1926 7.00 C 7194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 87 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 484 " distance=2.03 Simple disulfide: pdb=" SG CYS B 75 " - pdb=" SG CYS B 87 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 484 " distance=2.03 Simple disulfide: pdb=" SG CYS C 75 " - pdb=" SG CYS C 87 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 323 " distance=2.03 Simple disulfide: pdb=" SG CYS C 491 " - pdb=" SG CYS C 495 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-2 " BMA D 5 " - " BMA D 6 " " BMA F 5 " - " BMA F 6 " " BMA H 5 " - " BMA H 6 " BETA1-3 " BMA D 4 " - " BMA D 5 " " BMA F 4 " - " BMA F 5 " " BMA H 4 " - " BMA H 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " BETA1-6 " BMA D 3 " - " BMA D 4 " " BMA F 3 " - " BMA F 4 " " BMA H 3 " - " BMA H 4 " NAG-ASN " NAG A 601 " - " ASN A 35 " " NAG A 602 " - " ASN A 105 " " NAG A 603 " - " ASN A 203 " " NAG A 604 " - " ASN A 486 " " NAG B 601 " - " ASN B 35 " " NAG B 602 " - " ASN B 105 " " NAG B 603 " - " ASN B 203 " " NAG B 604 " - " ASN B 486 " " NAG C 601 " - " ASN C 35 " " NAG C 602 " - " ASN C 105 " " NAG C 603 " - " ASN C 203 " " NAG C 604 " - " ASN C 486 " " NAG D 1 " - " ASN A 124 " " NAG E 1 " - " ASN A 307 " " NAG F 1 " - " ASN B 124 " " NAG G 1 " - " ASN B 307 " " NAG H 1 " - " ASN C 124 " " NAG I 1 " - " ASN C 307 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 544.0 milliseconds 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2598 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 31 sheets defined 32.7% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 76 through 82 removed outlier: 3.507A pdb=" N HIS A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N HIS A 81 " --> pdb=" O ILE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.639A pdb=" N LEU A 92 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 127 removed outlier: 4.279A pdb=" N ILE A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TRP A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 removed outlier: 3.734A pdb=" N LEU A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 154 removed outlier: 4.025A pdb=" N GLY A 153 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 154 " --> pdb=" O SER A 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 150 through 154' Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 385 through 415 removed outlier: 3.805A pdb=" N ILE A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A 396 " --> pdb=" O VAL A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.595A pdb=" N LEU A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 474 removed outlier: 3.723A pdb=" N GLU A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 443 " --> pdb=" O PHE A 439 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE A 448 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS A 465 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A 468 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 472 " --> pdb=" O GLU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 502 removed outlier: 3.831A pdb=" N ILE A 499 " --> pdb=" O CYS A 495 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A 500 " --> pdb=" O VAL A 496 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 510 removed outlier: 3.882A pdb=" N ILE A 510 " --> pdb=" O GLU A 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 82 removed outlier: 3.923A pdb=" N HIS B 81 " --> pdb=" O ILE B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 92 removed outlier: 3.639A pdb=" N LEU B 92 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 127 removed outlier: 4.286A pdb=" N ILE B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N TRP B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 145 removed outlier: 3.735A pdb=" N LEU B 140 " --> pdb=" O PHE B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 154 removed outlier: 4.024A pdb=" N GLY B 153 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA B 154 " --> pdb=" O SER B 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 150 through 154' Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 229 through 237 Processing helix chain 'B' and resid 385 through 415 removed outlier: 3.796A pdb=" N ILE B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR B 396 " --> pdb=" O VAL B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 428 removed outlier: 3.604A pdb=" N LEU B 427 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 474 removed outlier: 3.721A pdb=" N GLU B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B 441 " --> pdb=" O GLU B 437 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE B 442 " --> pdb=" O THR B 438 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 443 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 444 " --> pdb=" O THR B 440 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE B 448 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 464 " --> pdb=" O ALA B 460 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS B 465 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU B 467 " --> pdb=" O SER B 463 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 469 " --> pdb=" O LYS B 465 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 472 " --> pdb=" O GLU B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 502 removed outlier: 3.839A pdb=" N ILE B 499 " --> pdb=" O CYS B 495 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 500 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG B 501 " --> pdb=" O ASN B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 removed outlier: 3.894A pdb=" N ILE B 510 " --> pdb=" O GLU B 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 82 removed outlier: 3.916A pdb=" N HIS C 81 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.630A pdb=" N LEU C 92 " --> pdb=" O PHE C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 127 removed outlier: 4.313A pdb=" N ILE C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TRP C 127 " --> pdb=" O MET C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 145 removed outlier: 3.728A pdb=" N LEU C 140 " --> pdb=" O PHE C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 154 removed outlier: 4.034A pdb=" N GLY C 153 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA C 154 " --> pdb=" O SER C 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 150 through 154' Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 229 through 237 Processing helix chain 'C' and resid 385 through 415 removed outlier: 3.793A pdb=" N ILE C 395 " --> pdb=" O ALA C 391 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR C 396 " --> pdb=" O VAL C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 428 removed outlier: 3.588A pdb=" N LEU C 427 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY C 428 " --> pdb=" O LEU C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 474 removed outlier: 3.718A pdb=" N GLU C 437 " --> pdb=" O ASP C 433 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU C 441 " --> pdb=" O GLU C 437 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE C 442 " --> pdb=" O THR C 438 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE C 443 " --> pdb=" O PHE C 439 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 444 " --> pdb=" O THR C 440 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE C 448 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS C 465 " --> pdb=" O ILE C 461 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS C 466 " --> pdb=" O GLY C 462 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU C 467 " --> pdb=" O SER C 463 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 472 " --> pdb=" O GLU C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 501 removed outlier: 3.766A pdb=" N ILE C 499 " --> pdb=" O CYS C 495 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER C 500 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG C 501 " --> pdb=" O ASN C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 510 removed outlier: 3.849A pdb=" N ILE C 510 " --> pdb=" O GLU C 507 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.178A pdb=" N ILE A 362 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LYS A 29 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.178A pdb=" N ILE A 362 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LYS A 29 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE A 25 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 486 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 478 " --> pdb=" O ASN A 486 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 36 through 39 Processing sheet with id=AA4, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.555A pdb=" N ILE A 313 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE A 312 " --> pdb=" O ILE A 327 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 61 through 62 removed outlier: 5.636A pdb=" N ILE A 61 " --> pdb=" O ASP A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 112 through 114 removed outlier: 3.842A pdb=" N THR A 182 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE A 277 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N TYR A 184 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR A 275 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA9, first strand: chain 'A' and resid 171 through 176 removed outlier: 4.538A pdb=" N ARG A 211 " --> pdb=" O SER A 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.612A pdb=" N GLY A 303 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.195A pdb=" N ILE B 362 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LYS B 29 " --> pdb=" O ILE B 362 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.195A pdb=" N ILE B 362 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LYS B 29 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 25 " --> pdb=" O PHE B 485 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 486 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU B 478 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 36 through 39 Processing sheet with id=AB5, first strand: chain 'B' and resid 50 through 52 Processing sheet with id=AB6, first strand: chain 'B' and resid 61 through 62 removed outlier: 5.627A pdb=" N ILE B 61 " --> pdb=" O ASP B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 112 through 114 removed outlier: 3.854A pdb=" N THR B 182 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE B 277 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TYR B 184 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR B 275 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AB9, first strand: chain 'B' and resid 171 through 176 removed outlier: 4.573A pdb=" N ARG B 211 " --> pdb=" O SER B 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 303 through 304 removed outlier: 3.610A pdb=" N GLY B 303 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 312 through 313 removed outlier: 6.161A pdb=" N ILE B 312 " --> pdb=" O ILE B 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.191A pdb=" N ILE C 362 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LYS C 29 " --> pdb=" O ILE C 362 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.191A pdb=" N ILE C 362 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LYS C 29 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE C 25 " --> pdb=" O PHE C 485 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN C 486 " --> pdb=" O LEU C 478 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU C 478 " --> pdb=" O ASN C 486 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 36 through 39 Processing sheet with id=AC6, first strand: chain 'C' and resid 50 through 52 Processing sheet with id=AC7, first strand: chain 'C' and resid 61 through 62 removed outlier: 5.629A pdb=" N ILE C 61 " --> pdb=" O ASP C 291 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 68 through 70 Processing sheet with id=AC9, first strand: chain 'C' and resid 112 through 114 removed outlier: 3.836A pdb=" N THR C 182 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE C 277 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TYR C 184 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR C 275 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AD2, first strand: chain 'C' and resid 171 through 176 removed outlier: 4.544A pdb=" N ARG C 211 " --> pdb=" O SER C 265 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 303 through 304 removed outlier: 3.627A pdb=" N GLY C 303 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 312 through 313 removed outlier: 6.194A pdb=" N ILE C 312 " --> pdb=" O ILE C 327 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 432 hydrogen bonds defined for protein. 1215 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: 2.20 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3717 1.34 - 1.46: 2789 1.46 - 1.58: 5158 1.58 - 1.70: 3 1.70 - 1.82: 72 Bond restraints: 11739 Sorted by residual: bond pdb=" C1 BMA D 5 " pdb=" C2 BMA D 5 " ideal model delta sigma weight residual 1.519 1.583 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C1 BMA H 5 " pdb=" C2 BMA H 5 " ideal model delta sigma weight residual 1.519 1.583 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C1 BMA F 5 " pdb=" C2 BMA F 5 " ideal model delta sigma weight residual 1.519 1.583 -0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C2 BMA D 5 " pdb=" O2 BMA D 5 " ideal model delta sigma weight residual 1.402 1.463 -0.061 2.00e-02 2.50e+03 9.39e+00 bond pdb=" C2 BMA F 5 " pdb=" O2 BMA F 5 " ideal model delta sigma weight residual 1.402 1.463 -0.061 2.00e-02 2.50e+03 9.39e+00 ... (remaining 11734 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 15185 1.35 - 2.70: 532 2.70 - 4.05: 121 4.05 - 5.40: 29 5.40 - 6.75: 24 Bond angle restraints: 15891 Sorted by residual: angle pdb=" N LYS A 379 " pdb=" CA LYS A 379 " pdb=" C LYS A 379 " ideal model delta sigma weight residual 114.75 111.39 3.36 1.26e+00 6.30e-01 7.10e+00 angle pdb=" N LYS B 379 " pdb=" CA LYS B 379 " pdb=" C LYS B 379 " ideal model delta sigma weight residual 114.75 111.40 3.35 1.26e+00 6.30e-01 7.07e+00 angle pdb=" C3 BMA H 3 " pdb=" C2 BMA H 3 " pdb=" O2 BMA H 3 " ideal model delta sigma weight residual 112.95 106.20 6.75 3.00e+00 1.11e-01 5.06e+00 angle pdb=" C3 BMA D 3 " pdb=" C2 BMA D 3 " pdb=" O2 BMA D 3 " ideal model delta sigma weight residual 112.95 106.21 6.74 3.00e+00 1.11e-01 5.05e+00 angle pdb=" C3 BMA F 3 " pdb=" C2 BMA F 3 " pdb=" O2 BMA F 3 " ideal model delta sigma weight residual 112.95 106.23 6.72 3.00e+00 1.11e-01 5.02e+00 ... (remaining 15886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.45: 6800 22.45 - 44.91: 505 44.91 - 67.36: 27 67.36 - 89.81: 78 89.81 - 112.27: 45 Dihedral angle restraints: 7455 sinusoidal: 3375 harmonic: 4080 Sorted by residual: dihedral pdb=" O4 BMA D 5 " pdb=" C4 BMA D 5 " pdb=" C5 BMA D 5 " pdb=" O5 BMA D 5 " ideal model delta sinusoidal sigma weight residual 288.71 176.44 112.27 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" O4 BMA H 5 " pdb=" C4 BMA H 5 " pdb=" C5 BMA H 5 " pdb=" O5 BMA H 5 " ideal model delta sinusoidal sigma weight residual 288.71 176.73 111.98 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" O4 BMA F 5 " pdb=" C4 BMA F 5 " pdb=" C5 BMA F 5 " pdb=" O5 BMA F 5 " ideal model delta sinusoidal sigma weight residual 288.71 176.73 111.98 1 3.00e+01 1.11e-03 1.47e+01 ... (remaining 7452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1712 0.088 - 0.176: 154 0.176 - 0.264: 10 0.264 - 0.352: 5 0.352 - 0.439: 3 Chirality restraints: 1884 Sorted by residual: chirality pdb=" C1 NAG C 604 " pdb=" ND2 ASN C 486 " pdb=" C2 NAG C 604 " pdb=" O5 NAG C 604 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" C1 NAG B 604 " pdb=" ND2 ASN B 486 " pdb=" C2 NAG B 604 " pdb=" O5 NAG B 604 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" C1 NAG A 604 " pdb=" ND2 ASN A 486 " pdb=" C2 NAG A 604 " pdb=" O5 NAG A 604 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.76e+00 ... (remaining 1881 not shown) Planarity restraints: 2019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 324 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO C 325 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 325 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 325 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 324 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO B 325 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 325 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 325 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 324 " 0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO A 325 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 325 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 325 " 0.022 5.00e-02 4.00e+02 ... (remaining 2016 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2390 2.78 - 3.31: 9640 3.31 - 3.84: 16741 3.84 - 4.37: 18983 4.37 - 4.90: 34551 Nonbonded interactions: 82305 Sorted by model distance: nonbonded pdb=" OE2 GLU A 422 " pdb=" ND2 ASN A 426 " model vdw 2.251 3.120 nonbonded pdb=" OE2 GLU C 422 " pdb=" ND2 ASN C 426 " model vdw 2.256 3.120 nonbonded pdb=" OE2 GLU B 422 " pdb=" ND2 ASN B 426 " model vdw 2.258 3.120 nonbonded pdb=" O CYS C 495 " pdb=" OG SER C 498 " model vdw 2.314 3.040 nonbonded pdb=" NZ LYS C 470 " pdb=" OD2 ASP C 479 " model vdw 2.317 3.120 ... (remaining 82300 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.480 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.550 Find NCS groups from input model: 0.110 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:8.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5710 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 : 0.004 0.064 11790 Z= 0.199 Angle : 0.678 7.165 16029 Z= 0.315 Chirality : 0.053 0.439 1884 Planarity : 0.003 0.041 2001 Dihedral : 19.133 112.265 4812 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.70 (0.22), residues: 1425 helix: 2.26 (0.29), residues: 357 sheet: 0.27 (0.35), residues: 231 loop : -2.06 (0.18), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 501 TYR 0.006 0.001 TYR A 509 PHE 0.011 0.001 PHE B 282 TRP 0.012 0.001 TRP B 208 HIS 0.002 0.000 HIS C 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.20 (11739) covalent geometry : angle 0.65069 / 0.31 (15891) SS BOND : bond 0.00161 / 0.09 ( 15) SS BOND : angle 1.24171 / 0.87 ( 30) hydrogen bonds : bond 0.19092 / 13.47 ( 396) hydrogen bonds : angle 5.74247 / 3.97 ( 1215) link_BETA1-2 : bond 0.00589 / 0.30 ( 3) link_BETA1-2 : angle 4.39519 / 3.00 ( 9) link_BETA1-3 : bond 0.00598 / 0.30 ( 3) link_BETA1-3 : angle 3.76030 / 2.60 ( 9) link_BETA1-4 : bond 0.00457 / 0.27 ( 9) link_BETA1-4 : angle 1.69539 / 1.14 ( 27) link_BETA1-6 : bond 0.01452 / 0.73 ( 3) link_BETA1-6 : angle 0.76137 / 0.55 ( 9) link_NAG-ASN : bond 0.00387 / 0.27 ( 18) link_NAG-ASN : angle 2.00083 / 1.36 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.5972 (pttm) cc_final: 0.5680 (pttm) REVERT: A 67 GLN cc_start: 0.6150 (mt0) cc_final: 0.5416 (pt0) REVERT: A 85 GLU cc_start: 0.5991 (tp30) cc_final: 0.5076 (tm-30) REVERT: A 174 GLU cc_start: 0.6289 (mt-10) cc_final: 0.5761 (mt-10) REVERT: A 209 ASP cc_start: 0.5984 (m-30) cc_final: 0.5577 (m-30) REVERT: A 217 GLU cc_start: 0.4596 (tm-30) cc_final: 0.4381 (tm-30) REVERT: A 291 ASP cc_start: 0.6369 (t0) cc_final: 0.5923 (t0) REVERT: A 408 GLN cc_start: 0.4166 (mt0) cc_final: 0.3764 (tp40) REVERT: A 437 GLU cc_start: 0.5118 (mm-30) cc_final: 0.4091 (tm-30) REVERT: B 60 LYS cc_start: 0.6087 (pttt) cc_final: 0.5864 (pttm) REVERT: B 85 GLU cc_start: 0.6413 (tp30) cc_final: 0.5487 (tm-30) REVERT: B 174 GLU cc_start: 0.6143 (mt-10) cc_final: 0.5766 (mt-10) REVERT: B 209 ASP cc_start: 0.5927 (m-30) cc_final: 0.5504 (m-30) REVERT: B 232 GLU cc_start: 0.4959 (tt0) cc_final: 0.4580 (tt0) REVERT: B 260 GLU cc_start: 0.6888 (mp0) cc_final: 0.6531 (mp0) REVERT: B 291 ASP cc_start: 0.6541 (t0) cc_final: 0.6248 (t0) REVERT: B 408 GLN cc_start: 0.4103 (mt0) cc_final: 0.3751 (tp40) REVERT: C 60 LYS cc_start: 0.6412 (pttt) cc_final: 0.6188 (pttm) REVERT: C 67 GLN cc_start: 0.6072 (mt0) cc_final: 0.5467 (pt0) REVERT: C 85 GLU cc_start: 0.6174 (tp30) cc_final: 0.5208 (tm-30) REVERT: C 146 GLU cc_start: 0.6544 (mm-30) cc_final: 0.6290 (mm-30) REVERT: C 174 GLU cc_start: 0.6408 (mt-10) cc_final: 0.6172 (mt-10) REVERT: C 209 ASP cc_start: 0.6213 (m-30) cc_final: 0.5855 (m-30) REVERT: C 232 GLU cc_start: 0.4855 (tt0) cc_final: 0.4109 (mt-10) REVERT: C 291 ASP cc_start: 0.6432 (t0) cc_final: 0.5930 (t0) REVERT: C 408 GLN cc_start: 0.4559 (mt0) cc_final: 0.4157 (tp40) REVERT: C 437 GLU cc_start: 0.5039 (mm-30) cc_final: 0.4009 (tm-30) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.5294 time to fit residues: 96.5108 Evaluate side-chains 133 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 72.8943 > 50:) chunk 55 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.174386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.132892 restraints weight = 10015.570| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.63 r_work: 0.3102 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11790 Z= 0.228 Angle : 0.807 10.205 16029 Z= 0.413 Chirality : 0.057 0.436 1884 Planarity : 0.005 0.048 2001 Dihedral : 15.608 86.421 2268 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.23 % Allowed : 6.62 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.21), residues: 1425 helix: 1.60 (0.28), residues: 378 sheet: 1.57 (0.38), residues: 168 loop : -2.03 (0.18), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 202 TYR 0.017 0.002 TYR A 185 PHE 0.023 0.003 PHE B 111 TRP 0.015 0.002 TRP B 208 HIS 0.005 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.23 (11739) covalent geometry : angle 0.75979 / 0.40 (15891) SS BOND : bond 0.00440 / 0.26 ( 15) SS BOND : angle 1.45749 / 0.98 ( 30) hydrogen bonds : bond 0.09322 / 6.35 ( 396) hydrogen bonds : angle 4.81635 / 3.42 ( 1215) link_BETA1-2 : bond 0.00502 / 0.25 ( 3) link_BETA1-2 : angle 5.72482 / 3.92 ( 9) link_BETA1-3 : bond 0.00464 / 0.23 ( 3) link_BETA1-3 : angle 6.12017 / 4.21 ( 9) link_BETA1-4 : bond 0.01060 / 0.61 ( 9) link_BETA1-4 : angle 3.21347 / 2.13 ( 27) link_BETA1-6 : bond 0.00955 / 0.48 ( 3) link_BETA1-6 : angle 1.83696 / 1.26 ( 9) link_NAG-ASN : bond 0.00866 / 0.55 ( 18) link_NAG-ASN : angle 2.19937 / 1.52 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8244 (mt0) cc_final: 0.7606 (pt0) REVERT: A 209 ASP cc_start: 0.8755 (m-30) cc_final: 0.8462 (m-30) REVERT: A 404 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7799 (tm-30) REVERT: A 408 GLN cc_start: 0.8349 (mt0) cc_final: 0.7991 (tp40) REVERT: A 456 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: A 459 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7614 (tt0) REVERT: B 85 GLU cc_start: 0.7917 (tp30) cc_final: 0.7388 (tm-30) REVERT: B 209 ASP cc_start: 0.8695 (m-30) cc_final: 0.8381 (m-30) REVERT: B 291 ASP cc_start: 0.7798 (t0) cc_final: 0.7571 (t0) REVERT: B 404 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7993 (tm-30) REVERT: B 408 GLN cc_start: 0.8329 (mt0) cc_final: 0.7949 (tp40) REVERT: B 456 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: C 67 GLN cc_start: 0.8312 (mt0) cc_final: 0.7736 (pt0) REVERT: C 213 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8352 (m) REVERT: C 291 ASP cc_start: 0.7927 (t0) cc_final: 0.7693 (t0) REVERT: C 404 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7736 (tm-30) REVERT: C 408 GLN cc_start: 0.8402 (mt0) cc_final: 0.8080 (tp40) REVERT: C 437 GLU cc_start: 0.8490 (mm-30) cc_final: 0.7987 (tm-30) REVERT: C 456 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7690 (tm-30) outliers start: 27 outliers final: 14 residues processed: 144 average time/residue: 0.4908 time to fit residues: 76.4930 Evaluate side-chains 140 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 459 GLN Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 456 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 31 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.177879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.139732 restraints weight = 10209.371| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.00 r_work: 0.3165 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11790 Z= 0.169 Angle : 0.701 9.832 16029 Z= 0.350 Chirality : 0.054 0.418 1884 Planarity : 0.004 0.047 2001 Dihedral : 12.821 73.151 2268 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.73 % Allowed : 9.76 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.70 (0.21), residues: 1425 helix: 1.72 (0.28), residues: 381 sheet: 1.33 (0.37), residues: 180 loop : -2.05 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 202 TYR 0.012 0.002 TYR A 185 PHE 0.017 0.002 PHE B 282 TRP 0.011 0.001 TRP B 208 HIS 0.003 0.001 HIS B 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.17 (11739) covalent geometry : angle 0.64844 / 0.34 (15891) SS BOND : bond 0.00422 / 0.25 ( 15) SS BOND : angle 1.21131 / 0.83 ( 30) hydrogen bonds : bond 0.07346 / 5.00 ( 396) hydrogen bonds : angle 4.59565 / 3.27 ( 1215) link_BETA1-2 : bond 0.00715 / 0.36 ( 3) link_BETA1-2 : angle 6.62340 / 4.65 ( 9) link_BETA1-3 : bond 0.00039 / 0.02 ( 3) link_BETA1-3 : angle 6.04021 / 4.23 ( 9) link_BETA1-4 : bond 0.00831 / 0.47 ( 9) link_BETA1-4 : angle 2.94906 / 1.96 ( 27) link_BETA1-6 : bond 0.00974 / 0.49 ( 3) link_BETA1-6 : angle 1.29355 / 0.96 ( 9) link_NAG-ASN : bond 0.00723 / 0.46 ( 18) link_NAG-ASN : angle 1.86853 / 1.29 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8182 (mt0) cc_final: 0.7475 (pt0) REVERT: A 209 ASP cc_start: 0.8695 (m-30) cc_final: 0.8426 (m-30) REVERT: A 404 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: A 408 GLN cc_start: 0.8109 (mt0) cc_final: 0.7836 (tp40) REVERT: A 456 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7501 (tm-30) REVERT: B 404 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7997 (tm-30) REVERT: B 408 GLN cc_start: 0.8137 (mt0) cc_final: 0.7876 (tp40) REVERT: B 456 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: C 67 GLN cc_start: 0.8293 (mt0) cc_final: 0.7598 (pt0) REVERT: C 213 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8337 (m) REVERT: C 332 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8323 (m-30) REVERT: C 404 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: C 408 GLN cc_start: 0.8169 (mt0) cc_final: 0.7936 (tp40) REVERT: C 437 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7979 (tm-30) REVERT: C 456 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7529 (tm-30) outliers start: 33 outliers final: 17 residues processed: 144 average time/residue: 0.4858 time to fit residues: 76.0739 Evaluate side-chains 141 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 456 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 97 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.168825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.128948 restraints weight = 9956.821| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.01 r_work: 0.3042 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 11790 Z= 0.367 Angle : 1.091 12.516 16029 Z= 0.563 Chirality : 0.070 0.540 1884 Planarity : 0.007 0.075 2001 Dihedral : 14.978 85.365 2268 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.39 % Allowed : 10.67 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.20), residues: 1425 helix: 0.82 (0.27), residues: 381 sheet: 0.84 (0.41), residues: 171 loop : -2.21 (0.16), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 202 TYR 0.032 0.005 TYR C 185 PHE 0.029 0.005 PHE B 111 TRP 0.017 0.003 TRP C 127 HIS 0.009 0.002 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00762 / 0.37 (11739) covalent geometry : angle 1.03803 / 0.55 (15891) SS BOND : bond 0.00966 / 0.57 ( 15) SS BOND : angle 2.00540 / 1.32 ( 30) hydrogen bonds : bond 0.12937 / 8.82 ( 396) hydrogen bonds : angle 4.98644 / 3.55 ( 1215) link_BETA1-2 : bond 0.00111 / 0.06 ( 3) link_BETA1-2 : angle 6.54840 / 4.51 ( 9) link_BETA1-3 : bond 0.00269 / 0.13 ( 3) link_BETA1-3 : angle 6.02129 / 4.19 ( 9) link_BETA1-4 : bond 0.01325 / 0.76 ( 9) link_BETA1-4 : angle 4.51999 / 3.01 ( 27) link_BETA1-6 : bond 0.01002 / 0.50 ( 3) link_BETA1-6 : angle 3.04071 / 2.17 ( 9) link_NAG-ASN : bond 0.01140 / 0.70 ( 18) link_NAG-ASN : angle 3.00685 / 2.10 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7637 (tm-30) REVERT: A 408 GLN cc_start: 0.8420 (mt0) cc_final: 0.8053 (tp40) REVERT: A 456 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7607 (tm-30) REVERT: B 408 GLN cc_start: 0.8458 (mt0) cc_final: 0.8081 (tp40) REVERT: B 456 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7937 (tm-30) REVERT: C 230 MET cc_start: 0.8548 (tpt) cc_final: 0.8201 (tpt) REVERT: C 404 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: C 408 GLN cc_start: 0.8458 (mt0) cc_final: 0.8080 (tp40) REVERT: C 416 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7751 (tp) REVERT: C 422 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8379 (tt0) REVERT: C 456 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7705 (tm-30) outliers start: 41 outliers final: 26 residues processed: 145 average time/residue: 0.5250 time to fit residues: 82.3059 Evaluate side-chains 143 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 456 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 73 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 112 optimal weight: 0.4980 chunk 86 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 78 optimal weight: 0.2980 chunk 84 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.182240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.142058 restraints weight = 10583.464| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.59 r_work: 0.3266 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11790 Z= 0.202 Angle : 0.784 10.548 16029 Z= 0.392 Chirality : 0.057 0.443 1884 Planarity : 0.005 0.051 2001 Dihedral : 12.858 74.554 2268 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.06 % Allowed : 13.23 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.21), residues: 1425 helix: 1.26 (0.28), residues: 381 sheet: 1.35 (0.36), residues: 177 loop : -2.20 (0.17), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 202 TYR 0.014 0.002 TYR A 185 PHE 0.018 0.002 PHE C 113 TRP 0.012 0.002 TRP B 208 HIS 0.005 0.001 HIS C 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.20 (11739) covalent geometry : angle 0.72726 / 0.38 (15891) SS BOND : bond 0.00464 / 0.27 ( 15) SS BOND : angle 1.19575 / 0.81 ( 30) hydrogen bonds : bond 0.08666 / 5.90 ( 396) hydrogen bonds : angle 4.72820 / 3.37 ( 1215) link_BETA1-2 : bond 0.00742 / 0.37 ( 3) link_BETA1-2 : angle 7.16548 / 5.03 ( 9) link_BETA1-3 : bond 0.00241 / 0.12 ( 3) link_BETA1-3 : angle 6.29493 / 4.37 ( 9) link_BETA1-4 : bond 0.00991 / 0.56 ( 9) link_BETA1-4 : angle 3.37569 / 2.29 ( 27) link_BETA1-6 : bond 0.00885 / 0.44 ( 3) link_BETA1-6 : angle 1.52964 / 1.09 ( 9) link_NAG-ASN : bond 0.00828 / 0.51 ( 18) link_NAG-ASN : angle 2.16083 / 1.50 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: A 408 GLN cc_start: 0.8166 (mt0) cc_final: 0.7876 (tp40) REVERT: A 456 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7580 (tm-30) REVERT: B 260 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.7756 (mp0) REVERT: B 408 GLN cc_start: 0.8150 (mt0) cc_final: 0.7849 (tp40) REVERT: B 456 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8031 (tm-30) REVERT: B 459 GLN cc_start: 0.8165 (mt0) cc_final: 0.7916 (mt0) REVERT: C 332 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8397 (m-30) REVERT: C 404 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: C 408 GLN cc_start: 0.8185 (mt0) cc_final: 0.7896 (tp40) REVERT: C 416 LEU cc_start: 0.7970 (mt) cc_final: 0.7731 (tp) REVERT: C 456 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7587 (tm-30) outliers start: 37 outliers final: 25 residues processed: 138 average time/residue: 0.4896 time to fit residues: 73.5040 Evaluate side-chains 142 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 456 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 85 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 38 optimal weight: 0.0670 chunk 47 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 11 optimal weight: 0.0030 overall best weight: 0.5330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.189030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.150690 restraints weight = 10756.820| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.65 r_work: 0.3416 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11790 Z= 0.132 Angle : 0.626 11.578 16029 Z= 0.307 Chirality : 0.051 0.477 1884 Planarity : 0.004 0.045 2001 Dihedral : 10.313 61.623 2268 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.48 % Allowed : 14.31 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.72 (0.21), residues: 1425 helix: 1.71 (0.29), residues: 381 sheet: 1.19 (0.35), residues: 195 loop : -2.10 (0.18), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 202 TYR 0.008 0.001 TYR A 185 PHE 0.014 0.001 PHE B 113 TRP 0.010 0.001 TRP B 208 HIS 0.003 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 (11739) covalent geometry : angle 0.56736 / 0.29 (15891) SS BOND : bond 0.00249 / 0.15 ( 15) SS BOND : angle 0.72581 / 0.50 ( 30) hydrogen bonds : bond 0.05823 / 3.95 ( 396) hydrogen bonds : angle 4.45278 / 3.18 ( 1215) link_BETA1-2 : bond 0.00942 / 0.47 ( 3) link_BETA1-2 : angle 7.60211 / 5.36 ( 9) link_BETA1-3 : bond 0.00079 / 0.04 ( 3) link_BETA1-3 : angle 6.02702 / 4.16 ( 9) link_BETA1-4 : bond 0.00734 / 0.42 ( 9) link_BETA1-4 : angle 2.43240 / 1.63 ( 27) link_BETA1-6 : bond 0.00889 / 0.44 ( 3) link_BETA1-6 : angle 1.26709 / 0.97 ( 9) link_NAG-ASN : bond 0.00582 / 0.37 ( 18) link_NAG-ASN : angle 1.53668 / 1.05 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.8554 (m-30) cc_final: 0.8320 (m-30) REVERT: A 404 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7656 (tm-30) REVERT: A 456 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7445 (tm-30) REVERT: B 209 ASP cc_start: 0.8598 (m-30) cc_final: 0.8396 (m-30) REVERT: B 404 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: C 404 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: C 422 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8184 (tt0) REVERT: C 456 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7483 (tm-30) outliers start: 30 outliers final: 17 residues processed: 144 average time/residue: 0.4300 time to fit residues: 67.4942 Evaluate side-chains 135 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 456 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 92 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 76 optimal weight: 0.1980 chunk 125 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 126 optimal weight: 0.3980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.186776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.148172 restraints weight = 10586.976| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.48 r_work: 0.3324 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11790 Z= 0.158 Angle : 0.673 11.599 16029 Z= 0.334 Chirality : 0.053 0.480 1884 Planarity : 0.004 0.045 2001 Dihedral : 10.195 62.439 2268 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.40 % Allowed : 15.38 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.73 (0.21), residues: 1425 helix: 1.71 (0.28), residues: 384 sheet: 1.16 (0.35), residues: 195 loop : -2.10 (0.18), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 202 TYR 0.010 0.002 TYR A 185 PHE 0.015 0.002 PHE C 113 TRP 0.011 0.001 TRP A 208 HIS 0.003 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (11739) covalent geometry : angle 0.61806 / 0.32 (15891) SS BOND : bond 0.00320 / 0.19 ( 15) SS BOND : angle 0.86876 / 0.59 ( 30) hydrogen bonds : bond 0.06766 / 4.59 ( 396) hydrogen bonds : angle 4.47994 / 3.19 ( 1215) link_BETA1-2 : bond 0.00848 / 0.42 ( 3) link_BETA1-2 : angle 7.55897 / 5.31 ( 9) link_BETA1-3 : bond 0.00145 / 0.07 ( 3) link_BETA1-3 : angle 5.61867 / 3.86 ( 9) link_BETA1-4 : bond 0.00847 / 0.47 ( 9) link_BETA1-4 : angle 2.69706 / 1.81 ( 27) link_BETA1-6 : bond 0.00981 / 0.49 ( 3) link_BETA1-6 : angle 1.40677 / 1.04 ( 9) link_NAG-ASN : bond 0.00685 / 0.43 ( 18) link_NAG-ASN : angle 1.74031 / 1.20 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.8699 (m-30) cc_final: 0.8417 (m-30) REVERT: A 404 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7708 (tm-30) REVERT: A 456 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: B 297 ASP cc_start: 0.8016 (p0) cc_final: 0.7785 (p0) REVERT: C 332 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8338 (m-30) REVERT: C 404 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: C 422 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: C 456 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7537 (tm-30) outliers start: 29 outliers final: 20 residues processed: 132 average time/residue: 0.4259 time to fit residues: 61.9231 Evaluate side-chains 136 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 456 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 31 optimal weight: 4.9990 chunk 24 optimal weight: 0.0040 chunk 34 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 48 optimal weight: 0.1980 chunk 119 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.187107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.148608 restraints weight = 10570.427| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.65 r_work: 0.3416 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11790 Z= 0.154 Angle : 0.665 11.962 16029 Z= 0.330 Chirality : 0.052 0.496 1884 Planarity : 0.004 0.044 2001 Dihedral : 9.622 59.217 2268 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.81 % Allowed : 15.05 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.68 (0.21), residues: 1425 helix: 1.77 (0.28), residues: 384 sheet: 1.24 (0.35), residues: 195 loop : -2.10 (0.18), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 202 TYR 0.009 0.002 TYR A 185 PHE 0.014 0.002 PHE B 282 TRP 0.011 0.001 TRP B 208 HIS 0.003 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (11739) covalent geometry : angle 0.60921 / 0.32 (15891) SS BOND : bond 0.00303 / 0.18 ( 15) SS BOND : angle 0.85289 / 0.58 ( 30) hydrogen bonds : bond 0.06608 / 4.48 ( 396) hydrogen bonds : angle 4.46645 / 3.19 ( 1215) link_BETA1-2 : bond 0.00847 / 0.42 ( 3) link_BETA1-2 : angle 7.75262 / 5.44 ( 9) link_BETA1-3 : bond 0.00158 / 0.08 ( 3) link_BETA1-3 : angle 5.30952 / 3.63 ( 9) link_BETA1-4 : bond 0.00813 / 0.46 ( 9) link_BETA1-4 : angle 2.61829 / 1.76 ( 27) link_BETA1-6 : bond 0.01051 / 0.53 ( 3) link_BETA1-6 : angle 1.44300 / 1.08 ( 9) link_NAG-ASN : bond 0.00679 / 0.42 ( 18) link_NAG-ASN : angle 1.75480 / 1.20 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 114 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.8692 (m-30) cc_final: 0.8395 (m-30) REVERT: A 456 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7541 (tm-30) REVERT: C 332 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8334 (m-30) REVERT: C 456 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: C 467 GLU cc_start: 0.6209 (tp30) cc_final: 0.5997 (pt0) outliers start: 34 outliers final: 26 residues processed: 140 average time/residue: 0.4544 time to fit residues: 69.8396 Evaluate side-chains 143 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 456 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 9 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.176946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.137677 restraints weight = 10350.690| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.85 r_work: 0.3209 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 11790 Z= 0.338 Angle : 1.032 11.972 16029 Z= 0.530 Chirality : 0.068 0.497 1884 Planarity : 0.007 0.074 2001 Dihedral : 12.859 78.223 2268 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.64 % Allowed : 14.72 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.20), residues: 1425 helix: 1.01 (0.28), residues: 384 sheet: 1.61 (0.40), residues: 153 loop : -2.17 (0.16), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 202 TYR 0.030 0.004 TYR C 185 PHE 0.026 0.004 PHE B 111 TRP 0.016 0.003 TRP A 127 HIS 0.007 0.002 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.34 (11739) covalent geometry : angle 0.97917 / 0.52 (15891) SS BOND : bond 0.00840 / 0.50 ( 15) SS BOND : angle 1.76737 / 1.15 ( 30) hydrogen bonds : bond 0.11964 / 8.14 ( 396) hydrogen bonds : angle 4.86851 / 3.47 ( 1215) link_BETA1-2 : bond 0.00277 / 0.14 ( 3) link_BETA1-2 : angle 7.64040 / 5.34 ( 9) link_BETA1-3 : bond 0.00728 / 0.36 ( 3) link_BETA1-3 : angle 5.10180 / 3.55 ( 9) link_BETA1-4 : bond 0.01080 / 0.60 ( 9) link_BETA1-4 : angle 4.11334 / 2.76 ( 27) link_BETA1-6 : bond 0.01041 / 0.52 ( 3) link_BETA1-6 : angle 3.26628 / 2.30 ( 9) link_NAG-ASN : bond 0.01035 / 0.64 ( 18) link_NAG-ASN : angle 2.81669 / 1.96 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 110 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7753 (mt0) REVERT: A 260 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: A 456 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: B 456 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8046 (tp30) REVERT: C 230 MET cc_start: 0.8506 (tpt) cc_final: 0.8205 (tpt) REVERT: C 404 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: C 456 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7589 (tm-30) REVERT: C 467 GLU cc_start: 0.6091 (tp30) cc_final: 0.5782 (pt0) outliers start: 44 outliers final: 30 residues processed: 137 average time/residue: 0.5543 time to fit residues: 82.5823 Evaluate side-chains 146 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 456 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 0.1980 chunk 114 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 31 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.185525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.146630 restraints weight = 10576.568| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.56 r_work: 0.3372 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11790 Z= 0.160 Angle : 0.694 11.991 16029 Z= 0.344 Chirality : 0.053 0.498 1884 Planarity : 0.004 0.047 2001 Dihedral : 11.013 66.745 2268 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.32 % Allowed : 15.96 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.21), residues: 1425 helix: 1.53 (0.28), residues: 384 sheet: 1.35 (0.36), residues: 195 loop : -2.21 (0.17), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 202 TYR 0.008 0.001 TYR A 410 PHE 0.014 0.002 PHE C 282 TRP 0.013 0.001 TRP B 208 HIS 0.003 0.001 HIS C 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.16 (11739) covalent geometry : angle 0.63709 / 0.33 (15891) SS BOND : bond 0.00276 / 0.16 ( 15) SS BOND : angle 0.97359 / 0.67 ( 30) hydrogen bonds : bond 0.07281 / 4.94 ( 396) hydrogen bonds : angle 4.61601 / 3.29 ( 1215) link_BETA1-2 : bond 0.00930 / 0.47 ( 3) link_BETA1-2 : angle 7.86686 / 5.52 ( 9) link_BETA1-3 : bond 0.00241 / 0.12 ( 3) link_BETA1-3 : angle 5.33081 / 3.65 ( 9) link_BETA1-4 : bond 0.00872 / 0.49 ( 9) link_BETA1-4 : angle 2.83197 / 1.91 ( 27) link_BETA1-6 : bond 0.00875 / 0.44 ( 3) link_BETA1-6 : angle 1.69864 / 1.24 ( 9) link_NAG-ASN : bond 0.00729 / 0.45 ( 18) link_NAG-ASN : angle 1.90418 / 1.30 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.8669 (m-30) cc_final: 0.8440 (m-30) REVERT: A 404 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7656 (tm-30) REVERT: A 456 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7579 (tm-30) REVERT: C 456 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7483 (tm-30) REVERT: C 467 GLU cc_start: 0.6085 (tp30) cc_final: 0.5846 (pt0) outliers start: 28 outliers final: 21 residues processed: 132 average time/residue: 0.4626 time to fit residues: 66.6227 Evaluate side-chains 137 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 456 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 65 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 0.4980 chunk 118 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.185663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.147005 restraints weight = 10611.081| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.53 r_work: 0.3389 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11790 Z= 0.162 Angle : 0.688 12.020 16029 Z= 0.342 Chirality : 0.053 0.490 1884 Planarity : 0.004 0.045 2001 Dihedral : 10.134 62.306 2268 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.40 % Allowed : 15.72 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.76 (0.21), residues: 1425 helix: 1.66 (0.28), residues: 384 sheet: 1.32 (0.36), residues: 195 loop : -2.17 (0.17), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 202 TYR 0.009 0.002 TYR A 185 PHE 0.015 0.002 PHE B 113 TRP 0.011 0.001 TRP B 208 HIS 0.003 0.001 HIS A 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 (11739) covalent geometry : angle 0.63206 / 0.33 (15891) SS BOND : bond 0.00362 / 0.20 ( 15) SS BOND : angle 1.06429 / 0.71 ( 30) hydrogen bonds : bond 0.07036 / 4.77 ( 396) hydrogen bonds : angle 4.53620 / 3.24 ( 1215) link_BETA1-2 : bond 0.00821 / 0.41 ( 3) link_BETA1-2 : angle 7.85320 / 5.51 ( 9) link_BETA1-3 : bond 0.00230 / 0.11 ( 3) link_BETA1-3 : angle 5.23741 / 3.58 ( 9) link_BETA1-4 : bond 0.00829 / 0.47 ( 9) link_BETA1-4 : angle 2.71543 / 1.83 ( 27) link_BETA1-6 : bond 0.00896 / 0.45 ( 3) link_BETA1-6 : angle 1.73386 / 1.28 ( 9) link_NAG-ASN : bond 0.00694 / 0.44 ( 18) link_NAG-ASN : angle 1.83970 / 1.26 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3707.09 seconds wall clock time: 63 minutes 44.59 seconds (3824.59 seconds total)