Starting phenix.real_space_refine on Sat Jul 4 03:50:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fyj_29580/07_2026/8fyj_29580.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fyj_29580/07_2026/8fyj_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fyj_29580/07_2026/8fyj_29580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fyj_29580/07_2026/8fyj_29580.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fyj_29580/07_2026/8fyj_29580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fyj_29580/07_2026/8fyj_29580.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8fyj_29580/07_2026/8fyj_29580.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fyj_29580/07_2026/8fyj_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-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 3.28, per 1000 atoms: 0.22 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: 1.05 Conformation dependent library (CDL) restraints added in 498.6 milliseconds 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: 2.46 Time building geometry restraints manager: 1.38 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 - 17.93: 7740 17.93 - 35.86: 995 35.86 - 53.80: 215 53.80 - 71.73: 30 71.73 - 89.66: 25 Dihedral angle restraints: 9005 sinusoidal: 3688 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 9002 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: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 13.380 Find NCS groups from input model: 0.360 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 : 16.322 89.659 5455 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 are 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/Z covalent geometry : bond 0.00487 / 0.23 (15314) covalent geometry : angle 0.86530 / 0.44 (20757) SS BOND : bond 0.00348 / 0.21 ( 32) SS BOND : angle 1.75264 / 0.87 ( 64) hydrogen bonds : bond 0.18311 / 12.42 ( 506) hydrogen bonds : angle 8.07755 / 5.56 ( 1374) link_ALPHA1-3 : bond 0.00549 / 0.28 ( 3) link_ALPHA1-3 : angle 2.50862 / 1.08 ( 9) link_ALPHA1-6 : bond 0.01363 / 0.72 ( 1) link_ALPHA1-6 : angle 2.50567 / 1.07 ( 3) link_BETA1-4 : bond 0.01768 / 1.01 ( 14) link_BETA1-4 : angle 7.08071 / 4.69 ( 42) link_NAG-ASN : bond 0.00775 / 0.36 ( 15) link_NAG-ASN : angle 3.74747 / 2.32 ( 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 : 0.613 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: 0.8794 (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: 0.1018 time to fit residues: 35.5374 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 : 0.625 ------------------------------------------------------------------------------- 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... 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 = 0.126566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.095655 restraints weight = 41832.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.093925 restraints weight = 29707.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.094814 restraints weight = 32240.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.094723 restraints weight = 25327.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.094859 restraints weight = 21546.828| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 15379 Z= 0.214 Angle : 0.809 20.007 20920 Z= 0.380 Chirality : 0.049 0.505 2457 Planarity : 0.005 0.053 2585 Dihedral : 5.559 59.023 1950 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.96 % Allowed : 24.62 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (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 0.009 0.001 ARG Z 131 TYR 0.015 0.002 TYR A 217 PHE 0.027 0.002 PHE C 382 TRP 0.024 0.002 TRP A 479 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (15314) covalent geometry : angle 0.73595 / 0.36 (20757) SS BOND : bond 0.00317 / 0.21 ( 32) SS BOND : angle 1.02275 / 0.60 ( 64) hydrogen bonds : bond 0.05116 / 3.50 ( 506) hydrogen bonds : angle 6.11758 / 4.22 ( 1374) link_ALPHA1-3 : bond 0.00811 / 0.41 ( 3) link_ALPHA1-3 : angle 1.98463 / 0.79 ( 9) link_ALPHA1-6 : bond 0.01584 / 0.83 ( 1) link_ALPHA1-6 : angle 3.35915 / 1.40 ( 3) link_BETA1-4 : bond 0.01761 / 0.92 ( 14) link_BETA1-4 : angle 6.23917 / 4.17 ( 42) link_NAG-ASN : bond 0.00839 / 0.39 ( 15) link_NAG-ASN : angle 3.84042 / 2.46 ( 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 289 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 224 time to evaluate : 0.609 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: 0.8318 (OUTLIER) cc_final: 0.8073 (pp) REVERT: A 252 LYS cc_start: 0.8315 (mmtp) cc_final: 0.8012 (mmtm) REVERT: B 111 LEU cc_start: 0.8626 (tp) cc_final: 0.8363 (tt) REVERT: B 271 MET cc_start: 0.8049 (mmm) cc_final: 0.7819 (mmt) REVERT: C 95 MET cc_start: 0.8815 (ppp) cc_final: 0.8101 (ppp) REVERT: C 96 TRP cc_start: 0.8802 (m100) cc_final: 0.8424 (m100) REVERT: C 479 TRP cc_start: 0.7325 (m-90) cc_final: 0.6845 (m-90) REVERT: C 483 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7325 (pp) REVERT: D 530 MET cc_start: 0.6004 (ppp) cc_final: 0.5745 (ppp) REVERT: E 530 MET cc_start: 0.7491 (mtm) cc_final: 0.7179 (mtm) REVERT: E 647 GLU cc_start: 0.6813 (tp30) cc_final: 0.6595 (tp30) REVERT: F 626 MET cc_start: 0.8199 (mmm) cc_final: 0.7986 (tmm) outliers start: 65 outliers final: 40 residues processed: 270 average time/residue: 0.0921 time to fit residues: 40.0837 Evaluate side-chains 239 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 197 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 109 ILE 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: 10.0000 chunk 52 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 chunk 165 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 154 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN C 332 ASN C 352 HIS ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.123414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.093140 restraints weight = 41872.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.090975 restraints weight = 31673.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.092127 restraints weight = 34715.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.092298 restraints weight = 24303.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.092517 restraints weight = 21240.239| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 15379 Z= 0.283 Angle : 0.854 19.804 20920 Z= 0.406 Chirality : 0.051 0.482 2457 Planarity : 0.005 0.058 2585 Dihedral : 5.467 42.131 1944 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 6.40 % Allowed : 23.89 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.18), residues: 1798 helix: 0.15 (0.24), residues: 450 sheet: -0.98 (0.26), residues: 383 loop : -1.98 (0.18), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 476 TYR 0.019 0.002 TYR B 40 PHE 0.024 0.002 PHE B 53 TRP 0.040 0.003 TRP D 623 HIS 0.007 0.002 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.28 (15314) covalent geometry : angle 0.78104 / 0.39 (20757) SS BOND : bond 0.00530 / 0.30 ( 32) SS BOND : angle 1.28828 / 0.73 ( 64) hydrogen bonds : bond 0.05207 / 3.55 ( 506) hydrogen bonds : angle 5.91971 / 4.06 ( 1374) link_ALPHA1-3 : bond 0.00711 / 0.36 ( 3) link_ALPHA1-3 : angle 2.04877 / 0.83 ( 9) link_ALPHA1-6 : bond 0.01244 / 0.65 ( 1) link_ALPHA1-6 : angle 2.97462 / 1.24 ( 3) link_BETA1-4 : bond 0.01849 / 0.99 ( 14) link_BETA1-4 : angle 6.33030 / 4.19 ( 42) link_NAG-ASN : bond 0.00848 / 0.40 ( 15) link_NAG-ASN : angle 4.06718 / 2.61 ( 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 305 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 200 time to evaluate : 0.512 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: 0.9057 (OUTLIER) cc_final: 0.8649 (m110) REVERT: A 193 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8181 (pp) REVERT: A 252 LYS cc_start: 0.8448 (mmtp) cc_final: 0.8024 (mmtm) REVERT: A 479 TRP cc_start: 0.8319 (m-90) cc_final: 0.7834 (m-90) REVERT: B 66 HIS cc_start: 0.7701 (OUTLIER) cc_final: 0.7464 (t-170) REVERT: B 80 ASN cc_start: 0.8847 (t0) cc_final: 0.8607 (t0) REVERT: C 96 TRP cc_start: 0.8906 (m100) cc_final: 0.8437 (m100) REVERT: C 318 TYR cc_start: 0.7618 (t80) cc_final: 0.6691 (t80) REVERT: C 479 TRP cc_start: 0.7506 (m-90) cc_final: 0.7245 (m-90) REVERT: D 530 MET cc_start: 0.6282 (ppp) cc_final: 0.5897 (ppp) REVERT: E 530 MET cc_start: 0.7699 (mtm) cc_final: 0.7443 (mtm) REVERT: Y 54 ARG cc_start: 0.8566 (ttp-110) cc_final: 0.8359 (ttm-80) outliers start: 105 outliers final: 65 residues processed: 282 average time/residue: 0.0961 time to fit residues: 43.5221 Evaluate side-chains 252 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 184 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 193 LEU 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 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 66 HIS 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 260 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 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 234 ASN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 396 ILE 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 566 LEU Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 610 TRP Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 580 VAL Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 577 GLN Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain Y residue 11 THR Chi-restraints excluded: chain Y residue 17 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 11 THR Chi-restraints excluded: chain Z residue 24 ILE 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: 20.0000 chunk 98 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 161 optimal weight: 50.0000 chunk 134 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN C 330 HIS C 352 HIS C 440 GLN E 656 ASN Z 25 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.124405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.093537 restraints weight = 41706.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.091707 restraints weight = 29042.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.092721 restraints weight = 33124.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.092930 restraints weight = 22100.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.093609 restraints weight = 20192.924| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 15379 Z= 0.206 Angle : 0.795 19.753 20920 Z= 0.371 Chirality : 0.049 0.485 2457 Planarity : 0.004 0.055 2585 Dihedral : 5.282 42.538 1944 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 5.85 % Allowed : 26.33 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.19), residues: 1798 helix: 0.30 (0.24), residues: 447 sheet: -0.93 (0.27), residues: 369 loop : -1.94 (0.18), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 131 TYR 0.016 0.002 TYR B 40 PHE 0.020 0.002 PHE C 233 TRP 0.041 0.002 TRP D 623 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (15314) covalent geometry : angle 0.72130 / 0.35 (20757) SS BOND : bond 0.00520 / 0.33 ( 32) SS BOND : angle 1.07074 / 0.65 ( 64) hydrogen bonds : bond 0.04549 / 3.13 ( 506) hydrogen bonds : angle 5.73099 / 3.93 ( 1374) link_ALPHA1-3 : bond 0.00693 / 0.35 ( 3) link_ALPHA1-3 : angle 1.90957 / 0.79 ( 9) link_ALPHA1-6 : bond 0.01269 / 0.67 ( 1) link_ALPHA1-6 : angle 2.94174 / 1.20 ( 3) link_BETA1-4 : bond 0.01770 / 0.96 ( 14) link_BETA1-4 : angle 6.15293 / 4.09 ( 42) link_NAG-ASN : bond 0.00778 / 0.36 ( 15) link_NAG-ASN : angle 3.93455 / 2.50 ( 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 297 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 201 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: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.6076 (pp20) REVERT: A 67 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8645 (m110) REVERT: A 252 LYS cc_start: 0.8348 (mmtp) cc_final: 0.7954 (mmtm) REVERT: A 474 ASP cc_start: 0.7894 (t0) cc_final: 0.7619 (t70) REVERT: A 479 TRP cc_start: 0.8315 (m-90) cc_final: 0.7846 (m-90) REVERT: B 66 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.7538 (t-170) REVERT: B 80 ASN cc_start: 0.8743 (t0) cc_final: 0.8537 (t0) REVERT: B 210 PHE cc_start: 0.8148 (t80) cc_final: 0.7638 (t80) REVERT: C 95 MET cc_start: 0.8815 (ppp) cc_final: 0.8300 (ppp) REVERT: C 96 TRP cc_start: 0.8901 (m100) cc_final: 0.8412 (m100) REVERT: C 479 TRP cc_start: 0.7435 (m-90) cc_final: 0.6908 (m-90) REVERT: C 483 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7641 (pp) REVERT: D 530 MET cc_start: 0.6086 (ppp) cc_final: 0.5638 (ppp) REVERT: E 530 MET cc_start: 0.7582 (mtm) cc_final: 0.7378 (mtm) REVERT: E 585 ARG cc_start: 0.8230 (tpt170) cc_final: 0.7975 (tmt170) REVERT: E 622 ILE cc_start: 0.9555 (mm) cc_final: 0.9338 (tt) REVERT: F 577 GLN cc_start: 0.9096 (OUTLIER) cc_final: 0.8884 (mt0) REVERT: Y 54 ARG cc_start: 0.8518 (ttp-110) cc_final: 0.8287 (ttm-80) outliers start: 96 outliers final: 59 residues processed: 279 average time/residue: 0.0916 time to fit residues: 40.8109 Evaluate side-chains 250 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 186 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 72 HIS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 483 LEU 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 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 112 TRP Chi-restraints excluded: chain B residue 198 THR 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 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 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 326 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 570 VAL 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 573 ILE Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 577 GLN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain Y residue 44 LEU 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 Y residue 117 THR Chi-restraints excluded: chain Y residue 160 THR Chi-restraints excluded: chain Z residue 44 LEU Chi-restraints excluded: chain Z residue 45 THR 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: 0.5980 chunk 80 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 158 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 125 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** 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 E 575 GLN E 652 GLN E 656 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.125264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.094407 restraints weight = 42820.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.092189 restraints weight = 31947.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.092978 restraints weight = 29724.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.093117 restraints weight = 24397.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.093305 restraints weight = 22853.615| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15379 Z= 0.165 Angle : 0.768 19.667 20920 Z= 0.356 Chirality : 0.048 0.484 2457 Planarity : 0.004 0.050 2585 Dihedral : 5.149 43.174 1944 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 5.42 % Allowed : 26.51 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.19), residues: 1798 helix: 0.43 (0.25), residues: 441 sheet: -1.11 (0.26), residues: 388 loop : -1.82 (0.18), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Z 131 TYR 0.026 0.002 TYR C 318 PHE 0.014 0.001 PHE B 53 TRP 0.035 0.002 TRP C 316 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (15314) covalent geometry : angle 0.69394 / 0.34 (20757) SS BOND : bond 0.00377 / 0.24 ( 32) SS BOND : angle 1.23965 / 0.71 ( 64) hydrogen bonds : bond 0.04181 / 2.87 ( 506) hydrogen bonds : angle 5.59025 / 3.82 ( 1374) link_ALPHA1-3 : bond 0.00658 / 0.33 ( 3) link_ALPHA1-3 : angle 1.83096 / 0.78 ( 9) link_ALPHA1-6 : bond 0.01228 / 0.65 ( 1) link_ALPHA1-6 : angle 2.80335 / 1.13 ( 3) link_BETA1-4 : bond 0.01722 / 0.95 ( 14) link_BETA1-4 : angle 6.06166 / 4.03 ( 42) link_NAG-ASN : bond 0.00754 / 0.35 ( 15) link_NAG-ASN : angle 3.83415 / 2.42 ( 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 298 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 209 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5935 (pp20) REVERT: A 67 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8596 (m110) REVERT: A 72 HIS cc_start: 0.7570 (OUTLIER) cc_final: 0.7300 (t70) REVERT: A 252 LYS cc_start: 0.8230 (mmtp) cc_final: 0.7929 (mmtm) REVERT: A 474 ASP cc_start: 0.7904 (t0) cc_final: 0.7578 (t70) REVERT: A 479 TRP cc_start: 0.8175 (m-10) cc_final: 0.7706 (m-90) REVERT: B 80 ASN cc_start: 0.8759 (t0) cc_final: 0.8549 (t0) REVERT: B 210 PHE cc_start: 0.8231 (t80) cc_final: 0.7694 (t80) REVERT: C 96 TRP cc_start: 0.8890 (m100) cc_final: 0.8390 (m100) REVERT: C 113 ASP cc_start: 0.8048 (m-30) cc_final: 0.7693 (t0) REVERT: C 479 TRP cc_start: 0.7400 (m-90) cc_final: 0.6937 (m-90) REVERT: C 483 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7581 (pp) REVERT: E 585 ARG cc_start: 0.8200 (tpt170) cc_final: 0.7965 (tmt170) REVERT: E 622 ILE cc_start: 0.9547 (mm) cc_final: 0.9334 (tt) REVERT: E 656 ASN cc_start: 0.7510 (m-40) cc_final: 0.7223 (m110) REVERT: Y 54 ARG cc_start: 0.8597 (ttp-110) cc_final: 0.8346 (ttm-80) outliers start: 89 outliers final: 69 residues processed: 281 average time/residue: 0.0982 time to fit residues: 44.5463 Evaluate side-chains 262 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 189 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 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 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 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 119 CYS Chi-restraints excluded: chain B residue 198 THR 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 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 103 GLN Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 387 THR 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 570 VAL 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 E residue 637 ASN Chi-restraints excluded: chain F residue 534 SER 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 87 GLU 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 44 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 160 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 38 optimal weight: 0.4980 chunk 152 optimal weight: 2.9990 chunk 98 optimal weight: 0.0270 chunk 175 optimal weight: 20.0000 chunk 79 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 overall best weight: 2.1044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 ASN C 352 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.124105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.093108 restraints weight = 41391.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.090695 restraints weight = 28611.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.091562 restraints weight = 31085.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.092061 restraints weight = 21967.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.092437 restraints weight = 20474.782| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15379 Z= 0.197 Angle : 0.780 19.635 20920 Z= 0.362 Chirality : 0.049 0.484 2457 Planarity : 0.004 0.048 2585 Dihedral : 5.116 41.335 1944 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 6.58 % Allowed : 26.45 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.19), residues: 1798 helix: 0.43 (0.25), residues: 441 sheet: -1.09 (0.26), residues: 394 loop : -1.78 (0.18), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG Z 131 TYR 0.025 0.002 TYR C 318 PHE 0.017 0.002 PHE B 53 TRP 0.034 0.002 TRP C 316 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 (15314) covalent geometry : angle 0.70755 / 0.35 (20757) SS BOND : bond 0.00347 / 0.23 ( 32) SS BOND : angle 0.88200 / 0.57 ( 64) hydrogen bonds : bond 0.04203 / 2.88 ( 506) hydrogen bonds : angle 5.52752 / 3.78 ( 1374) link_ALPHA1-3 : bond 0.00596 / 0.30 ( 3) link_ALPHA1-3 : angle 1.87096 / 0.79 ( 9) link_ALPHA1-6 : bond 0.01187 / 0.62 ( 1) link_ALPHA1-6 : angle 2.64302 / 1.07 ( 3) link_BETA1-4 : bond 0.01722 / 0.95 ( 14) link_BETA1-4 : angle 6.07664 / 4.03 ( 42) link_NAG-ASN : bond 0.00765 / 0.36 ( 15) link_NAG-ASN : angle 3.87223 / 2.46 ( 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 303 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 195 time to evaluate : 0.707 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: A 64 GLU cc_start: 0.6346 (OUTLIER) cc_final: 0.6093 (pp20) REVERT: A 67 ASN cc_start: 0.9112 (OUTLIER) cc_final: 0.8665 (m110) REVERT: A 72 HIS cc_start: 0.7558 (OUTLIER) cc_final: 0.7288 (t70) REVERT: A 252 LYS cc_start: 0.8271 (mmtp) cc_final: 0.7945 (mmtm) REVERT: A 434 MET cc_start: 0.5386 (OUTLIER) cc_final: 0.5174 (mmt) REVERT: A 474 ASP cc_start: 0.7980 (t0) cc_final: 0.7633 (t70) REVERT: A 479 TRP cc_start: 0.8259 (m-10) cc_final: 0.7776 (m-90) REVERT: B 80 ASN cc_start: 0.8732 (t0) cc_final: 0.8510 (t0) REVERT: B 210 PHE cc_start: 0.8337 (t80) cc_final: 0.7862 (t80) REVERT: B 446 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.8169 (p) REVERT: C 96 TRP cc_start: 0.8954 (m100) cc_final: 0.8434 (m100) REVERT: C 113 ASP cc_start: 0.7950 (m-30) cc_final: 0.7555 (t0) REVERT: C 342 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8508 (tt) REVERT: C 479 TRP cc_start: 0.7470 (m-90) cc_final: 0.6954 (m-90) REVERT: C 483 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7628 (pp) REVERT: F 577 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8890 (mt0) REVERT: Y 54 ARG cc_start: 0.8596 (ttp-110) cc_final: 0.8382 (ttp-110) outliers start: 108 outliers final: 78 residues processed: 285 average time/residue: 0.0980 time to fit residues: 45.1962 Evaluate side-chains 268 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 182 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 72 HIS 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 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 68 VAL 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 260 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 439 ILE Chi-restraints excluded: chain B residue 446 VAL 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 234 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 387 THR 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 570 VAL Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 608 VAL 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 E residue 637 ASN Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 577 GLN 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 19 SER 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 87 GLU 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 44 LEU Chi-restraints excluded: chain Z residue 45 THR 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: 0.4980 chunk 180 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 127 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS E 656 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.125298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.088841 restraints weight = 41339.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.089326 restraints weight = 29745.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.089757 restraints weight = 19689.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.090366 restraints weight = 19090.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.090591 restraints weight = 17364.304| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15379 Z= 0.149 Angle : 0.759 19.583 20920 Z= 0.351 Chirality : 0.048 0.483 2457 Planarity : 0.004 0.047 2585 Dihedral : 5.039 42.881 1944 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 5.48 % Allowed : 26.93 % Favored : 67.58 % 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 are not related in a simple way. whole: -1.47 (0.19), residues: 1798 helix: 0.53 (0.25), residues: 440 sheet: -1.02 (0.26), residues: 388 loop : -1.71 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Z 131 TYR 0.027 0.002 TYR C 318 PHE 0.013 0.001 PHE C 233 TRP 0.036 0.002 TRP C 316 HIS 0.006 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (15314) covalent geometry : angle 0.68635 / 0.33 (20757) SS BOND : bond 0.00346 / 0.25 ( 32) SS BOND : angle 1.19616 / 0.75 ( 64) hydrogen bonds : bond 0.03913 / 2.70 ( 506) hydrogen bonds : angle 5.45253 / 3.71 ( 1374) link_ALPHA1-3 : bond 0.00657 / 0.33 ( 3) link_ALPHA1-3 : angle 1.77441 / 0.77 ( 9) link_ALPHA1-6 : bond 0.00976 / 0.51 ( 1) link_ALPHA1-6 : angle 2.51100 / 1.00 ( 3) link_BETA1-4 : bond 0.01779 / 0.99 ( 14) link_BETA1-4 : angle 5.96412 / 3.97 ( 42) link_NAG-ASN : bond 0.00755 / 0.36 ( 15) link_NAG-ASN : angle 3.78531 / 2.38 ( 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 288 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 198 time to evaluate : 0.764 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: 0.9057 (OUTLIER) cc_final: 0.8611 (m110) REVERT: A 72 HIS cc_start: 0.7534 (OUTLIER) cc_final: 0.6861 (t70) REVERT: A 102 GLU cc_start: 0.7471 (tm-30) cc_final: 0.6817 (tm-30) REVERT: A 252 LYS cc_start: 0.8270 (mmtp) cc_final: 0.7879 (mmtm) REVERT: A 479 TRP cc_start: 0.8246 (m-10) cc_final: 0.7801 (m-90) REVERT: B 57 ASP cc_start: 0.8184 (p0) cc_final: 0.7613 (p0) REVERT: B 210 PHE cc_start: 0.8306 (t80) cc_final: 0.7830 (t80) REVERT: C 95 MET cc_start: 0.8782 (ppp) cc_final: 0.8169 (ppp) REVERT: C 96 TRP cc_start: 0.8874 (m100) cc_final: 0.8434 (m100) REVERT: C 113 ASP cc_start: 0.7975 (m-30) cc_final: 0.7572 (t0) REVERT: C 318 TYR cc_start: 0.7685 (t80) cc_final: 0.6846 (t80) REVERT: C 479 TRP cc_start: 0.7498 (m-90) cc_final: 0.6975 (m-90) REVERT: C 483 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7696 (pp) REVERT: D 602 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8760 (mp) REVERT: E 622 ILE cc_start: 0.9555 (mm) cc_final: 0.9301 (tt) REVERT: E 656 ASN cc_start: 0.7496 (m-40) cc_final: 0.7235 (m110) REVERT: Y 54 ARG cc_start: 0.8649 (ttp-110) cc_final: 0.8330 (ttm-80) outliers start: 90 outliers final: 72 residues processed: 267 average time/residue: 0.0978 time to fit residues: 42.6043 Evaluate side-chains 265 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 189 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 72 HIS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 254 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 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 112 TRP Chi-restraints excluded: chain B residue 215 ILE 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 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 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 270 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 452 LEU 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 602 LEU Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 608 VAL 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 584 GLU Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain F residue 534 SER 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 19 SER Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 87 GLU 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 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: 1.9990 chunk 168 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 2 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS Y 129 GLN Y 139 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.124905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.094119 restraints weight = 41670.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.091978 restraints weight = 29020.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.092665 restraints weight = 32484.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.093385 restraints weight = 22161.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.093586 restraints weight = 19834.969| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15379 Z= 0.167 Angle : 0.762 19.556 20920 Z= 0.353 Chirality : 0.048 0.484 2457 Planarity : 0.004 0.046 2585 Dihedral : 5.010 41.762 1944 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 5.48 % Allowed : 27.30 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.19), residues: 1798 helix: 0.46 (0.25), residues: 445 sheet: -0.98 (0.26), residues: 388 loop : -1.69 (0.18), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Z 131 TYR 0.025 0.002 TYR C 318 PHE 0.014 0.001 PHE B 53 TRP 0.037 0.002 TRP C 316 HIS 0.005 0.001 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (15314) covalent geometry : angle 0.69049 / 0.34 (20757) SS BOND : bond 0.00312 / 0.21 ( 32) SS BOND : angle 1.00916 / 0.64 ( 64) hydrogen bonds : bond 0.04064 / 2.81 ( 506) hydrogen bonds : angle 5.40856 / 3.68 ( 1374) link_ALPHA1-3 : bond 0.00567 / 0.29 ( 3) link_ALPHA1-3 : angle 1.77353 / 0.77 ( 9) link_ALPHA1-6 : bond 0.01068 / 0.56 ( 1) link_ALPHA1-6 : angle 2.42626 / 0.97 ( 3) link_BETA1-4 : bond 0.01757 / 0.96 ( 14) link_BETA1-4 : angle 5.97317 / 3.96 ( 42) link_NAG-ASN : bond 0.00748 / 0.35 ( 15) link_NAG-ASN : angle 3.80336 / 2.40 ( 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 280 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 190 time to evaluate : 0.624 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 67 ASN cc_start: 0.9090 (OUTLIER) cc_final: 0.8706 (m110) REVERT: A 72 HIS cc_start: 0.7422 (OUTLIER) cc_final: 0.6728 (t70) REVERT: A 252 LYS cc_start: 0.8231 (mmtp) cc_final: 0.7958 (mmtm) REVERT: A 474 ASP cc_start: 0.7802 (t0) cc_final: 0.7525 (t70) REVERT: A 479 TRP cc_start: 0.8205 (m-10) cc_final: 0.7755 (m-90) REVERT: B 57 ASP cc_start: 0.8164 (p0) cc_final: 0.7615 (p0) REVERT: B 210 PHE cc_start: 0.8372 (t80) cc_final: 0.7901 (t80) REVERT: B 446 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8185 (p) REVERT: C 96 TRP cc_start: 0.8850 (m100) cc_final: 0.8370 (m100) REVERT: C 479 TRP cc_start: 0.7535 (m-90) cc_final: 0.7068 (m-90) REVERT: C 483 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7574 (pp) REVERT: E 622 ILE cc_start: 0.9546 (mm) cc_final: 0.9280 (tt) outliers start: 90 outliers final: 74 residues processed: 263 average time/residue: 0.0927 time to fit residues: 39.7672 Evaluate side-chains 262 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 184 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 208 VAL Chi-restraints excluded: chain A residue 254 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 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 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 260 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 439 ILE Chi-restraints excluded: chain B residue 446 VAL 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 234 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 452 LEU 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 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 E residue 637 ASN Chi-restraints excluded: chain F residue 534 SER 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 19 SER 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 Z residue 11 THR 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: 3.9990 chunk 131 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 72 optimal weight: 0.0970 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN C 352 HIS ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.125303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.094136 restraints weight = 41646.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.092706 restraints weight = 28970.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.093297 restraints weight = 32961.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.093859 restraints weight = 22721.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.094273 restraints weight = 20339.854| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15379 Z= 0.158 Angle : 0.768 19.546 20920 Z= 0.355 Chirality : 0.048 0.484 2457 Planarity : 0.004 0.046 2585 Dihedral : 4.979 40.904 1944 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 5.06 % Allowed : 28.28 % 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 are not related in a simple way. whole: -1.43 (0.19), residues: 1798 helix: 0.45 (0.25), residues: 445 sheet: -0.91 (0.27), residues: 387 loop : -1.66 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 131 TYR 0.031 0.002 TYR A 217 PHE 0.013 0.001 PHE C 382 TRP 0.054 0.002 TRP D 623 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (15314) covalent geometry : angle 0.69822 / 0.34 (20757) SS BOND : bond 0.00291 / 0.19 ( 32) SS BOND : angle 0.91780 / 0.60 ( 64) hydrogen bonds : bond 0.03910 / 2.67 ( 506) hydrogen bonds : angle 5.38294 / 3.66 ( 1374) link_ALPHA1-3 : bond 0.00552 / 0.28 ( 3) link_ALPHA1-3 : angle 1.73955 / 0.75 ( 9) link_ALPHA1-6 : bond 0.01043 / 0.55 ( 1) link_ALPHA1-6 : angle 2.34382 / 0.93 ( 3) link_BETA1-4 : bond 0.01753 / 0.96 ( 14) link_BETA1-4 : angle 5.92069 / 3.92 ( 42) link_NAG-ASN : bond 0.00747 / 0.35 ( 15) link_NAG-ASN : angle 3.77247 / 2.38 ( 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 279 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 196 time to evaluate : 0.604 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 67 ASN cc_start: 0.9110 (OUTLIER) cc_final: 0.8712 (m110) REVERT: A 72 HIS cc_start: 0.7319 (OUTLIER) cc_final: 0.5903 (t70) REVERT: A 252 LYS cc_start: 0.8216 (mmtp) cc_final: 0.7970 (mmtm) REVERT: A 474 ASP cc_start: 0.7695 (t0) cc_final: 0.7444 (t70) REVERT: A 479 TRP cc_start: 0.8214 (m-10) cc_final: 0.7774 (m-90) REVERT: B 57 ASP cc_start: 0.8117 (p0) cc_final: 0.7571 (p0) REVERT: B 210 PHE cc_start: 0.8384 (t80) cc_final: 0.7885 (t80) REVERT: B 446 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8211 (p) REVERT: C 96 TRP cc_start: 0.8841 (m100) cc_final: 0.8411 (m100) REVERT: C 479 TRP cc_start: 0.7496 (m-90) cc_final: 0.7032 (m-90) REVERT: C 483 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7560 (pp) REVERT: E 622 ILE cc_start: 0.9531 (mm) cc_final: 0.9275 (tt) REVERT: E 656 ASN cc_start: 0.7500 (m-40) cc_final: 0.7239 (m-40) outliers start: 83 outliers final: 72 residues processed: 264 average time/residue: 0.0936 time to fit residues: 40.2431 Evaluate side-chains 263 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 187 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 72 HIS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 254 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 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 215 ILE 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 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 446 VAL 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 254 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 452 LEU 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 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 E residue 637 ASN Chi-restraints excluded: chain F residue 534 SER 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 638 TYR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain Y residue 11 THR Chi-restraints excluded: chain Y residue 19 SER 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 Z residue 11 THR 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: 8.9990 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 81 optimal weight: 0.2980 chunk 92 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.126224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.094874 restraints weight = 41793.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.092864 restraints weight = 30531.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.093766 restraints weight = 28339.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.094697 restraints weight = 21615.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.094771 restraints weight = 20406.597| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15379 Z= 0.137 Angle : 0.763 19.515 20920 Z= 0.352 Chirality : 0.048 0.484 2457 Planarity : 0.004 0.045 2585 Dihedral : 4.754 37.021 1942 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.20 % Allowed : 29.25 % Favored : 66.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.19), residues: 1798 helix: 0.44 (0.25), residues: 443 sheet: -0.86 (0.27), residues: 378 loop : -1.62 (0.18), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Z 131 TYR 0.024 0.002 TYR C 318 PHE 0.013 0.001 PHE C 382 TRP 0.058 0.002 TRP C 338 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (15314) covalent geometry : angle 0.69585 / 0.34 (20757) SS BOND : bond 0.00280 / 0.18 ( 32) SS BOND : angle 0.84841 / 0.56 ( 64) hydrogen bonds : bond 0.03831 / 2.63 ( 506) hydrogen bonds : angle 5.31464 / 3.61 ( 1374) link_ALPHA1-3 : bond 0.00572 / 0.29 ( 3) link_ALPHA1-3 : angle 1.68005 / 0.74 ( 9) link_ALPHA1-6 : bond 0.00995 / 0.52 ( 1) link_ALPHA1-6 : angle 2.25921 / 0.88 ( 3) link_BETA1-4 : bond 0.01753 / 0.96 ( 14) link_BETA1-4 : angle 5.84720 / 3.88 ( 42) link_NAG-ASN : bond 0.00743 / 0.35 ( 15) link_NAG-ASN : angle 3.71049 / 2.33 ( 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 273 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 204 time to evaluate : 0.634 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 72 HIS cc_start: 0.7305 (OUTLIER) cc_final: 0.5949 (t70) REVERT: A 102 GLU cc_start: 0.7362 (tm-30) cc_final: 0.6870 (tm-30) REVERT: A 252 LYS cc_start: 0.8201 (mmtp) cc_final: 0.7949 (mmtm) REVERT: A 474 ASP cc_start: 0.7669 (t0) cc_final: 0.7419 (t70) REVERT: A 479 TRP cc_start: 0.8185 (m-10) cc_final: 0.7731 (m-90) REVERT: B 57 ASP cc_start: 0.8138 (p0) cc_final: 0.7589 (p0) REVERT: B 210 PHE cc_start: 0.8298 (t80) cc_final: 0.7849 (t80) REVERT: B 446 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8205 (p) REVERT: C 96 TRP cc_start: 0.8828 (m100) cc_final: 0.8622 (m100) REVERT: C 342 LEU cc_start: 0.8662 (mp) cc_final: 0.8387 (tt) REVERT: C 479 TRP cc_start: 0.7420 (m-90) cc_final: 0.7150 (m-90) REVERT: C 483 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7568 (pp) REVERT: E 622 ILE cc_start: 0.9516 (mm) cc_final: 0.9275 (tt) REVERT: E 654 GLU cc_start: 0.8235 (pp20) cc_final: 0.7507 (pp20) outliers start: 69 outliers final: 63 residues processed: 259 average time/residue: 0.0976 time to fit residues: 41.0199 Evaluate side-chains 259 residues out of total 1641 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 193 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 254 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 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 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 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 446 VAL 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 270 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 452 LEU 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 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 570 VAL 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 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 Z residue 11 THR 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: 9.9990 chunk 43 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 159 optimal weight: 0.7980 chunk 176 optimal weight: 2.9990 chunk 147 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS E 652 GLN E 656 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.125665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.094098 restraints weight = 41624.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.092686 restraints weight = 27722.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.093258 restraints weight = 30044.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.093849 restraints weight = 21235.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.094113 restraints weight = 19074.698| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15379 Z= 0.154 Angle : 0.766 19.511 20920 Z= 0.356 Chirality : 0.048 0.485 2457 Planarity : 0.004 0.044 2585 Dihedral : 4.792 36.801 1942 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.33 % Allowed : 29.07 % 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 are not related in a simple way. whole: -1.33 (0.19), residues: 1798 helix: 0.44 (0.25), residues: 442 sheet: -0.68 (0.27), residues: 366 loop : -1.62 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Z 131 TYR 0.019 0.002 TYR C 318 PHE 0.021 0.001 PHE Y 43 TRP 0.052 0.002 TRP C 338 HIS 0.003 0.001 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (15314) covalent geometry : angle 0.69802 / 0.34 (20757) SS BOND : bond 0.00261 / 0.17 ( 32) SS BOND : angle 0.86808 / 0.56 ( 64) hydrogen bonds : bond 0.03939 / 2.69 ( 506) hydrogen bonds : angle 5.31555 / 3.61 ( 1374) link_ALPHA1-3 : bond 0.00524 / 0.27 ( 3) link_ALPHA1-3 : angle 1.68849 / 0.73 ( 9) link_ALPHA1-6 : bond 0.00958 / 0.50 ( 1) link_ALPHA1-6 : angle 2.16869 / 0.85 ( 3) link_BETA1-4 : bond 0.01740 / 0.95 ( 14) link_BETA1-4 : angle 5.85898 / 3.88 ( 42) link_NAG-ASN : bond 0.00753 / 0.35 ( 15) link_NAG-ASN : angle 3.69981 / 2.32 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2335.36 seconds wall clock time: 41 minutes 34.10 seconds (2494.10 seconds total)