Starting phenix.real_space_refine on Wed May 14 09:36:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wh7_37532/05_2025/8wh7_37532.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wh7_37532/05_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_37532/05_2025/8wh7_37532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wh7_37532/05_2025/8wh7_37532.map" model { file = "/net/cci-nas-00/data/ceres_data/8wh7_37532/05_2025/8wh7_37532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wh7_37532/05_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-5687/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: 7.39, per 1000 atoms: 0.64 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: 3.26 Conformation dependent library (CDL) restraints added in 1.6 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: 1.58 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: 3.60 Time building geometry restraints manager: 3.77 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: 0.08 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: 2.520 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.770 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: 0.010 Load rotamer database and sin/cos tables:11.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.240 ------------------------------------------------------------------------------- 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 : 1.262 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: 1.2141 time to fit residues: 222.0398 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 : 1.154 ------------------------------------------------------------------------------- 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 = 0.144128 restraints weight = 10086.905| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.32 r_work: 0.3226 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 1.53026 ( 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 : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLN cc_start: 0.8213 (mt0) cc_final: 0.7623 (pt0) REVERT: A 209 ASP cc_start: 0.8414 (m-30) cc_final: 0.8126 (m-30) REVERT: A 408 GLN cc_start: 0.8211 (mt0) cc_final: 0.7909 (tp40) REVERT: A 456 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7629 (tm-30) REVERT: B 66 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6975 (mm-30) REVERT: B 85 GLU cc_start: 0.7919 (tp30) cc_final: 0.7405 (tm-30) REVERT: B 209 ASP cc_start: 0.8345 (m-30) cc_final: 0.8046 (m-30) REVERT: B 291 ASP cc_start: 0.7685 (t0) cc_final: 0.7483 (t0) REVERT: B 408 GLN cc_start: 0.8185 (mt0) cc_final: 0.7892 (tp40) REVERT: B 456 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: C 67 GLN cc_start: 0.8266 (mt0) cc_final: 0.7747 (pt0) REVERT: C 291 ASP cc_start: 0.7720 (t0) cc_final: 0.7513 (t0) REVERT: C 404 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7849 (tm-30) REVERT: C 408 GLN cc_start: 0.8246 (mt0) cc_final: 0.8020 (tp40) REVERT: C 437 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8008 (tm-30) REVERT: C 456 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7612 (tm-30) outliers start: 17 outliers final: 7 residues processed: 148 average time/residue: 1.1933 time to fit residues: 193.4342 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 : 1.253 ------------------------------------------------------------------------------- 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: 6.9990 chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 127 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 38 optimal weight: 0.0170 chunk 44 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.169804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.131083 restraints weight = 9961.522| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.90 r_work: 0.3031 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 11790 Z= 0.361 Angle : 1.079 12.439 16029 Z= 0.558 Chirality : 0.070 0.539 1884 Planarity : 0.007 0.074 2001 Dihedral : 15.955 87.403 2268 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.98 % Allowed : 9.76 % 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: -1.25 (0.20), residues: 1425 helix: 0.92 (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 0.003 TRP C 127 HIS 0.008 0.002 HIS A 81 PHE 0.030 0.005 PHE B 111 TYR 0.032 0.005 TYR C 185 ARG 0.007 0.001 ARG B 202 Details of bonding type rmsd link_NAG-ASN : bond 0.01116 ( 18) link_NAG-ASN : angle 2.92634 ( 54) link_BETA1-2 : bond 0.00165 ( 3) link_BETA1-2 : angle 6.02951 ( 9) link_BETA1-4 : bond 0.01245 ( 9) link_BETA1-4 : angle 4.34766 ( 27) hydrogen bonds : bond 0.12742 ( 396) hydrogen bonds : angle 4.97763 ( 1215) link_BETA1-6 : bond 0.01094 ( 3) link_BETA1-6 : angle 2.83863 ( 9) SS BOND : bond 0.00886 ( 15) SS BOND : angle 2.04341 ( 30) link_BETA1-3 : bond 0.00145 ( 3) link_BETA1-3 : angle 5.84119 ( 9) covalent geometry : bond 0.00747 (11739) covalent geometry : angle 1.02942 (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 154 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 CYS cc_start: 0.7553 (p) cc_final: 0.7342 (t) REVERT: A 404 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: A 408 GLN cc_start: 0.8441 (mt0) cc_final: 0.8106 (tp40) REVERT: A 456 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: B 408 GLN cc_start: 0.8475 (mt0) cc_final: 0.8099 (tp40) REVERT: B 456 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7942 (tm-30) REVERT: C 174 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: C 404 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: C 408 GLN cc_start: 0.8523 (mt0) cc_final: 0.8145 (tp40) REVERT: C 456 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7771 (tm-30) outliers start: 36 outliers final: 19 residues processed: 142 average time/residue: 1.2548 time to fit residues: 192.7088 Evaluate side-chains 136 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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: 0.6980 chunk 47 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 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: 0.0370 overall best weight: 2.3464 ------------------------------------------------------------------------------- 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 = 0.3927 r_free = 0.3927 target = 0.179607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.140003 restraints weight = 10499.384| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.11 r_work: 0.3246 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 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 : 0.005 0.061 11790 Z= 0.277 Angle : 0.928 10.343 16029 Z= 0.472 Chirality : 0.062 0.458 1884 Planarity : 0.006 0.060 2001 Dihedral : 14.441 79.981 2268 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.39 % Allowed : 11.58 % Favored : 85.03 % 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: -1.17 (0.20), residues: 1425 helix: 0.93 (0.28), residues: 381 sheet: 1.33 (0.37), residues: 177 loop : -2.19 (0.17), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 208 HIS 0.007 0.002 HIS A 81 PHE 0.024 0.003 PHE B 111 TYR 0.021 0.003 TYR A 185 ARG 0.006 0.001 ARG B 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00964 ( 18) link_NAG-ASN : angle 2.57595 ( 54) link_BETA1-2 : bond 0.00150 ( 3) link_BETA1-2 : angle 6.70318 ( 9) link_BETA1-4 : bond 0.01099 ( 9) link_BETA1-4 : angle 3.92815 ( 27) hydrogen bonds : bond 0.10679 ( 396) hydrogen bonds : angle 4.85591 ( 1215) link_BETA1-6 : bond 0.00912 ( 3) link_BETA1-6 : angle 1.87190 ( 9) SS BOND : bond 0.00686 ( 15) SS BOND : angle 1.65319 ( 30) link_BETA1-3 : bond 0.00223 ( 3) link_BETA1-3 : angle 6.37113 ( 9) covalent geometry : bond 0.00546 (11739) covalent geometry : angle 0.87472 (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 155 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: A 408 GLN cc_start: 0.8254 (mt0) cc_final: 0.7906 (tp40) REVERT: A 456 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7479 (tm-30) REVERT: B 408 GLN cc_start: 0.8214 (mt0) cc_final: 0.7876 (tp40) REVERT: B 456 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7975 (tm-30) REVERT: C 174 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7933 (mt-10) REVERT: C 230 MET cc_start: 0.8423 (tpt) cc_final: 0.8040 (tpt) REVERT: C 404 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: C 408 GLN cc_start: 0.8247 (mt0) cc_final: 0.7903 (tp40) REVERT: C 416 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7802 (tp) REVERT: C 422 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8284 (tt0) REVERT: C 456 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7594 (tm-30) outliers start: 41 outliers final: 24 residues processed: 142 average time/residue: 1.2238 time to fit residues: 188.3197 Evaluate side-chains 141 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 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 60 LYS 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 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 422 GLU 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: 5.9990 chunk 77 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.182809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.143399 restraints weight = 10516.972| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.68 r_work: 0.3286 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11790 Z= 0.203 Angle : 0.783 10.455 16029 Z= 0.392 Chirality : 0.057 0.443 1884 Planarity : 0.005 0.050 2001 Dihedral : 12.945 74.376 2268 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.23 % Allowed : 12.99 % Favored : 83.79 % 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: -1.00 (0.21), residues: 1425 helix: 1.27 (0.28), residues: 381 sheet: 1.40 (0.36), residues: 177 loop : -2.18 (0.17), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 208 HIS 0.005 0.001 HIS A 81 PHE 0.018 0.002 PHE C 113 TYR 0.014 0.002 TYR A 185 ARG 0.004 0.000 ARG B 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00832 ( 18) link_NAG-ASN : angle 2.16920 ( 54) link_BETA1-2 : bond 0.00676 ( 3) link_BETA1-2 : angle 7.02526 ( 9) link_BETA1-4 : bond 0.01034 ( 9) link_BETA1-4 : angle 3.39769 ( 27) hydrogen bonds : bond 0.08632 ( 396) hydrogen bonds : angle 4.70934 ( 1215) link_BETA1-6 : bond 0.00939 ( 3) link_BETA1-6 : angle 1.54905 ( 9) SS BOND : bond 0.00483 ( 15) SS BOND : angle 1.19212 ( 30) link_BETA1-3 : bond 0.00180 ( 3) link_BETA1-3 : angle 6.24704 ( 9) covalent geometry : bond 0.00382 (11739) covalent geometry : angle 0.72701 (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 151 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: A 408 GLN cc_start: 0.8110 (mt0) cc_final: 0.7833 (tp40) REVERT: A 456 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7483 (tm-30) REVERT: B 408 GLN cc_start: 0.8090 (mt0) cc_final: 0.7802 (tp40) REVERT: B 456 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: C 174 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7860 (mt-10) REVERT: C 332 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8376 (m-30) REVERT: C 404 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: C 408 GLN cc_start: 0.8125 (mt0) cc_final: 0.7876 (tp40) REVERT: C 416 LEU cc_start: 0.8030 (mt) cc_final: 0.7792 (tp) REVERT: C 422 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: C 456 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7489 (tm-30) outliers start: 39 outliers final: 23 residues processed: 139 average time/residue: 1.1733 time to fit residues: 177.7701 Evaluate side-chains 142 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 404 GLU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 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 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 251 LEU Chi-restraints excluded: chain C residue 297 ASP 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: 1.9990 chunk 95 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 126 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 overall best weight: 1.5742 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.181604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.142914 restraints weight = 10512.913| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.87 r_work: 0.3355 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11790 Z= 0.221 Angle : 0.820 10.787 16029 Z= 0.412 Chirality : 0.058 0.455 1884 Planarity : 0.005 0.050 2001 Dihedral : 12.579 74.107 2268 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.80 % Allowed : 13.48 % 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: -1.02 (0.21), residues: 1425 helix: 1.24 (0.28), residues: 381 sheet: 1.41 (0.36), residues: 177 loop : -2.20 (0.17), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 208 HIS 0.005 0.001 HIS B 81 PHE 0.019 0.003 PHE C 113 TYR 0.016 0.002 TYR A 185 ARG 0.004 0.000 ARG B 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00884 ( 18) link_NAG-ASN : angle 2.29665 ( 54) link_BETA1-2 : bond 0.00623 ( 3) link_BETA1-2 : angle 7.28674 ( 9) link_BETA1-4 : bond 0.01030 ( 9) link_BETA1-4 : angle 3.55182 ( 27) hydrogen bonds : bond 0.09174 ( 396) hydrogen bonds : angle 4.73036 ( 1215) link_BETA1-6 : bond 0.00974 ( 3) link_BETA1-6 : angle 1.83719 ( 9) SS BOND : bond 0.00528 ( 15) SS BOND : angle 1.27086 ( 30) link_BETA1-3 : bond 0.00313 ( 3) link_BETA1-3 : angle 5.91645 ( 9) covalent geometry : bond 0.00422 (11739) covalent geometry : angle 0.76399 (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 158 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 112 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7610 (tm-30) REVERT: A 408 GLN cc_start: 0.8141 (mt0) cc_final: 0.7855 (tp40) REVERT: A 456 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7436 (tm-30) REVERT: B 68 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8341 (mt) REVERT: B 297 ASP cc_start: 0.8073 (p0) cc_final: 0.7817 (p0) REVERT: B 408 GLN cc_start: 0.8084 (mt0) cc_final: 0.7822 (tp40) REVERT: B 456 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7938 (tm-30) REVERT: B 459 GLN cc_start: 0.8024 (mt0) cc_final: 0.7795 (mt0) REVERT: C 174 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7839 (mt-10) REVERT: C 294 CYS cc_start: 0.7359 (p) cc_final: 0.7125 (t) REVERT: C 332 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8349 (m-30) REVERT: C 404 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: C 408 GLN cc_start: 0.8153 (mt0) cc_final: 0.7907 (tp40) REVERT: C 416 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7820 (tp) REVERT: C 422 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: C 456 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7402 (tm-30) outliers start: 46 outliers final: 28 residues processed: 143 average time/residue: 1.1126 time to fit residues: 173.9074 Evaluate side-chains 148 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain B residue 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 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 216 SER Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 456 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 0.0010 chunk 140 optimal weight: 0.2980 chunk 136 optimal weight: 0.4980 chunk 39 optimal weight: 0.0270 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 112 optimal weight: 0.7980 overall best weight: 0.2844 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.191314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.153446 restraints weight = 10879.844| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.66 r_work: 0.3471 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11790 Z= 0.117 Angle : 0.600 11.949 16029 Z= 0.291 Chirality : 0.051 0.493 1884 Planarity : 0.004 0.044 2001 Dihedral : 9.522 56.157 2268 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.82 % Allowed : 15.55 % Favored : 82.63 % 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: -0.77 (0.21), residues: 1425 helix: 1.69 (0.29), residues: 384 sheet: 0.75 (0.34), residues: 219 loop : -2.11 (0.18), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 208 HIS 0.003 0.001 HIS C 81 PHE 0.014 0.001 PHE B 113 TYR 0.007 0.001 TYR B 504 ARG 0.002 0.000 ARG A 255 Details of bonding type rmsd link_NAG-ASN : bond 0.00507 ( 18) link_NAG-ASN : angle 1.50164 ( 54) link_BETA1-2 : bond 0.00935 ( 3) link_BETA1-2 : angle 7.83719 ( 9) link_BETA1-4 : bond 0.00707 ( 9) link_BETA1-4 : angle 2.14571 ( 27) hydrogen bonds : bond 0.05083 ( 396) hydrogen bonds : angle 4.41919 ( 1215) link_BETA1-6 : bond 0.00982 ( 3) link_BETA1-6 : angle 1.27108 ( 9) SS BOND : bond 0.00176 ( 15) SS BOND : angle 0.56382 ( 30) link_BETA1-3 : bond 0.00198 ( 3) link_BETA1-3 : angle 6.03003 ( 9) covalent geometry : bond 0.00218 (11739) covalent geometry : angle 0.53976 (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 144 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.8464 (m-30) cc_final: 0.8226 (m-30) REVERT: A 404 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: A 456 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7405 (tm-30) REVERT: B 44 MET cc_start: 0.8390 (mmt) cc_final: 0.7930 (mmt) REVERT: C 404 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: C 456 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7349 (tm-30) outliers start: 22 outliers final: 15 residues processed: 138 average time/residue: 1.0832 time to fit residues: 165.7765 Evaluate side-chains 134 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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 271 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 291 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 39 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 101 optimal weight: 0.2980 chunk 55 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.186791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.147608 restraints weight = 10672.583| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.68 r_work: 0.3328 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2366 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= 0.157 Angle : 0.667 11.828 16029 Z= 0.331 Chirality : 0.053 0.491 1884 Planarity : 0.004 0.043 2001 Dihedral : 9.654 58.483 2268 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % 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: -0.66 (0.21), residues: 1425 helix: 1.74 (0.28), residues: 384 sheet: 1.28 (0.35), residues: 195 loop : -2.08 (0.18), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 208 HIS 0.003 0.001 HIS A 81 PHE 0.015 0.002 PHE C 282 TYR 0.009 0.002 TYR A 185 ARG 0.002 0.000 ARG B 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00661 ( 18) link_NAG-ASN : angle 1.71969 ( 54) link_BETA1-2 : bond 0.00817 ( 3) link_BETA1-2 : angle 7.66803 ( 9) link_BETA1-4 : bond 0.00784 ( 9) link_BETA1-4 : angle 2.61317 ( 27) hydrogen bonds : bond 0.06584 ( 396) hydrogen bonds : angle 4.44323 ( 1215) link_BETA1-6 : bond 0.01063 ( 3) link_BETA1-6 : angle 1.40477 ( 9) SS BOND : bond 0.00322 ( 15) SS BOND : angle 0.83921 ( 30) link_BETA1-3 : bond 0.00184 ( 3) link_BETA1-3 : angle 5.54126 ( 9) covalent geometry : bond 0.00295 (11739) covalent geometry : angle 0.61182 (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 143 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASP cc_start: 0.8707 (m-30) cc_final: 0.8418 (m-30) REVERT: A 404 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7647 (tm-30) REVERT: A 456 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7584 (tm-30) REVERT: B 404 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7991 (tm-30) REVERT: C 404 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: C 456 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7491 (tm-30) REVERT: C 467 GLU cc_start: 0.6201 (tp30) cc_final: 0.5887 (pt0) outliers start: 26 outliers final: 20 residues processed: 136 average time/residue: 1.0600 time to fit residues: 158.0691 Evaluate side-chains 136 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR 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 267 SER Chi-restraints excluded: chain A residue 291 ASP 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 A residue 495 CYS Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 297 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 445 LEU Chi-restraints excluded: chain C residue 456 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 107 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 138 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 23 optimal weight: 0.0670 chunk 16 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- 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 = 0.186214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.147113 restraints weight = 10609.998| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.61 r_work: 0.3381 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2411 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= 0.165 Angle : 0.688 12.027 16029 Z= 0.343 Chirality : 0.053 0.494 1884 Planarity : 0.004 0.045 2001 Dihedral : 9.688 58.620 2268 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.81 % Allowed : 15.80 % Favored : 81.39 % 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: -0.68 (0.21), residues: 1425 helix: 1.72 (0.28), residues: 384 sheet: 1.31 (0.35), residues: 195 loop : -2.09 (0.18), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 208 HIS 0.003 0.001 HIS A 81 PHE 0.016 0.002 PHE C 113 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 0.00697 ( 18) link_NAG-ASN : angle 1.82282 ( 54) link_BETA1-2 : bond 0.00799 ( 3) link_BETA1-2 : angle 7.78487 ( 9) link_BETA1-4 : bond 0.00826 ( 9) link_BETA1-4 : angle 2.72962 ( 27) hydrogen bonds : bond 0.06959 ( 396) hydrogen bonds : angle 4.49292 ( 1215) link_BETA1-6 : bond 0.01069 ( 3) link_BETA1-6 : angle 1.52691 ( 9) SS BOND : bond 0.00323 ( 15) SS BOND : angle 0.96371 ( 30) link_BETA1-3 : bond 0.00201 ( 3) link_BETA1-3 : angle 5.25109 ( 9) covalent geometry : bond 0.00310 (11739) covalent geometry : angle 0.63290 (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 143 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7627 (tm-30) REVERT: A 456 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7596 (tm-30) REVERT: C 422 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: C 456 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7460 (tm-30) REVERT: C 467 GLU cc_start: 0.6236 (tp30) cc_final: 0.5949 (pt0) outliers start: 34 outliers final: 27 residues processed: 136 average time/residue: 1.0872 time to fit residues: 161.9371 Evaluate side-chains 141 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 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 291 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 243 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 419 THR 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 297 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 322 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.182670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.143303 restraints weight = 10480.053| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.60 r_work: 0.3260 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11790 Z= 0.214 Angle : 0.791 11.985 16029 Z= 0.399 Chirality : 0.057 0.491 1884 Planarity : 0.005 0.048 2001 Dihedral : 10.745 65.200 2268 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.98 % Allowed : 15.55 % Favored : 81.47 % 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: -0.79 (0.21), residues: 1425 helix: 1.54 (0.28), residues: 384 sheet: 1.61 (0.37), residues: 177 loop : -2.14 (0.17), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 208 HIS 0.005 0.001 HIS A 81 PHE 0.019 0.003 PHE C 113 TYR 0.015 0.002 TYR A 185 ARG 0.004 0.000 ARG B 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00836 ( 18) link_NAG-ASN : angle 2.12990 ( 54) link_BETA1-2 : bond 0.00633 ( 3) link_BETA1-2 : angle 7.81585 ( 9) link_BETA1-4 : bond 0.00961 ( 9) link_BETA1-4 : angle 3.22515 ( 27) hydrogen bonds : bond 0.08653 ( 396) hydrogen bonds : angle 4.62687 ( 1215) link_BETA1-6 : bond 0.01062 ( 3) link_BETA1-6 : angle 2.17697 ( 9) SS BOND : bond 0.00514 ( 15) SS BOND : angle 1.21246 ( 30) link_BETA1-3 : bond 0.00371 ( 3) link_BETA1-3 : angle 4.96292 ( 9) covalent geometry : bond 0.00411 (11739) covalent geometry : angle 0.73731 (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 147 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: A 456 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: B 389 GLN cc_start: 0.6394 (OUTLIER) cc_final: 0.6147 (pp30) REVERT: C 422 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8332 (tt0) REVERT: C 456 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7558 (tm-30) REVERT: C 467 GLU cc_start: 0.6301 (tp30) cc_final: 0.5994 (pt0) outliers start: 36 outliers final: 30 residues processed: 138 average time/residue: 1.0485 time to fit residues: 158.7831 Evaluate side-chains 145 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 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 291 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 495 CYS Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 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 389 GLN Chi-restraints excluded: chain B residue 419 THR 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 291 ASP 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 76 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 140 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.183455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.144227 restraints weight = 10592.574| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.53 r_work: 0.3362 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2527 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 : 0.758 11.845 16029 Z= 0.381 Chirality : 0.055 0.490 1884 Planarity : 0.005 0.048 2001 Dihedral : 10.726 64.752 2268 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.73 % Allowed : 15.72 % 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: -0.79 (0.21), residues: 1425 helix: 1.53 (0.28), residues: 384 sheet: 1.57 (0.37), residues: 183 loop : -2.15 (0.17), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 208 HIS 0.004 0.001 HIS C 81 PHE 0.017 0.002 PHE B 282 TYR 0.014 0.002 TYR A 185 ARG 0.004 0.000 ARG B 202 Details of bonding type rmsd link_NAG-ASN : bond 0.00780 ( 18) link_NAG-ASN : angle 2.02852 ( 54) link_BETA1-2 : bond 0.00689 ( 3) link_BETA1-2 : angle 7.83871 ( 9) link_BETA1-4 : bond 0.00879 ( 9) link_BETA1-4 : angle 3.07564 ( 27) hydrogen bonds : bond 0.08145 ( 396) hydrogen bonds : angle 4.60906 ( 1215) link_BETA1-6 : bond 0.00970 ( 3) link_BETA1-6 : angle 1.94617 ( 9) SS BOND : bond 0.00438 ( 15) SS BOND : angle 1.21320 ( 30) link_BETA1-3 : bond 0.00374 ( 3) link_BETA1-3 : angle 5.04279 ( 9) covalent geometry : bond 0.00375 (11739) covalent geometry : angle 0.70375 (15891) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8244.00 seconds wall clock time: 142 minutes 39.03 seconds (8559.03 seconds total)