Starting phenix.real_space_refine on Sun Aug 24 07:49:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fyj_29580/08_2025/8fyj_29580.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fyj_29580/08_2025/8fyj_29580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fyj_29580/08_2025/8fyj_29580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fyj_29580/08_2025/8fyj_29580.map" model { file = "/net/cci-nas-00/data/ceres_data/8fyj_29580/08_2025/8fyj_29580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fyj_29580/08_2025/8fyj_29580.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3579 atoms to isotropic. 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 100 5.16 5 C 9454 2.51 5 N 2576 2.21 5 O 2897 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15027 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2802 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 20, 'TRANS': 336} Chain breaks: 4 Chain: "B" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2783 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 20, 'TRANS': 334} Chain breaks: 4 Chain: "C" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3255 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 21, 'TRANS': 390} Chain breaks: 7 Chain: "D" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 989 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "E" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 989 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "F" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1020 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain breaks: 1 Chain: "Y" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "Z" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.51, per 1000 atoms: 0.23 Number of scatterers: 15027 At special positions: 0 Unit cell: (109.824, 129.792, 189.696, 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 100 16.00 O 2897 8.00 N 2576 7.00 C 9454 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 16 " - pdb=" SG CYS Y 84 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 130 " - pdb=" SG CYS Y 159 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 16 " - pdb=" SG CYS Z 84 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 130 " - pdb=" SG CYS Z 159 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " BMA N 3 " - " MAN N 4 " ALPHA1-6 " BMA H 3 " - " MAN H 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG B 601 " - " ASN B 234 " " NAG B 602 " - " ASN B 386 " " NAG B 603 " - " ASN B 448 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 156 " " NAG C 603 " - " ASN C 295 " " NAG G 1 " - " ASN A 262 " " NAG H 1 " - " ASN A 276 " " NAG I 1 " - " ASN A 363 " " NAG J 1 " - " ASN B 262 " " NAG K 1 " - " ASN B 276 " " NAG L 1 " - " ASN B 363 " " NAG N 1 " - " ASN C 262 " " NAG O 1 " - " ASN C 276 " Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 710.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3454 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 32 sheets defined 26.2% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 337 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 474 through 483 removed outlier: 3.898A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 73 Processing helix chain 'B' and resid 99 through 116 Processing helix chain 'B' and resid 337 through 353 Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 474 through 483 removed outlier: 3.943A pdb=" N ASN B 478 " --> pdb=" O ASP B 474 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.652A pdb=" N LYS C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.682A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 334 through 354 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.551A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 392 removed outlier: 3.728A pdb=" N PHE C 391 " --> pdb=" O THR C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.876A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 483 removed outlier: 3.945A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 483 " --> pdb=" O TRP C 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 537 removed outlier: 3.551A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 540 No H-bonds generated for 'chain 'D' and resid 538 through 540' Processing helix chain 'D' and resid 564 through 596 removed outlier: 3.755A pdb=" N LEU D 568 " --> pdb=" O HIS D 564 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.604A pdb=" N MET D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 4.001A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 659 Processing helix chain 'E' and resid 521 through 526 Processing helix chain 'E' and resid 529 through 538 Processing helix chain 'E' and resid 562 through 596 removed outlier: 4.414A pdb=" N TRP E 571 " --> pdb=" O LYS E 567 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY E 572 " --> pdb=" O LEU E 568 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TRP E 596 " --> pdb=" O LEU E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 625 Processing helix chain 'E' and resid 627 through 637 removed outlier: 3.552A pdb=" N ASP E 632 " --> pdb=" O TRP E 628 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS E 633 " --> pdb=" O LEU E 629 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE E 635 " --> pdb=" O TRP E 631 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN E 637 " --> pdb=" O LYS E 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 659 removed outlier: 3.545A pdb=" N GLU E 647 " --> pdb=" O TYR E 643 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN E 650 " --> pdb=" O LEU E 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 542 Processing helix chain 'F' and resid 563 through 596 removed outlier: 3.606A pdb=" N LYS F 567 " --> pdb=" O GLN F 563 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 637 Processing helix chain 'F' and resid 638 through 654 Processing helix chain 'Y' and resid 58 through 62 removed outlier: 3.810A pdb=" N LEU Y 61 " --> pdb=" O ARG Y 58 " (cutoff:3.500A) Processing helix chain 'Y' and resid 75 through 79 Processing helix chain 'Y' and resid 150 through 154 removed outlier: 4.215A pdb=" N SER Y 154 " --> pdb=" O LEU Y 151 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 62 Processing helix chain 'Z' and resid 75 through 79 Processing helix chain 'Z' and resid 150 through 154 removed outlier: 4.060A pdb=" N SER Z 154 " --> pdb=" O LEU Z 151 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 39 removed outlier: 5.469A pdb=" N VAL A 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N THR D 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 4.161A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.969A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 199 through 202 Processing sheet with id=AA6, first strand: chain 'A' and resid 260 through 261 removed outlier: 7.648A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 11.172A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.421A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 12.298A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 12.007A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.035A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.909A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.564A pdb=" N CYS A 378 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 497 through 498 removed outlier: 4.691A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR E 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS E 604 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.792A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 53 through 55 Processing sheet with id=AB3, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.771A pdb=" N GLU B 91 " --> pdb=" O CYS B 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 198 through 199 Processing sheet with id=AB5, first strand: chain 'B' and resid 259 through 260 removed outlier: 3.987A pdb=" N VAL B 292 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N GLY B 451 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 10.530A pdb=" N THR B 290 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 11.830A pdb=" N ILE B 453 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 11.770A pdb=" N PHE B 288 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 10.892A pdb=" N THR B 455 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 11.490A pdb=" N VAL B 286 " --> pdb=" O THR B 455 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 259 through 260 removed outlier: 5.977A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 359 " --> pdb=" O TRP B 395 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 374 through 376 Processing sheet with id=AB8, first strand: chain 'C' and resid 38 through 40 removed outlier: 3.753A pdb=" N GLY C 495 " --> pdb=" O TYR C 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.570A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.373A pdb=" N LEU C 154 " --> pdb=" O VAL C 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.294A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 260 through 261 removed outlier: 3.819A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.565A pdb=" N MET C 271 " --> pdb=" O GLN C 287 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN C 295 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 301 through 307 removed outlier: 7.877A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.295A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Y' and resid 3 through 4 removed outlier: 3.640A pdb=" N VAL Y 4 " --> pdb=" O GLN Y 94 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP Y 28 " --> pdb=" O ILE Y 36 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN Y 40 " --> pdb=" O PHE Y 43 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE Y 43 " --> pdb=" O GLN Y 40 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Y' and resid 12 through 17 removed outlier: 3.584A pdb=" N CYS Y 16 " --> pdb=" O PHE Y 67 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE Y 67 " --> pdb=" O CYS Y 16 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Y' and resid 100 through 102 Processing sheet with id=AD2, first strand: chain 'Z' and resid 2 through 6 removed outlier: 6.549A pdb=" N LYS Z 2 " --> pdb=" O GLN Z 94 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU Z 96 " --> pdb=" O LYS Z 2 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL Z 4 " --> pdb=" O LEU Z 96 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU Z 37 " --> pdb=" O TRP Z 28 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASN Z 30 " --> pdb=" O LYS Z 35 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS Z 35 " --> pdb=" O ASN Z 30 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN Z 40 " --> pdb=" O PHE Z 43 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Z' and resid 13 through 14 Processing sheet with id=AD4, first strand: chain 'Z' and resid 99 through 102 removed outlier: 3.871A pdb=" N GLY Z 99 " --> pdb=" O GLU Z 119 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Z' and resid 137 through 139 510 hydrogen bonds defined for protein. 1374 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4811 1.35 - 1.47: 3652 1.47 - 1.59: 6718 1.59 - 1.71: 1 1.71 - 1.84: 132 Bond restraints: 15314 Sorted by residual: bond pdb=" C1 MAN H 4 " pdb=" O5 MAN H 4 " ideal model delta sigma weight residual 1.399 1.472 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" C1 BMA H 3 " pdb=" C2 BMA H 3 " ideal model delta sigma weight residual 1.519 1.591 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" CB PRO Y 68 " pdb=" CG PRO Y 68 " ideal model delta sigma weight residual 1.492 1.652 -0.160 5.00e-02 4.00e+02 1.02e+01 bond pdb=" C5 MAN H 4 " pdb=" O5 MAN H 4 " ideal model delta sigma weight residual 1.418 1.478 -0.060 2.00e-02 2.50e+03 8.97e+00 bond pdb=" C1 MAN H 4 " pdb=" C2 MAN H 4 " ideal model delta sigma weight residual 1.526 1.586 -0.060 2.00e-02 2.50e+03 8.96e+00 ... (remaining 15309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 20520 3.20 - 6.41: 202 6.41 - 9.61: 27 9.61 - 12.82: 6 12.82 - 16.02: 2 Bond angle restraints: 20757 Sorted by residual: angle pdb=" CA PRO Y 68 " pdb=" N PRO Y 68 " pdb=" CD PRO Y 68 " ideal model delta sigma weight residual 112.00 95.98 16.02 1.40e+00 5.10e-01 1.31e+02 angle pdb=" CA CYS A 205 " pdb=" CB CYS A 205 " pdb=" SG CYS A 205 " ideal model delta sigma weight residual 114.40 130.14 -15.74 2.30e+00 1.89e-01 4.68e+01 angle pdb=" C VAL Y 86 " pdb=" N GLU Y 87 " pdb=" CA GLU Y 87 " ideal model delta sigma weight residual 122.44 115.44 7.00 1.19e+00 7.06e-01 3.46e+01 angle pdb=" C ASN F 611 " pdb=" CA ASN F 611 " pdb=" CB ASN F 611 " ideal model delta sigma weight residual 116.54 110.55 5.99 1.15e+00 7.56e-01 2.72e+01 angle pdb=" N PRO Y 68 " pdb=" CD PRO Y 68 " pdb=" CG PRO Y 68 " ideal model delta sigma weight residual 103.20 96.40 6.80 1.50e+00 4.44e-01 2.05e+01 ... (remaining 20752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.79: 8752 23.79 - 47.58: 776 47.58 - 71.37: 92 71.37 - 95.15: 59 95.15 - 118.94: 22 Dihedral angle restraints: 9701 sinusoidal: 4384 harmonic: 5317 Sorted by residual: dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual 93.00 -178.81 -88.19 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 9.70 83.30 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 17.71 75.29 1 1.00e+01 1.00e-02 7.16e+01 ... (remaining 9698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2179 0.078 - 0.156: 259 0.156 - 0.234: 7 0.234 - 0.311: 9 0.311 - 0.389: 3 Chirality restraints: 2457 Sorted by residual: chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 5.10e+00 chirality pdb=" C4 NAG J 2 " pdb=" C3 NAG J 2 " pdb=" C5 NAG J 2 " pdb=" O4 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.53 -2.14 -0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" C1 NAG B 602 " pdb=" ND2 ASN B 386 " pdb=" C2 NAG B 602 " pdb=" O5 NAG B 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 2454 not shown) Planarity restraints: 2600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE Y 67 " 0.068 5.00e-02 4.00e+02 9.19e-02 1.35e+01 pdb=" N PRO Y 68 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO Y 68 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO Y 68 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 96 " -0.033 2.00e-02 2.50e+03 2.28e-02 1.30e+01 pdb=" CG TRP A 96 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP A 96 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 96 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 96 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 96 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 96 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 96 " -0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 96 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 96 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 304 " -0.248 9.50e-02 1.11e+02 1.11e-01 7.65e+00 pdb=" NE ARG C 304 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 304 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 304 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 304 " -0.010 2.00e-02 2.50e+03 ... (remaining 2597 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 314 2.66 - 3.22: 14651 3.22 - 3.78: 23397 3.78 - 4.34: 30428 4.34 - 4.90: 48920 Nonbonded interactions: 117710 Sorted by model distance: nonbonded pdb=" O SER E 528 " pdb=" OG1 THR E 627 " model vdw 2.105 3.040 nonbonded pdb=" OG SER B 365 " pdb=" O LYS Z 46 " model vdw 2.112 3.040 nonbonded pdb=" OG1 THR C 303 " pdb=" O ASP C 321A" model vdw 2.200 3.040 nonbonded pdb=" O MET E 535 " pdb=" OG1 THR E 538 " model vdw 2.206 3.040 nonbonded pdb=" OD1 ASN F 607 " pdb=" OG SER F 649 " model vdw 2.221 3.040 ... (remaining 117705 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 37 through 57 or resid 67 through 367 or resid 369 through \ 501 or resid 601)) selection = (chain 'B' and (resid 37 through 57 or resid 67 through 129 or resid 192 through \ 367 or resid 369 through 501 or resid 603)) selection = (chain 'C' and (resid 37 through 129 or resid 192 through 298 or resid 332 throu \ gh 367 or resid 369 through 459 or resid 463 through 501 or resid 601)) } ncs_group { reference = (chain 'D' and resid 519 through 657) selection = (chain 'E' and resid 519 through 657) selection = (chain 'F' and (resid 519 through 542 or resid 561 through 657)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.290 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.160 15379 Z= 0.229 Angle : 0.942 22.149 20920 Z= 0.457 Chirality : 0.050 0.389 2457 Planarity : 0.005 0.111 2585 Dihedral : 18.488 118.943 6151 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.61 % Allowed : 26.81 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.19), residues: 1798 helix: 0.05 (0.24), residues: 426 sheet: -0.46 (0.29), residues: 330 loop : -1.74 (0.17), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 327 TYR 0.022 0.002 TYR D 586 PHE 0.031 0.002 PHE C 382 TRP 0.061 0.003 TRP A 96 HIS 0.010 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00487 (15314) covalent geometry : angle 0.86530 (20757) SS BOND : bond 0.00348 ( 32) SS BOND : angle 1.75264 ( 64) hydrogen bonds : bond 0.18311 ( 506) hydrogen bonds : angle 8.07755 ( 1374) link_ALPHA1-3 : bond 0.00549 ( 3) link_ALPHA1-3 : angle 2.50862 ( 9) link_ALPHA1-6 : bond 0.01363 ( 1) link_ALPHA1-6 : angle 2.50567 ( 3) link_BETA1-4 : bond 0.01768 ( 14) link_BETA1-4 : angle 7.08071 ( 42) link_NAG-ASN : bond 0.00775 ( 15) link_NAG-ASN : angle 3.74747 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 217 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 MET cc_start: 0.8795 (ppp) cc_final: 0.8585 (ppp) REVERT: C 100 MET cc_start: 0.4823 (tpt) cc_final: 0.4551 (tpt) REVERT: C 424 ILE cc_start: 0.7266 (mt) cc_final: 0.6100 (mm) REVERT: C 479 TRP cc_start: 0.7337 (m-90) cc_final: 0.7062 (m-90) REVERT: E 530 MET cc_start: 0.7516 (mtm) cc_final: 0.7202 (mtm) outliers start: 10 outliers final: 6 residues processed: 222 average time/residue: 0.0938 time to fit residues: 33.0524 Evaluate side-chains 212 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 206 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain Y residue 71 ILE Chi-restraints excluded: chain Z residue 98 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 GLN C 80 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS D 656 ASN Y 139 GLN Z 27 HIS ** Z 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.126563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.095395 restraints weight = 41826.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.093210 restraints weight = 28964.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.094337 restraints weight = 31677.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.094313 restraints weight = 24099.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.094620 restraints weight = 21106.927| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 15379 Z= 0.216 Angle : 0.820 20.224 20920 Z= 0.383 Chirality : 0.049 0.465 2457 Planarity : 0.005 0.053 2585 Dihedral : 12.793 102.369 2646 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 4.02 % Allowed : 24.68 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.19), residues: 1798 helix: 0.31 (0.24), residues: 447 sheet: -0.71 (0.27), residues: 368 loop : -1.84 (0.18), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 298 TYR 0.016 0.002 TYR B 40 PHE 0.026 0.002 PHE C 382 TRP 0.025 0.002 TRP A 479 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00477 (15314) covalent geometry : angle 0.74425 (20757) SS BOND : bond 0.00353 ( 32) SS BOND : angle 1.07961 ( 64) hydrogen bonds : bond 0.05285 ( 506) hydrogen bonds : angle 6.12704 ( 1374) link_ALPHA1-3 : bond 0.01288 ( 3) link_ALPHA1-3 : angle 2.02753 ( 9) link_ALPHA1-6 : bond 0.03164 ( 1) link_ALPHA1-6 : angle 4.33645 ( 3) link_BETA1-4 : bond 0.01752 ( 14) link_BETA1-4 : angle 6.41654 ( 42) link_NAG-ASN : bond 0.00861 ( 15) link_NAG-ASN : angle 3.85623 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 224 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8072 (pp) REVERT: A 252 LYS cc_start: 0.8317 (mmtp) cc_final: 0.8003 (mmtm) REVERT: B 111 LEU cc_start: 0.8636 (tp) cc_final: 0.8364 (tt) REVERT: B 271 MET cc_start: 0.8037 (mmm) cc_final: 0.7744 (mmt) REVERT: C 95 MET cc_start: 0.8810 (ppp) cc_final: 0.8101 (ppp) REVERT: C 96 TRP cc_start: 0.8806 (m100) cc_final: 0.8432 (m100) REVERT: C 479 TRP cc_start: 0.7329 (m-90) cc_final: 0.6829 (m-90) REVERT: C 483 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7349 (pp) REVERT: D 530 MET cc_start: 0.6020 (ppp) cc_final: 0.5756 (ppp) REVERT: E 530 MET cc_start: 0.7507 (mtm) cc_final: 0.7190 (mtm) REVERT: E 647 GLU cc_start: 0.6833 (tp30) cc_final: 0.6623 (tp30) REVERT: F 626 MET cc_start: 0.8218 (mmm) cc_final: 0.7965 (tmm) REVERT: F 628 TRP cc_start: 0.6212 (OUTLIER) cc_final: 0.3894 (t60) outliers start: 66 outliers final: 38 residues processed: 271 average time/residue: 0.0991 time to fit residues: 42.8193 Evaluate side-chains 237 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 562 GLN Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain F residue 577 GLN Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 76 ILE Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain Y residue 160 THR Chi-restraints excluded: chain Z residue 98 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 149 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 156 optimal weight: 0.0030 chunk 53 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 165 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS C 440 GLN E 656 ASN Y 137 ASN Z 25 GLN ** Z 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.126310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.094599 restraints weight = 41886.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.092677 restraints weight = 27795.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.093441 restraints weight = 30057.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.094031 restraints weight = 21606.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.094342 restraints weight = 19675.924| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 15379 Z= 0.194 Angle : 0.783 20.011 20920 Z= 0.364 Chirality : 0.049 0.466 2457 Planarity : 0.004 0.052 2585 Dihedral : 10.942 95.341 2640 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.81 % Allowed : 24.98 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.19), residues: 1798 helix: 0.31 (0.24), residues: 447 sheet: -0.77 (0.27), residues: 377 loop : -1.84 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Z 131 TYR 0.021 0.002 TYR C 318 PHE 0.019 0.002 PHE C 317 TRP 0.036 0.002 TRP D 623 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00434 (15314) covalent geometry : angle 0.70482 (20757) SS BOND : bond 0.00484 ( 32) SS BOND : angle 1.17021 ( 64) hydrogen bonds : bond 0.04618 ( 506) hydrogen bonds : angle 5.78808 ( 1374) link_ALPHA1-3 : bond 0.01225 ( 3) link_ALPHA1-3 : angle 2.14567 ( 9) link_ALPHA1-6 : bond 0.02681 ( 1) link_ALPHA1-6 : angle 4.31067 ( 3) link_BETA1-4 : bond 0.01788 ( 14) link_BETA1-4 : angle 6.29100 ( 42) link_NAG-ASN : bond 0.00788 ( 15) link_NAG-ASN : angle 3.84390 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 212 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.9017 (OUTLIER) cc_final: 0.8611 (m110) REVERT: A 252 LYS cc_start: 0.8331 (mmtp) cc_final: 0.7947 (mmtm) REVERT: A 474 ASP cc_start: 0.7800 (t0) cc_final: 0.7461 (t70) REVERT: A 479 TRP cc_start: 0.8155 (m-90) cc_final: 0.7625 (m-90) REVERT: B 80 ASN cc_start: 0.8862 (t0) cc_final: 0.8617 (t0) REVERT: C 95 MET cc_start: 0.8742 (ppp) cc_final: 0.8376 (ppp) REVERT: C 96 TRP cc_start: 0.8790 (m100) cc_final: 0.8402 (m100) REVERT: C 318 TYR cc_start: 0.7588 (t80) cc_final: 0.6767 (t80) REVERT: C 479 TRP cc_start: 0.7446 (m-90) cc_final: 0.7116 (m-90) REVERT: D 530 MET cc_start: 0.5968 (ppp) cc_final: 0.5760 (ppp) REVERT: E 530 MET cc_start: 0.7711 (mtm) cc_final: 0.7408 (mtm) REVERT: F 577 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8841 (mt0) outliers start: 79 outliers final: 48 residues processed: 271 average time/residue: 0.0940 time to fit residues: 40.8498 Evaluate side-chains 242 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 192 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 562 GLN Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain F residue 577 GLN Chi-restraints excluded: chain Y residue 11 THR Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain Y residue 160 THR Chi-restraints excluded: chain Z residue 44 LEU Chi-restraints excluded: chain Z residue 98 PHE Chi-restraints excluded: chain Z residue 158 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 156 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 85 optimal weight: 0.0970 chunk 115 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.126931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.095545 restraints weight = 42747.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.094050 restraints weight = 27930.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.094836 restraints weight = 31055.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.095247 restraints weight = 21791.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.096116 restraints weight = 19853.403| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15379 Z= 0.159 Angle : 0.756 19.886 20920 Z= 0.348 Chirality : 0.048 0.469 2457 Planarity : 0.004 0.050 2585 Dihedral : 9.738 92.005 2640 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.12 % Allowed : 25.47 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.19), residues: 1798 helix: 0.48 (0.25), residues: 441 sheet: -0.69 (0.27), residues: 370 loop : -1.76 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Z 131 TYR 0.029 0.002 TYR C 318 PHE 0.014 0.002 PHE B 53 TRP 0.044 0.002 TRP D 623 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00352 (15314) covalent geometry : angle 0.67982 (20757) SS BOND : bond 0.00368 ( 32) SS BOND : angle 0.82156 ( 64) hydrogen bonds : bond 0.04228 ( 506) hydrogen bonds : angle 5.62618 ( 1374) link_ALPHA1-3 : bond 0.01275 ( 3) link_ALPHA1-3 : angle 2.29038 ( 9) link_ALPHA1-6 : bond 0.02609 ( 1) link_ALPHA1-6 : angle 4.48788 ( 3) link_BETA1-4 : bond 0.01758 ( 14) link_BETA1-4 : angle 6.16380 ( 42) link_NAG-ASN : bond 0.00758 ( 15) link_NAG-ASN : angle 3.74441 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 212 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.6027 (pp20) REVERT: A 67 ASN cc_start: 0.9030 (OUTLIER) cc_final: 0.8599 (m110) REVERT: A 479 TRP cc_start: 0.8084 (m-90) cc_final: 0.7623 (m-90) REVERT: B 80 ASN cc_start: 0.8774 (t0) cc_final: 0.8569 (t0) REVERT: C 95 MET cc_start: 0.8779 (ppp) cc_final: 0.8072 (ppp) REVERT: C 96 TRP cc_start: 0.8741 (m100) cc_final: 0.8170 (m100) REVERT: C 300 ASN cc_start: 0.6192 (OUTLIER) cc_final: 0.5062 (t0) REVERT: C 318 TYR cc_start: 0.7695 (t80) cc_final: 0.6870 (t80) REVERT: C 479 TRP cc_start: 0.7347 (m-90) cc_final: 0.6876 (m-90) REVERT: C 483 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7498 (pp) REVERT: C 484 TYR cc_start: 0.8327 (p90) cc_final: 0.8099 (p90) REVERT: E 530 MET cc_start: 0.7505 (mtm) cc_final: 0.7280 (mtm) REVERT: E 622 ILE cc_start: 0.9499 (mm) cc_final: 0.9251 (tt) REVERT: F 621 GLU cc_start: 0.8440 (pt0) cc_final: 0.8195 (pt0) REVERT: F 626 MET cc_start: 0.8055 (mmm) cc_final: 0.7842 (tpp) REVERT: F 630 GLN cc_start: 0.7995 (mt0) cc_final: 0.7788 (pt0) outliers start: 84 outliers final: 55 residues processed: 276 average time/residue: 0.0907 time to fit residues: 40.4906 Evaluate side-chains 255 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 196 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 562 GLN Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 610 TRP Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Y residue 160 THR Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 25 GLN Chi-restraints excluded: chain Z residue 44 LEU Chi-restraints excluded: chain Z residue 98 PHE Chi-restraints excluded: chain Z residue 158 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 115 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 158 optimal weight: 40.0000 chunk 135 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 70 optimal weight: 0.4980 chunk 125 optimal weight: 0.0010 chunk 88 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 656 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.128449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.097199 restraints weight = 42482.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.095213 restraints weight = 27800.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.096321 restraints weight = 27284.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.096591 restraints weight = 20572.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.096730 restraints weight = 19325.142| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15379 Z= 0.130 Angle : 0.735 19.817 20920 Z= 0.337 Chirality : 0.047 0.464 2457 Planarity : 0.004 0.047 2585 Dihedral : 8.966 92.332 2640 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.45 % Allowed : 26.63 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.19), residues: 1798 helix: 0.66 (0.25), residues: 433 sheet: -0.84 (0.27), residues: 389 loop : -1.62 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Z 131 TYR 0.026 0.001 TYR C 318 PHE 0.013 0.001 PHE C 159 TRP 0.032 0.001 TRP C 316 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00274 (15314) covalent geometry : angle 0.65813 (20757) SS BOND : bond 0.00596 ( 32) SS BOND : angle 1.01912 ( 64) hydrogen bonds : bond 0.03844 ( 506) hydrogen bonds : angle 5.45357 ( 1374) link_ALPHA1-3 : bond 0.01414 ( 3) link_ALPHA1-3 : angle 2.40085 ( 9) link_ALPHA1-6 : bond 0.02495 ( 1) link_ALPHA1-6 : angle 4.53480 ( 3) link_BETA1-4 : bond 0.01739 ( 14) link_BETA1-4 : angle 6.04044 ( 42) link_NAG-ASN : bond 0.00762 ( 15) link_NAG-ASN : angle 3.63890 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 214 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.9035 (OUTLIER) cc_final: 0.8601 (m110) REVERT: A 102 GLU cc_start: 0.7233 (tm-30) cc_final: 0.7031 (tm-30) REVERT: A 107 ASP cc_start: 0.8206 (t0) cc_final: 0.7864 (t0) REVERT: A 252 LYS cc_start: 0.8155 (mmtp) cc_final: 0.7773 (mmtm) REVERT: A 434 MET cc_start: 0.5401 (OUTLIER) cc_final: 0.5139 (mmt) REVERT: A 479 TRP cc_start: 0.7887 (m-10) cc_final: 0.7260 (m-90) REVERT: C 95 MET cc_start: 0.8629 (ppp) cc_final: 0.7969 (ppp) REVERT: C 96 TRP cc_start: 0.8642 (m100) cc_final: 0.8090 (m100) REVERT: C 453 ILE cc_start: 0.9579 (OUTLIER) cc_final: 0.9084 (tp) REVERT: C 479 TRP cc_start: 0.7279 (m-90) cc_final: 0.6886 (m-90) REVERT: C 483 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7493 (pp) REVERT: D 602 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8693 (mp) REVERT: E 530 MET cc_start: 0.7503 (mtm) cc_final: 0.7237 (mtm) REVERT: E 595 ILE cc_start: 0.9108 (mt) cc_final: 0.8795 (mt) REVERT: F 621 GLU cc_start: 0.8444 (pt0) cc_final: 0.8225 (pt0) outliers start: 73 outliers final: 49 residues processed: 268 average time/residue: 0.0963 time to fit residues: 41.6842 Evaluate side-chains 250 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 196 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 562 GLN Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 610 TRP Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain Y residue 11 THR Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain Y residue 93 VAL Chi-restraints excluded: chain Z residue 25 GLN Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 64 GLN Chi-restraints excluded: chain Z residue 98 PHE Chi-restraints excluded: chain Z residue 158 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 160 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 152 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 175 optimal weight: 20.0000 chunk 79 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.122579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.092298 restraints weight = 41682.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.089823 restraints weight = 32768.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.090701 restraints weight = 37606.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.090971 restraints weight = 27646.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.091181 restraints weight = 23150.727| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 15379 Z= 0.315 Angle : 0.883 19.811 20920 Z= 0.422 Chirality : 0.051 0.462 2457 Planarity : 0.005 0.064 2585 Dihedral : 9.251 98.416 2640 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 6.70 % Allowed : 25.29 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.19), residues: 1798 helix: 0.20 (0.24), residues: 446 sheet: -0.85 (0.27), residues: 365 loop : -1.87 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Z 131 TYR 0.029 0.003 TYR C 318 PHE 0.030 0.003 PHE B 53 TRP 0.034 0.003 TRP B 479 HIS 0.006 0.002 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00715 (15314) covalent geometry : angle 0.81338 (20757) SS BOND : bond 0.00479 ( 32) SS BOND : angle 1.01267 ( 64) hydrogen bonds : bond 0.05064 ( 506) hydrogen bonds : angle 5.72647 ( 1374) link_ALPHA1-3 : bond 0.01041 ( 3) link_ALPHA1-3 : angle 2.75215 ( 9) link_ALPHA1-6 : bond 0.02609 ( 1) link_ALPHA1-6 : angle 4.18354 ( 3) link_BETA1-4 : bond 0.01606 ( 14) link_BETA1-4 : angle 6.28058 ( 42) link_NAG-ASN : bond 0.00864 ( 15) link_NAG-ASN : angle 4.06421 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 192 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.9099 (OUTLIER) cc_final: 0.8768 (m110) REVERT: A 252 LYS cc_start: 0.8335 (mmtp) cc_final: 0.7880 (mmtm) REVERT: A 434 MET cc_start: 0.5315 (OUTLIER) cc_final: 0.5112 (mmt) REVERT: A 474 ASP cc_start: 0.8251 (t0) cc_final: 0.7883 (t0) REVERT: A 479 TRP cc_start: 0.8243 (m-10) cc_final: 0.7847 (m-90) REVERT: B 80 ASN cc_start: 0.8669 (t0) cc_final: 0.8456 (t0) REVERT: B 210 PHE cc_start: 0.8400 (t80) cc_final: 0.7904 (t80) REVERT: B 271 MET cc_start: 0.7777 (mmt) cc_final: 0.7512 (mmm) REVERT: C 95 MET cc_start: 0.8823 (ppp) cc_final: 0.8144 (ppp) REVERT: C 96 TRP cc_start: 0.8848 (m100) cc_final: 0.8162 (m100) REVERT: C 479 TRP cc_start: 0.7538 (m-90) cc_final: 0.7140 (m-90) REVERT: C 483 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7488 (pp) REVERT: D 631 TRP cc_start: 0.8026 (OUTLIER) cc_final: 0.6492 (t60) REVERT: E 530 MET cc_start: 0.7585 (mtm) cc_final: 0.7351 (mtm) REVERT: E 642 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7653 (mt) REVERT: F 564 HIS cc_start: 0.6973 (m170) cc_final: 0.6723 (m170) outliers start: 110 outliers final: 73 residues processed: 282 average time/residue: 0.0963 time to fit residues: 43.9913 Evaluate side-chains 259 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 181 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 562 GLN Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 610 TRP Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 631 TRP Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain Y residue 11 THR Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain Y residue 93 VAL Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 44 LEU Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 98 PHE Chi-restraints excluded: chain Z residue 158 THR Chi-restraints excluded: chain Z residue 174 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 164 optimal weight: 0.7980 chunk 180 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 20 optimal weight: 0.0770 chunk 74 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 656 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.126253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.095184 restraints weight = 41556.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.092912 restraints weight = 27190.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.093777 restraints weight = 30026.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.094400 restraints weight = 20716.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.095131 restraints weight = 18624.722| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15379 Z= 0.138 Angle : 0.767 19.685 20920 Z= 0.354 Chirality : 0.048 0.457 2457 Planarity : 0.004 0.050 2585 Dihedral : 8.398 96.037 2638 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.12 % Allowed : 26.63 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.19), residues: 1798 helix: 0.36 (0.25), residues: 440 sheet: -0.80 (0.27), residues: 377 loop : -1.70 (0.18), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Z 131 TYR 0.022 0.002 TYR C 318 PHE 0.015 0.001 PHE C 233 TRP 0.027 0.002 TRP C 316 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00297 (15314) covalent geometry : angle 0.69391 (20757) SS BOND : bond 0.00311 ( 32) SS BOND : angle 1.01250 ( 64) hydrogen bonds : bond 0.03907 ( 506) hydrogen bonds : angle 5.45756 ( 1374) link_ALPHA1-3 : bond 0.01446 ( 3) link_ALPHA1-3 : angle 2.72660 ( 9) link_ALPHA1-6 : bond 0.02352 ( 1) link_ALPHA1-6 : angle 4.31937 ( 3) link_BETA1-4 : bond 0.01701 ( 14) link_BETA1-4 : angle 5.95460 ( 42) link_NAG-ASN : bond 0.00774 ( 15) link_NAG-ASN : angle 3.75216 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 211 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.9065 (OUTLIER) cc_final: 0.8657 (m110) REVERT: A 72 HIS cc_start: 0.7464 (OUTLIER) cc_final: 0.6858 (t70) REVERT: A 102 GLU cc_start: 0.7462 (tm-30) cc_final: 0.6811 (tm-30) REVERT: A 252 LYS cc_start: 0.8232 (mmtp) cc_final: 0.7779 (mmtm) REVERT: A 479 TRP cc_start: 0.8069 (m-10) cc_final: 0.7680 (m-90) REVERT: B 57 ASP cc_start: 0.8165 (p0) cc_final: 0.7632 (p0) REVERT: B 66 HIS cc_start: 0.7423 (OUTLIER) cc_final: 0.7201 (t-170) REVERT: B 210 PHE cc_start: 0.8266 (t80) cc_final: 0.7665 (t80) REVERT: C 95 MET cc_start: 0.8667 (ppp) cc_final: 0.7912 (ppp) REVERT: C 96 TRP cc_start: 0.8675 (m100) cc_final: 0.8101 (m100) REVERT: C 479 TRP cc_start: 0.7424 (m-90) cc_final: 0.7031 (m-90) REVERT: C 483 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7678 (pp) REVERT: E 530 MET cc_start: 0.7609 (mtm) cc_final: 0.7378 (mtm) REVERT: E 589 ASP cc_start: 0.8945 (m-30) cc_final: 0.8667 (m-30) REVERT: F 645 LEU cc_start: 0.9079 (mm) cc_final: 0.8674 (tp) outliers start: 84 outliers final: 63 residues processed: 274 average time/residue: 0.0935 time to fit residues: 41.5702 Evaluate side-chains 253 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 186 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 562 GLN Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 610 TRP Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain E residue 519 PHE Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain Y residue 11 THR Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain Y residue 93 VAL Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Y residue 160 THR Chi-restraints excluded: chain Z residue 25 GLN Chi-restraints excluded: chain Z residue 44 LEU Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 98 PHE Chi-restraints excluded: chain Z residue 158 THR Chi-restraints excluded: chain Z residue 174 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 19 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 161 optimal weight: 40.0000 chunk 60 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 169 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 22 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN E 656 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.125155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.094926 restraints weight = 42767.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.093120 restraints weight = 29215.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.093902 restraints weight = 34296.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.094308 restraints weight = 23065.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.095127 restraints weight = 20303.471| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 15379 Z= 0.180 Angle : 0.784 19.601 20920 Z= 0.363 Chirality : 0.048 0.457 2457 Planarity : 0.004 0.048 2585 Dihedral : 8.120 95.541 2638 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.17 % Favored : 93.77 % Rotamer: Outliers : 4.88 % Allowed : 28.09 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.19), residues: 1798 helix: 0.34 (0.25), residues: 437 sheet: -0.81 (0.27), residues: 377 loop : -1.72 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Z 131 TYR 0.024 0.002 TYR C 318 PHE 0.016 0.002 PHE B 53 TRP 0.037 0.002 TRP C 316 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00408 (15314) covalent geometry : angle 0.71208 (20757) SS BOND : bond 0.00313 ( 32) SS BOND : angle 0.96198 ( 64) hydrogen bonds : bond 0.04152 ( 506) hydrogen bonds : angle 5.42773 ( 1374) link_ALPHA1-3 : bond 0.01292 ( 3) link_ALPHA1-3 : angle 2.94556 ( 9) link_ALPHA1-6 : bond 0.02182 ( 1) link_ALPHA1-6 : angle 4.22212 ( 3) link_BETA1-4 : bond 0.01627 ( 14) link_BETA1-4 : angle 5.96688 ( 42) link_NAG-ASN : bond 0.00747 ( 15) link_NAG-ASN : angle 3.81137 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 182 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.7469 (OUTLIER) cc_final: 0.6868 (t70) REVERT: A 102 GLU cc_start: 0.7541 (tm-30) cc_final: 0.6878 (tm-30) REVERT: A 252 LYS cc_start: 0.8227 (mmtp) cc_final: 0.7929 (mmtm) REVERT: A 474 ASP cc_start: 0.8218 (t0) cc_final: 0.7780 (t0) REVERT: A 479 TRP cc_start: 0.8144 (m-10) cc_final: 0.7743 (m-90) REVERT: B 57 ASP cc_start: 0.8155 (p0) cc_final: 0.7653 (p0) REVERT: B 210 PHE cc_start: 0.8317 (t80) cc_final: 0.7806 (t80) REVERT: C 95 MET cc_start: 0.8589 (ppp) cc_final: 0.7478 (ppp) REVERT: C 96 TRP cc_start: 0.8676 (m100) cc_final: 0.8237 (m100) REVERT: C 479 TRP cc_start: 0.7463 (m-90) cc_final: 0.6995 (m-90) REVERT: C 483 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7609 (pp) REVERT: E 530 MET cc_start: 0.7531 (mtm) cc_final: 0.7249 (mtm) REVERT: E 589 ASP cc_start: 0.8865 (m-30) cc_final: 0.8627 (m-30) outliers start: 80 outliers final: 61 residues processed: 247 average time/residue: 0.1058 time to fit residues: 41.9632 Evaluate side-chains 236 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 173 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 562 GLN Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 610 TRP Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 519 PHE Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain Y residue 11 THR Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain Y residue 93 VAL Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Y residue 160 THR Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 25 GLN Chi-restraints excluded: chain Z residue 44 LEU Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 98 PHE Chi-restraints excluded: chain Z residue 158 THR Chi-restraints excluded: chain Z residue 174 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 158 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.124925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.094477 restraints weight = 41933.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.092438 restraints weight = 30242.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.093572 restraints weight = 32768.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.093803 restraints weight = 22290.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.095011 restraints weight = 20387.269| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15379 Z= 0.191 Angle : 0.794 19.523 20920 Z= 0.368 Chirality : 0.049 0.452 2457 Planarity : 0.004 0.047 2585 Dihedral : 7.955 94.111 2638 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.95 % Favored : 93.99 % Rotamer: Outliers : 4.51 % Allowed : 28.88 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.19), residues: 1798 helix: 0.26 (0.25), residues: 437 sheet: -0.83 (0.27), residues: 376 loop : -1.71 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Z 131 TYR 0.023 0.002 TYR C 318 PHE 0.016 0.002 PHE B 53 TRP 0.052 0.002 TRP C 338 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00435 (15314) covalent geometry : angle 0.72273 (20757) SS BOND : bond 0.00333 ( 32) SS BOND : angle 0.90071 ( 64) hydrogen bonds : bond 0.04109 ( 506) hydrogen bonds : angle 5.41172 ( 1374) link_ALPHA1-3 : bond 0.01124 ( 3) link_ALPHA1-3 : angle 3.10090 ( 9) link_ALPHA1-6 : bond 0.02085 ( 1) link_ALPHA1-6 : angle 4.18091 ( 3) link_BETA1-4 : bond 0.01591 ( 14) link_BETA1-4 : angle 5.93592 ( 42) link_NAG-ASN : bond 0.00746 ( 15) link_NAG-ASN : angle 3.83531 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 177 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7551 (tm-30) cc_final: 0.6896 (tm-30) REVERT: A 252 LYS cc_start: 0.8239 (mmtp) cc_final: 0.7924 (mmtm) REVERT: A 474 ASP cc_start: 0.8277 (t0) cc_final: 0.7853 (t0) REVERT: A 479 TRP cc_start: 0.8183 (m-10) cc_final: 0.7771 (m-90) REVERT: B 57 ASP cc_start: 0.8197 (p0) cc_final: 0.7688 (p0) REVERT: B 210 PHE cc_start: 0.8358 (t80) cc_final: 0.7913 (t80) REVERT: C 95 MET cc_start: 0.8579 (ppp) cc_final: 0.7410 (ppp) REVERT: C 96 TRP cc_start: 0.8717 (m100) cc_final: 0.8356 (m100) REVERT: C 342 LEU cc_start: 0.8620 (mp) cc_final: 0.8278 (tp) REVERT: C 352 HIS cc_start: 0.7528 (OUTLIER) cc_final: 0.7274 (m90) REVERT: C 479 TRP cc_start: 0.7476 (m-90) cc_final: 0.7118 (m-90) REVERT: C 483 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7480 (pp) REVERT: E 530 MET cc_start: 0.7553 (mtm) cc_final: 0.7283 (mtm) REVERT: E 654 GLU cc_start: 0.8271 (pp20) cc_final: 0.7628 (pp20) outliers start: 74 outliers final: 65 residues processed: 238 average time/residue: 0.0975 time to fit residues: 37.6303 Evaluate side-chains 241 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 174 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 352 HIS Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 562 GLN Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 610 TRP Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 519 PHE Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain Y residue 11 THR Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain Y residue 93 VAL Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Y residue 160 THR Chi-restraints excluded: chain Z residue 25 GLN Chi-restraints excluded: chain Z residue 44 LEU Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 98 PHE Chi-restraints excluded: chain Z residue 158 THR Chi-restraints excluded: chain Z residue 174 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 7 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 92 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.126680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.095858 restraints weight = 42021.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.093779 restraints weight = 29452.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.094918 restraints weight = 29644.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.095409 restraints weight = 20735.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.096018 restraints weight = 19241.964| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15379 Z= 0.138 Angle : 0.761 19.394 20920 Z= 0.350 Chirality : 0.048 0.449 2457 Planarity : 0.004 0.049 2585 Dihedral : 7.602 89.799 2638 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.45 % Favored : 94.49 % Rotamer: Outliers : 4.14 % Allowed : 29.19 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.19), residues: 1798 helix: 0.38 (0.25), residues: 437 sheet: -0.71 (0.27), residues: 375 loop : -1.62 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Z 131 TYR 0.022 0.002 TYR C 318 PHE 0.013 0.001 PHE C 382 TRP 0.046 0.002 TRP C 338 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00306 (15314) covalent geometry : angle 0.69055 (20757) SS BOND : bond 0.00270 ( 32) SS BOND : angle 0.79268 ( 64) hydrogen bonds : bond 0.03814 ( 506) hydrogen bonds : angle 5.32867 ( 1374) link_ALPHA1-3 : bond 0.01093 ( 3) link_ALPHA1-3 : angle 3.03233 ( 9) link_ALPHA1-6 : bond 0.01953 ( 1) link_ALPHA1-6 : angle 4.19785 ( 3) link_BETA1-4 : bond 0.01606 ( 14) link_BETA1-4 : angle 5.79213 ( 42) link_NAG-ASN : bond 0.00742 ( 15) link_NAG-ASN : angle 3.73218 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3596 Ramachandran restraints generated. 1798 Oldfield, 0 Emsley, 1798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 190 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7808 (m-30) REVERT: A 102 GLU cc_start: 0.7486 (tm-30) cc_final: 0.6831 (tm-30) REVERT: A 252 LYS cc_start: 0.8158 (mmtp) cc_final: 0.7908 (mmtm) REVERT: A 474 ASP cc_start: 0.8175 (t0) cc_final: 0.7725 (t0) REVERT: A 479 TRP cc_start: 0.8071 (m-10) cc_final: 0.7690 (m-90) REVERT: B 57 ASP cc_start: 0.8152 (p0) cc_final: 0.7620 (p0) REVERT: B 210 PHE cc_start: 0.8330 (t80) cc_final: 0.7875 (t80) REVERT: C 95 MET cc_start: 0.8489 (ppp) cc_final: 0.7734 (ppp) REVERT: C 96 TRP cc_start: 0.8628 (m100) cc_final: 0.8206 (m100) REVERT: C 342 LEU cc_start: 0.8583 (mp) cc_final: 0.8176 (tt) REVERT: C 352 HIS cc_start: 0.7498 (OUTLIER) cc_final: 0.7257 (m90) REVERT: C 416 LEU cc_start: 0.7136 (pt) cc_final: 0.6829 (pt) REVERT: C 479 TRP cc_start: 0.7358 (m-90) cc_final: 0.6888 (m-90) REVERT: C 483 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7290 (pp) REVERT: E 530 MET cc_start: 0.7581 (mtm) cc_final: 0.7322 (mtm) REVERT: E 654 GLU cc_start: 0.8191 (pp20) cc_final: 0.7457 (pp20) outliers start: 68 outliers final: 60 residues processed: 242 average time/residue: 0.0967 time to fit residues: 37.8375 Evaluate side-chains 247 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 184 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 352 HIS Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 562 GLN Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 610 TRP Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 519 PHE Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain Y residue 11 THR Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain Y residue 93 VAL Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Y residue 160 THR Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 25 GLN Chi-restraints excluded: chain Z residue 44 LEU Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 98 PHE Chi-restraints excluded: chain Z residue 158 THR Chi-restraints excluded: chain Z residue 174 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 76 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 28 optimal weight: 0.0670 chunk 113 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 159 optimal weight: 20.0000 chunk 176 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 129 GLN Y 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.124363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.093781 restraints weight = 41674.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.091843 restraints weight = 29137.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.092629 restraints weight = 34330.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.093157 restraints weight = 22614.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.093581 restraints weight = 19877.957| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15379 Z= 0.206 Angle : 0.807 19.318 20920 Z= 0.376 Chirality : 0.049 0.446 2457 Planarity : 0.004 0.046 2585 Dihedral : 7.707 87.004 2638 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.28 % Favored : 93.66 % Rotamer: Outliers : 4.45 % Allowed : 29.07 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.19), residues: 1798 helix: 0.36 (0.25), residues: 431 sheet: -0.70 (0.27), residues: 370 loop : -1.64 (0.18), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Z 131 TYR 0.023 0.002 TYR C 318 PHE 0.020 0.002 PHE Y 43 TRP 0.044 0.002 TRP C 338 HIS 0.004 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00470 (15314) covalent geometry : angle 0.73772 (20757) SS BOND : bond 0.00311 ( 32) SS BOND : angle 0.92463 ( 64) hydrogen bonds : bond 0.04288 ( 506) hydrogen bonds : angle 5.36230 ( 1374) link_ALPHA1-3 : bond 0.00873 ( 3) link_ALPHA1-3 : angle 3.02581 ( 9) link_ALPHA1-6 : bond 0.01901 ( 1) link_ALPHA1-6 : angle 4.09356 ( 3) link_BETA1-4 : bond 0.01525 ( 14) link_BETA1-4 : angle 5.87654 ( 42) link_NAG-ASN : bond 0.00754 ( 15) link_NAG-ASN : angle 3.87424 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2303.96 seconds wall clock time: 40 minutes 54.88 seconds (2454.88 seconds total)