Starting phenix.real_space_refine on Tue Jun 10 12:13:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wh7_37532/06_2025/8wh7_37532.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wh7_37532/06_2025/8wh7_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wh7_37532/06_2025/8wh7_37532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wh7_37532/06_2025/8wh7_37532.map" model { file = "/net/cci-nas-00/data/ceres_data/8wh7_37532/06_2025/8wh7_37532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wh7_37532/06_2025/8wh7_37532.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.99, per 1000 atoms: 0.61 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: 2.78 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.45 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: 3.53 Time building geometry restraints manager: 3.29 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: 0.07 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 27.260 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 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:10.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5436 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (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 TRP 0.012 0.001 TRP B 208 HIS 0.002 0.000 HIS C 489 PHE 0.011 0.001 PHE B 282 TYR 0.006 0.001 TYR A 509 ARG 0.006 0.000 ARG C 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 18) link_NAG-ASN : angle 2.00083 ( 54) link_BETA1-2 : bond 0.00589 ( 3) link_BETA1-2 : angle 4.39519 ( 9) link_BETA1-4 : bond 0.00457 ( 9) link_BETA1-4 : angle 1.69539 ( 27) hydrogen bonds : bond 0.19092 ( 396) hydrogen bonds : angle 5.74247 ( 1215) link_BETA1-6 : bond 0.01452 ( 3) link_BETA1-6 : angle 0.76137 ( 9) SS BOND : bond 0.00161 ( 15) SS BOND : angle 1.24171 ( 30) link_BETA1-3 : bond 0.00598 ( 3) link_BETA1-3 : angle 3.76030 ( 9) covalent geometry : bond 0.00415 (11739) covalent geometry : angle 0.65069 (15891) *********************** 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 : 1.290 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: 1.3122 time to fit residues: 239.0283 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 : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 chunk 36 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 57 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 128 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.182737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.144127 restraints weight = 10086.892| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.32 r_work: 0.3225 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1111 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= 0.140 Angle : 0.638 9.358 16029 Z= 0.315 Chirality : 0.051 0.424 1884 Planarity : 0.004 0.042 2001 Dihedral : 14.802 81.076 2268 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.41 % Allowed : 6.70 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.22), residues: 1425 helix: 2.00 (0.29), residues: 378 sheet: 0.40 (0.35), residues: 231 loop : -2.00 (0.19), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 208 HIS 0.002 0.001 HIS A 489 PHE 0.017 0.002 PHE B 282 TYR 0.009 0.001 TYR B 160 ARG 0.003 0.000 ARG C 501 Details of bonding type rmsd link_NAG-ASN : bond 0.00578 ( 18) link_NAG-ASN : angle 1.70514 ( 54) link_BETA1-2 : bond 0.00632 ( 3) link_BETA1-2 : angle 5.99591 ( 9) link_BETA1-4 : bond 0.00670 ( 9) link_BETA1-4 : angle 2.21784 ( 27) hydrogen bonds : bond 0.06382 ( 396) hydrogen bonds : angle 4.63540 ( 1215) link_BETA1-6 : bond 0.01016 ( 3) link_BETA1-6 : angle 1.53027 ( 9) SS BOND : bond 0.00255 ( 15) SS BOND : angle 0.99321 ( 30) link_BETA1-3 : bond 0.00413 ( 3) link_BETA1-3 : angle 5.97431 ( 9) covalent geometry : bond 0.00260 (11739) covalent geometry : angle 0.58994 (15891) *********************** 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 158 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8221 (mt0) cc_final: 0.7632 (pt0) REVERT: A 209 ASP cc_start: 0.8417 (m-30) cc_final: 0.8130 (m-30) REVERT: A 408 GLN cc_start: 0.8219 (mt0) cc_final: 0.7910 (tp40) REVERT: A 456 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7625 (tm-30) REVERT: B 66 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6980 (mm-30) REVERT: B 85 GLU cc_start: 0.7929 (tp30) cc_final: 0.7410 (tm-30) REVERT: B 209 ASP cc_start: 0.8345 (m-30) cc_final: 0.8048 (m-30) REVERT: B 291 ASP cc_start: 0.7685 (t0) cc_final: 0.7485 (t0) REVERT: B 408 GLN cc_start: 0.8195 (mt0) cc_final: 0.7896 (tp40) REVERT: B 456 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7775 (tm-30) REVERT: C 67 GLN cc_start: 0.8273 (mt0) cc_final: 0.7753 (pt0) REVERT: C 291 ASP cc_start: 0.7721 (t0) cc_final: 0.7519 (t0) REVERT: C 404 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: C 408 GLN cc_start: 0.8255 (mt0) cc_final: 0.8020 (tp40) REVERT: C 437 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8001 (tm-30) REVERT: C 456 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7607 (tm-30) outliers start: 17 outliers final: 7 residues processed: 148 average time/residue: 1.2633 time to fit residues: 203.9852 Evaluate side-chains 129 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 THR 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 312 ILE 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 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 17 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 38 optimal weight: 0.0000 chunk 44 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 overall best weight: 3.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.169498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.129811 restraints weight = 9944.680| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.03 r_work: 0.3026 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 11790 Z= 0.377 Angle : 1.113 13.014 16029 Z= 0.577 Chirality : 0.071 0.547 1884 Planarity : 0.007 0.079 2001 Dihedral : 16.092 88.542 2268 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.06 % Allowed : 9.68 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.20), residues: 1425 helix: 0.83 (0.27), residues: 381 sheet: 1.07 (0.41), residues: 165 loop : -2.17 (0.16), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP A 127 HIS 0.008 0.002 HIS C 80 PHE 0.030 0.005 PHE B 111 TYR 0.033 0.005 TYR C 185 ARG 0.008 0.001 ARG B 202 Details of bonding type rmsd link_NAG-ASN : bond 0.01128 ( 18) link_NAG-ASN : angle 3.00442 ( 54) link_BETA1-2 : bond 0.00477 ( 3) link_BETA1-2 : angle 6.06134 ( 9) link_BETA1-4 : bond 0.01179 ( 9) link_BETA1-4 : angle 4.49586 ( 27) hydrogen bonds : bond 0.13102 ( 396) hydrogen bonds : angle 4.99949 ( 1215) link_BETA1-6 : bond 0.01175 ( 3) link_BETA1-6 : angle 2.92823 ( 9) SS BOND : bond 0.00935 ( 15) SS BOND : angle 2.10528 ( 30) link_BETA1-3 : bond 0.00223 ( 3) link_BETA1-3 : angle 5.90790 ( 9) covalent geometry : bond 0.00781 (11739) covalent geometry : angle 1.06301 (15891) *********************** 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 156 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: A 408 GLN cc_start: 0.8418 (mt0) cc_final: 0.8069 (tp40) REVERT: A 456 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: B 408 GLN cc_start: 0.8450 (mt0) cc_final: 0.8055 (tp40) REVERT: B 456 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: C 174 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8002 (mt-10) REVERT: C 404 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7628 (tm-30) REVERT: C 408 GLN cc_start: 0.8502 (mt0) cc_final: 0.8113 (tp40) REVERT: C 456 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7757 (tm-30) outliers start: 37 outliers final: 19 residues processed: 143 average time/residue: 1.2588 time to fit residues: 194.4965 Evaluate side-chains 137 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 1.315 ------------------------------------------------------------------------------- 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 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 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 60 LYS Chi-restraints excluded: chain B residue 126 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 445 LEU Chi-restraints excluded: chain B residue 456 GLU Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 174 GLU 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 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 140 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.178472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.139335 restraints weight = 10460.197| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.94 r_work: 0.3252 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 11790 Z= 0.308 Angle : 0.992 11.162 16029 Z= 0.507 Chirality : 0.065 0.490 1884 Planarity : 0.006 0.067 2001 Dihedral : 14.874 82.079 2268 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.97 % Allowed : 11.17 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.20), residues: 1425 helix: 0.74 (0.27), residues: 381 sheet: 1.28 (0.42), residues: 147 loop : -2.17 (0.16), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP C 127 HIS 0.008 0.002 HIS C 81 PHE 0.026 0.004 PHE B 111 TYR 0.027 0.004 TYR A 185 ARG 0.007 0.001 ARG B 202 Details of bonding type rmsd link_NAG-ASN : bond 0.01066 ( 18) link_NAG-ASN : angle 2.77760 ( 54) link_BETA1-2 : bond 0.00084 ( 3) link_BETA1-2 : angle 6.63534 ( 9) link_BETA1-4 : bond 0.01212 ( 9) link_BETA1-4 : angle 4.15458 ( 27) hydrogen bonds : bond 0.11497 ( 396) hydrogen bonds : angle 4.92098 ( 1215) link_BETA1-6 : bond 0.00988 ( 3) link_BETA1-6 : angle 2.12147 ( 9) SS BOND : bond 0.00743 ( 15) SS BOND : angle 1.80850 ( 30) link_BETA1-3 : bond 0.00210 ( 3) link_BETA1-3 : angle 6.41565 ( 9) covalent geometry : bond 0.00620 (11739) covalent geometry : angle 0.93837 (15891) *********************** 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 167 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 119 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: A 408 GLN cc_start: 0.8254 (mt0) cc_final: 0.7934 (tp40) REVERT: A 456 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7495 (tm-30) REVERT: B 174 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: B 297 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7806 (p0) REVERT: B 408 GLN cc_start: 0.8201 (mt0) cc_final: 0.7891 (tp40) REVERT: B 456 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7938 (tm-30) REVERT: B 459 GLN cc_start: 0.8270 (mt0) cc_final: 0.8006 (mt0) REVERT: C 174 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7894 (mt-10) REVERT: C 404 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: C 408 GLN cc_start: 0.8271 (mt0) cc_final: 0.7944 (tp40) REVERT: C 416 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7833 (tp) REVERT: C 456 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7616 (tm-30) outliers start: 48 outliers final: 26 residues processed: 151 average time/residue: 1.2482 time to fit residues: 204.6028 Evaluate side-chains 148 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 271 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 389 GLN 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 60 LYS Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 297 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 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 174 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 271 VAL 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 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 12 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 21 optimal weight: 0.2980 chunk 74 optimal weight: 9.9990 chunk 113 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.182982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.143853 restraints weight = 10517.221| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.61 r_work: 0.3292 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11790 Z= 0.197 Angle : 0.772 10.540 16029 Z= 0.386 Chirality : 0.056 0.445 1884 Planarity : 0.005 0.051 2001 Dihedral : 13.011 74.146 2268 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.31 % Allowed : 13.56 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.21), residues: 1425 helix: 1.24 (0.28), residues: 381 sheet: 1.20 (0.35), residues: 189 loop : -2.18 (0.17), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 208 HIS 0.004 0.001 HIS C 81 PHE 0.017 0.002 PHE C 113 TYR 0.013 0.002 TYR A 185 ARG 0.004 0.000 ARG B 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00823 ( 18) link_NAG-ASN : angle 2.13582 ( 54) link_BETA1-2 : bond 0.00689 ( 3) link_BETA1-2 : angle 7.03728 ( 9) link_BETA1-4 : bond 0.01019 ( 9) link_BETA1-4 : angle 3.37987 ( 27) hydrogen bonds : bond 0.08456 ( 396) hydrogen bonds : angle 4.71086 ( 1215) link_BETA1-6 : bond 0.00914 ( 3) link_BETA1-6 : angle 1.49701 ( 9) SS BOND : bond 0.00457 ( 15) SS BOND : angle 1.15046 ( 30) link_BETA1-3 : bond 0.00147 ( 3) link_BETA1-3 : angle 6.36544 ( 9) covalent geometry : bond 0.00369 (11739) covalent geometry : angle 0.71565 (15891) *********************** 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 156 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: A 408 GLN cc_start: 0.8079 (mt0) cc_final: 0.7804 (tp40) REVERT: A 456 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7496 (tm-30) REVERT: B 68 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8205 (mp) REVERT: B 408 GLN cc_start: 0.8064 (mt0) cc_final: 0.7804 (tp40) REVERT: B 456 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7968 (tm-30) REVERT: B 459 GLN cc_start: 0.8052 (mt0) cc_final: 0.7835 (mt0) REVERT: C 174 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7839 (mt-10) REVERT: C 332 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8368 (m-30) REVERT: C 404 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: C 408 GLN cc_start: 0.8072 (mt0) cc_final: 0.7809 (tp40) REVERT: C 416 LEU cc_start: 0.8032 (mt) cc_final: 0.7794 (tp) REVERT: C 422 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: C 456 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7489 (tm-30) outliers start: 40 outliers final: 23 residues processed: 143 average time/residue: 1.2324 time to fit residues: 192.1559 Evaluate side-chains 145 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 312 ILE 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 37 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 151 SER 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 174 GLU 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 332 ASP Chi-restraints excluded: chain C residue 404 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 62 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 126 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.179581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.140236 restraints weight = 10466.138| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 3.23 r_work: 0.3251 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11790 Z= 0.268 Angle : 0.917 10.369 16029 Z= 0.464 Chirality : 0.062 0.452 1884 Planarity : 0.006 0.058 2001 Dihedral : 13.509 78.643 2268 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.14 % Allowed : 12.82 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.20), residues: 1425 helix: 1.01 (0.28), residues: 381 sheet: 1.37 (0.41), residues: 147 loop : -2.18 (0.16), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 208 HIS 0.006 0.002 HIS A 81 PHE 0.021 0.003 PHE C 113 TYR 0.020 0.003 TYR A 185 ARG 0.006 0.001 ARG B 202 Details of bonding type rmsd link_NAG-ASN : bond 0.01004 ( 18) link_NAG-ASN : angle 2.60000 ( 54) link_BETA1-2 : bond 0.00426 ( 3) link_BETA1-2 : angle 7.08201 ( 9) link_BETA1-4 : bond 0.01177 ( 9) link_BETA1-4 : angle 3.99933 ( 27) hydrogen bonds : bond 0.10565 ( 396) hydrogen bonds : angle 4.83241 ( 1215) link_BETA1-6 : bond 0.00986 ( 3) link_BETA1-6 : angle 2.10722 ( 9) SS BOND : bond 0.00666 ( 15) SS BOND : angle 1.47600 ( 30) link_BETA1-3 : bond 0.00351 ( 3) link_BETA1-3 : angle 6.09576 ( 9) covalent geometry : bond 0.00526 (11739) covalent geometry : angle 0.86092 (15891) *********************** 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 160 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 110 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: A 408 GLN cc_start: 0.8246 (mt0) cc_final: 0.7919 (tp40) REVERT: A 456 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7505 (tm-30) REVERT: B 68 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8338 (mt) REVERT: B 408 GLN cc_start: 0.8144 (mt0) cc_final: 0.7836 (tp40) REVERT: B 456 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7973 (tm-30) REVERT: B 459 GLN cc_start: 0.8132 (mt0) cc_final: 0.7921 (mt0) REVERT: C 174 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: C 260 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: C 294 CYS cc_start: 0.7424 (p) cc_final: 0.7128 (t) REVERT: C 332 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8398 (m-30) REVERT: C 404 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: C 408 GLN cc_start: 0.8270 (mt0) cc_final: 0.7970 (tp40) REVERT: C 416 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7815 (tp) REVERT: C 422 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: C 456 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7491 (tm-30) outliers start: 50 outliers final: 33 residues processed: 147 average time/residue: 1.5528 time to fit residues: 248.6758 Evaluate side-chains 153 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 109 time to evaluate : 1.403 ------------------------------------------------------------------------------- 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 267 SER 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 389 GLN 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 68 ILE Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 271 VAL 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 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 174 GLU Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 260 GLU 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 332 ASP Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 419 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 140 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 chunk 39 optimal weight: 0.0670 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.186361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.147962 restraints weight = 10788.046| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.71 r_work: 0.3408 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2364 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= 0.144 Angle : 0.665 11.513 16029 Z= 0.326 Chirality : 0.052 0.473 1884 Planarity : 0.004 0.046 2001 Dihedral : 11.023 64.607 2268 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.23 % Allowed : 15.05 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.21), residues: 1425 helix: 1.46 (0.28), residues: 384 sheet: 1.26 (0.35), residues: 195 loop : -2.17 (0.18), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 208 HIS 0.004 0.001 HIS C 81 PHE 0.015 0.002 PHE B 113 TYR 0.008 0.001 TYR B 504 ARG 0.002 0.000 ARG A 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00658 ( 18) link_NAG-ASN : angle 1.77172 ( 54) link_BETA1-2 : bond 0.00951 ( 3) link_BETA1-2 : angle 7.65241 ( 9) link_BETA1-4 : bond 0.00804 ( 9) link_BETA1-4 : angle 2.74338 ( 27) hydrogen bonds : bond 0.06524 ( 396) hydrogen bonds : angle 4.55498 ( 1215) link_BETA1-6 : bond 0.00858 ( 3) link_BETA1-6 : angle 1.33454 ( 9) SS BOND : bond 0.00253 ( 15) SS BOND : angle 0.76909 ( 30) link_BETA1-3 : bond 0.00112 ( 3) link_BETA1-3 : angle 6.13448 ( 9) covalent geometry : bond 0.00262 (11739) covalent geometry : angle 0.60525 (15891) *********************** 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 149 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8264 (mt0) cc_final: 0.7590 (pt0) REVERT: A 209 ASP cc_start: 0.8607 (m-30) cc_final: 0.8346 (m-30) REVERT: A 404 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7533 (tm-30) REVERT: A 456 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7453 (tm-30) REVERT: B 209 ASP cc_start: 0.8559 (m-30) cc_final: 0.8327 (m-30) REVERT: B 408 GLN cc_start: 0.7854 (mt0) cc_final: 0.7645 (tp40) REVERT: C 67 GLN cc_start: 0.8234 (mt0) cc_final: 0.7442 (pt0) REVERT: C 404 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7639 (tm-30) REVERT: C 456 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7358 (tm-30) outliers start: 27 outliers final: 15 residues processed: 143 average time/residue: 1.1549 time to fit residues: 180.6603 Evaluate side-chains 135 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 251 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 GLN 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 216 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 216 SER Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 271 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 39 optimal weight: 6.9990 chunk 115 optimal weight: 0.4980 chunk 101 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.186350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.148190 restraints weight = 10654.689| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.55 r_work: 0.3388 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2398 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= 0.152 Angle : 0.665 11.749 16029 Z= 0.329 Chirality : 0.052 0.492 1884 Planarity : 0.004 0.043 2001 Dihedral : 9.970 60.505 2268 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.15 % Allowed : 15.80 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.21), residues: 1425 helix: 1.66 (0.28), residues: 384 sheet: 1.30 (0.35), residues: 195 loop : -2.11 (0.18), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 208 HIS 0.003 0.001 HIS A 81 PHE 0.015 0.002 PHE B 113 TYR 0.009 0.001 TYR A 185 ARG 0.002 0.000 ARG B 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00684 ( 18) link_NAG-ASN : angle 1.75623 ( 54) link_BETA1-2 : bond 0.00862 ( 3) link_BETA1-2 : angle 7.64579 ( 9) link_BETA1-4 : bond 0.00831 ( 9) link_BETA1-4 : angle 2.66584 ( 27) hydrogen bonds : bond 0.06542 ( 396) hydrogen bonds : angle 4.48488 ( 1215) link_BETA1-6 : bond 0.01002 ( 3) link_BETA1-6 : angle 1.39683 ( 9) SS BOND : bond 0.00280 ( 15) SS BOND : angle 0.85036 ( 30) link_BETA1-3 : bond 0.00124 ( 3) link_BETA1-3 : angle 5.56152 ( 9) covalent geometry : bond 0.00281 (11739) covalent geometry : angle 0.60822 (15891) *********************** 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 144 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8289 (mt0) cc_final: 0.7607 (pt0) REVERT: A 209 ASP cc_start: 0.8703 (m-30) cc_final: 0.8398 (m-30) REVERT: A 404 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: A 456 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: C 67 GLN cc_start: 0.8297 (mt0) cc_final: 0.7510 (pt0) REVERT: C 174 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7793 (mt-10) REVERT: C 332 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8359 (m-30) REVERT: C 404 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7692 (tm-30) REVERT: C 422 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: C 456 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7440 (tm-30) REVERT: C 467 GLU cc_start: 0.6049 (tp30) cc_final: 0.5812 (pt0) outliers start: 26 outliers final: 17 residues processed: 136 average time/residue: 1.2120 time to fit residues: 179.6601 Evaluate side-chains 138 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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 251 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 GLN 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 A residue 495 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 151 SER 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 174 GLU Chi-restraints excluded: chain C residue 251 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 107 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 5 optimal weight: 0.8980 chunk 138 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 105 optimal weight: 0.4980 chunk 84 optimal weight: 0.1980 chunk 3 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 459 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.189246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.151388 restraints weight = 10717.387| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.49 r_work: 0.3434 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11790 Z= 0.127 Angle : 0.610 12.097 16029 Z= 0.300 Chirality : 0.051 0.500 1884 Planarity : 0.004 0.041 2001 Dihedral : 8.747 52.559 2268 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.07 % Allowed : 16.38 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.21), residues: 1425 helix: 1.85 (0.28), residues: 384 sheet: 1.27 (0.36), residues: 180 loop : -2.02 (0.18), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 208 HIS 0.002 0.001 HIS C 81 PHE 0.013 0.001 PHE B 113 TYR 0.007 0.001 TYR B 504 ARG 0.002 0.000 ARG B 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00584 ( 18) link_NAG-ASN : angle 1.59089 ( 54) link_BETA1-2 : bond 0.00891 ( 3) link_BETA1-2 : angle 7.78927 ( 9) link_BETA1-4 : bond 0.00733 ( 9) link_BETA1-4 : angle 2.25247 ( 27) hydrogen bonds : bond 0.05493 ( 396) hydrogen bonds : angle 4.36450 ( 1215) link_BETA1-6 : bond 0.01077 ( 3) link_BETA1-6 : angle 1.20106 ( 9) SS BOND : bond 0.00204 ( 15) SS BOND : angle 0.77346 ( 30) link_BETA1-3 : bond 0.00054 ( 3) link_BETA1-3 : angle 5.50859 ( 9) covalent geometry : bond 0.00238 (11739) covalent geometry : angle 0.55243 (15891) *********************** 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 142 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8285 (mt0) cc_final: 0.7622 (pt0) REVERT: A 209 ASP cc_start: 0.8595 (m-30) cc_final: 0.8328 (m-30) REVERT: A 404 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: A 456 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7520 (tm-30) REVERT: B 209 ASP cc_start: 0.8550 (m-30) cc_final: 0.8318 (m-30) REVERT: C 332 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8343 (m-30) REVERT: C 456 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: C 467 GLU cc_start: 0.6239 (tp30) cc_final: 0.5961 (pt0) outliers start: 25 outliers final: 19 residues processed: 135 average time/residue: 1.0561 time to fit residues: 156.4400 Evaluate side-chains 139 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 251 LEU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 GLN 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 495 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 151 SER 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 251 LEU Chi-restraints excluded: chain C residue 320 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 11 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.181513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.141975 restraints weight = 10429.622| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.77 r_work: 0.3318 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11790 Z= 0.249 Angle : 0.856 12.002 16029 Z= 0.436 Chirality : 0.059 0.491 1884 Planarity : 0.006 0.057 2001 Dihedral : 10.699 65.068 2268 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.48 % Allowed : 15.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.21), residues: 1425 helix: 1.43 (0.28), residues: 384 sheet: 1.56 (0.36), residues: 177 loop : -2.13 (0.17), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 208 HIS 0.006 0.001 HIS A 81 PHE 0.022 0.003 PHE C 113 TYR 0.019 0.003 TYR A 185 ARG 0.005 0.001 ARG B 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00889 ( 18) link_NAG-ASN : angle 2.27736 ( 54) link_BETA1-2 : bond 0.00505 ( 3) link_BETA1-2 : angle 7.80512 ( 9) link_BETA1-4 : bond 0.00919 ( 9) link_BETA1-4 : angle 3.42922 ( 27) hydrogen bonds : bond 0.09456 ( 396) hydrogen bonds : angle 4.66323 ( 1215) link_BETA1-6 : bond 0.01156 ( 3) link_BETA1-6 : angle 2.37355 ( 9) SS BOND : bond 0.00620 ( 15) SS BOND : angle 1.42714 ( 30) link_BETA1-3 : bond 0.00438 ( 3) link_BETA1-3 : angle 4.99780 ( 9) covalent geometry : bond 0.00490 (11739) covalent geometry : angle 0.80388 (15891) ********************** 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: 30 poor density : 112 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8306 (mt0) cc_final: 0.7628 (pt0) REVERT: A 404 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7654 (tm-30) REVERT: A 456 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: B 297 ASP cc_start: 0.8066 (p0) cc_final: 0.7849 (p0) REVERT: C 174 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7631 (tp30) REVERT: C 456 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7503 (tm-30) REVERT: C 467 GLU cc_start: 0.6111 (tp30) cc_final: 0.5791 (pt0) outliers start: 30 outliers final: 21 residues processed: 132 average time/residue: 1.1373 time to fit residues: 164.0489 Evaluate side-chains 132 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 251 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 389 GLN 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 126 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 216 SER 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 C residue 129 VAL Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 312 ILE 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 76 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.186054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.147818 restraints weight = 10600.088| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.68 r_work: 0.3402 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2508 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= 0.164 Angle : 0.692 11.939 16029 Z= 0.345 Chirality : 0.053 0.497 1884 Planarity : 0.004 0.047 2001 Dihedral : 9.940 59.658 2268 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.07 % Allowed : 16.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1425 helix: 1.63 (0.28), residues: 384 sheet: 1.34 (0.36), residues: 195 loop : -2.13 (0.17), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 208 HIS 0.003 0.001 HIS A 81 PHE 0.016 0.002 PHE C 282 TYR 0.010 0.002 TYR A 185 ARG 0.003 0.000 ARG B 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00696 ( 18) link_NAG-ASN : angle 1.85133 ( 54) link_BETA1-2 : bond 0.00763 ( 3) link_BETA1-2 : angle 7.84331 ( 9) link_BETA1-4 : bond 0.00820 ( 9) link_BETA1-4 : angle 2.75000 ( 27) hydrogen bonds : bond 0.07076 ( 396) hydrogen bonds : angle 4.53528 ( 1215) link_BETA1-6 : bond 0.01011 ( 3) link_BETA1-6 : angle 1.57105 ( 9) SS BOND : bond 0.00324 ( 15) SS BOND : angle 1.06196 ( 30) link_BETA1-3 : bond 0.00232 ( 3) link_BETA1-3 : angle 5.14701 ( 9) covalent geometry : bond 0.00307 (11739) covalent geometry : angle 0.63613 (15891) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8942.61 seconds wall clock time: 154 minutes 46.01 seconds (9286.01 seconds total)