Starting phenix.real_space_refine on Sat Feb 17 12:11:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyj_29580/02_2024/8fyj_29580.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyj_29580/02_2024/8fyj_29580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyj_29580/02_2024/8fyj_29580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyj_29580/02_2024/8fyj_29580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyj_29580/02_2024/8fyj_29580.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyj_29580/02_2024/8fyj_29580.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A ASP 57": "OD1" <-> "OD2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 230": "OD1" <-> "OD2" Residue "A PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 474": "OD1" <-> "OD2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B ASP 368": "OD1" <-> "OD2" Residue "B PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 457": "OD1" <-> "OD2" Residue "B ASP 477": "OD1" <-> "OD2" Residue "B TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C ASP 113": "OD1" <-> "OD2" Residue "C PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 180": "OD1" <-> "OD2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C ASP 477": "OD1" <-> "OD2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 584": "OE1" <-> "OE2" Residue "D TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 589": "OD1" <-> "OD2" Residue "D ASP 624": "OD1" <-> "OD2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "D GLU 657": "OE1" <-> "OE2" Residue "E PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 654": "OE1" <-> "OE2" Residue "E GLU 657": "OE1" <-> "OE2" Residue "F ASP 589": "OD1" <-> "OD2" Residue "F GLU 621": "OE1" <-> "OE2" Residue "F ASP 632": "OD1" <-> "OD2" Residue "F GLU 634": "OE1" <-> "OE2" Residue "Y PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 85": "OE1" <-> "OE2" Residue "Y ASP 88": "OD1" <-> "OD2" Residue "Y GLU 91": "OE1" <-> "OE2" Residue "Z ASP 10": "OD1" <-> "OD2" Residue "Z ASP 78": "OD1" <-> "OD2" Residue "Z GLU 85": "OE1" <-> "OE2" Residue "Z GLU 92": "OE1" <-> "OE2" Residue "Z PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15027 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2802 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 20, 'TRANS': 336} Chain breaks: 4 Chain: "B" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2783 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 20, 'TRANS': 334} Chain breaks: 4 Chain: "C" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3255 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 21, 'TRANS': 390} Chain breaks: 7 Chain: "D" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 989 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "E" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 989 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "F" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1020 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain breaks: 1 Chain: "Y" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "Z" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1370 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.14, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 5.71 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.78 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: 4.97 Time building geometry restraints manager: 6.22 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: 95.98 - 104.06: 209 104.06 - 112.15: 8114 112.15 - 120.24: 5754 120.24 - 128.32: 6524 128.32 - 136.41: 156 Bond angle restraints: 20757 Sorted by residual: angle pdb=" CA PRO Y 68 " pdb=" N PRO Y 68 " pdb=" CD PRO Y 68 " ideal model delta sigma weight residual 112.00 95.98 16.02 1.40e+00 5.10e-01 1.31e+02 angle pdb=" CA CYS A 205 " pdb=" CB CYS A 205 " pdb=" SG CYS A 205 " ideal model delta sigma weight residual 114.40 130.14 -15.74 2.30e+00 1.89e-01 4.68e+01 angle pdb=" C VAL Y 86 " pdb=" N GLU Y 87 " pdb=" CA GLU Y 87 " ideal model delta sigma weight residual 122.44 115.44 7.00 1.19e+00 7.06e-01 3.46e+01 angle pdb=" C ASN F 611 " pdb=" CA ASN F 611 " pdb=" CB ASN F 611 " ideal model delta sigma weight residual 116.54 110.55 5.99 1.15e+00 7.56e-01 2.72e+01 angle pdb=" N PRO Y 68 " pdb=" CD PRO Y 68 " pdb=" CG PRO Y 68 " ideal model delta sigma weight residual 103.20 96.40 6.80 1.50e+00 4.44e-01 2.05e+01 ... (remaining 20752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.79: 8752 23.79 - 47.58: 776 47.58 - 71.37: 92 71.37 - 95.15: 59 95.15 - 118.94: 22 Dihedral angle restraints: 9701 sinusoidal: 4384 harmonic: 5317 Sorted by residual: dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual 93.00 -178.81 -88.19 1 1.00e+01 1.00e-02 9.30e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 9.70 83.30 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 17.71 75.29 1 1.00e+01 1.00e-02 7.16e+01 ... (remaining 9698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2179 0.078 - 0.156: 259 0.156 - 0.234: 7 0.234 - 0.311: 9 0.311 - 0.389: 3 Chirality restraints: 2457 Sorted by residual: chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 5.10e+00 chirality pdb=" C4 NAG J 2 " pdb=" C3 NAG J 2 " pdb=" C5 NAG J 2 " pdb=" O4 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.53 -2.14 -0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" C1 NAG B 602 " pdb=" ND2 ASN B 386 " pdb=" C2 NAG B 602 " pdb=" O5 NAG B 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 2454 not shown) Planarity restraints: 2600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE Y 67 " 0.068 5.00e-02 4.00e+02 9.19e-02 1.35e+01 pdb=" N PRO Y 68 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO Y 68 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO Y 68 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 96 " -0.033 2.00e-02 2.50e+03 2.28e-02 1.30e+01 pdb=" CG TRP A 96 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP A 96 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 96 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 96 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 96 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 96 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 96 " -0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 96 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 96 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 304 " -0.248 9.50e-02 1.11e+02 1.11e-01 7.65e+00 pdb=" NE ARG C 304 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 304 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 304 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG C 304 " -0.010 2.00e-02 2.50e+03 ... (remaining 2597 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 314 2.66 - 3.22: 14651 3.22 - 3.78: 23397 3.78 - 4.34: 30428 4.34 - 4.90: 48920 Nonbonded interactions: 117710 Sorted by model distance: nonbonded pdb=" O SER E 528 " pdb=" OG1 THR E 627 " model vdw 2.105 2.440 nonbonded pdb=" OG SER B 365 " pdb=" O LYS Z 46 " model vdw 2.112 2.440 nonbonded pdb=" OG1 THR C 303 " pdb=" O ASP C 321A" model vdw 2.200 2.440 nonbonded pdb=" O MET E 535 " pdb=" OG1 THR E 538 " model vdw 2.206 2.440 nonbonded pdb=" OD1 ASN F 607 " pdb=" OG SER F 649 " model vdw 2.221 2.440 ... (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 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: 3.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 10.420 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 41.420 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.130 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.160 15314 Z= 0.324 Angle : 0.865 16.022 20757 Z= 0.439 Chirality : 0.050 0.389 2457 Planarity : 0.005 0.111 2585 Dihedral : 18.488 118.943 6151 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.61 % Allowed : 26.81 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (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 TRP 0.061 0.003 TRP A 96 HIS 0.010 0.001 HIS A 66 PHE 0.031 0.002 PHE C 382 TYR 0.022 0.002 TYR D 586 ARG 0.004 0.000 ARG C 327 *********************** 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 fitting. rotamer outliers: 10 poor density : 217 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 MET cc_start: 0.8795 (ppp) cc_final: 0.8585 (ppp) REVERT: C 100 MET cc_start: 0.4823 (tpt) cc_final: 0.4551 (tpt) REVERT: C 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: 0.2446 time to fit residues: 83.4770 Evaluate side-chains 212 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 206 time to evaluate : 1.811 ------------------------------------------------------------------------------- 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 152 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 73 optimal weight: 0.3980 chunk 141 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 164 optimal weight: 8.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS A 258 GLN ** 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 234 ASN C 332 ASN C 352 HIS D 640 GLN D 656 ASN ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 139 GLN Z 27 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 15314 Z= 0.386 Angle : 0.779 11.706 20757 Z= 0.383 Chirality : 0.050 0.480 2457 Planarity : 0.005 0.054 2585 Dihedral : 12.676 101.631 2646 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 5.30 % Allowed : 24.56 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.19), residues: 1798 helix: 0.32 (0.24), residues: 447 sheet: -0.89 (0.26), residues: 376 loop : -1.88 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 479 HIS 0.008 0.002 HIS A 66 PHE 0.028 0.002 PHE C 382 TYR 0.034 0.002 TYR C 318 ARG 0.007 0.001 ARG Z 131 *********************** 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 304 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 217 time to evaluate : 1.757 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 193 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8113 (pp) REVERT: A 252 LYS cc_start: 0.8388 (mmtp) cc_final: 0.7969 (mmtm) REVERT: B 57 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.7710 (p0) REVERT: C 95 MET cc_start: 0.8880 (ppp) cc_final: 0.8124 (ppp) REVERT: C 96 TRP cc_start: 0.8813 (m100) cc_final: 0.8512 (m100) REVERT: C 476 ARG cc_start: 0.8486 (ptm160) cc_final: 0.8274 (ptp-110) REVERT: C 479 TRP cc_start: 0.7473 (m-90) cc_final: 0.6869 (m-90) REVERT: C 483 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7370 (pp) REVERT: E 530 MET cc_start: 0.7736 (mtm) cc_final: 0.7443 (mtm) outliers start: 87 outliers final: 54 residues processed: 279 average time/residue: 0.2244 time to fit residues: 97.8548 Evaluate side-chains 253 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 196 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 57 ASP 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 198 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 345 VAL 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 566 LEU 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 629 LEU Chi-restraints excluded: chain F residue 566 LEU Chi-restraints excluded: chain F residue 577 GLN Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain Y residue 160 THR Chi-restraints excluded: chain Z residue 44 LEU Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 73 ASN 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 91 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 136 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 163 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15314 Z= 0.222 Angle : 0.677 11.741 20757 Z= 0.329 Chirality : 0.048 0.463 2457 Planarity : 0.004 0.052 2585 Dihedral : 10.844 95.195 2640 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.81 % Allowed : 26.26 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.19), residues: 1798 helix: 0.38 (0.24), residues: 449 sheet: -0.81 (0.27), residues: 375 loop : -1.81 (0.18), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 623 HIS 0.008 0.001 HIS A 66 PHE 0.023 0.002 PHE C 382 TYR 0.013 0.002 TYR C 39 ARG 0.005 0.000 ARG Z 131 *********************** 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 fitting. rotamer outliers: 79 poor density : 226 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASN cc_start: 0.9044 (OUTLIER) cc_final: 0.8602 (m110) REVERT: A 252 LYS cc_start: 0.8330 (mmtp) cc_final: 0.7953 (mmtm) REVERT: A 479 TRP cc_start: 0.8170 (m-90) cc_final: 0.7682 (m-90) REVERT: B 80 ASN cc_start: 0.8866 (t0) cc_final: 0.8635 (t0) REVERT: B 116 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8755 (tp) REVERT: C 96 TRP cc_start: 0.8750 (m100) cc_final: 0.8408 (m100) REVERT: C 300 ASN cc_start: 0.6291 (OUTLIER) cc_final: 0.5026 (t0) REVERT: C 318 TYR cc_start: 0.7411 (t80) cc_final: 0.6728 (t80) REVERT: C 479 TRP cc_start: 0.7379 (m-90) cc_final: 0.6859 (m-90) REVERT: E 530 MET cc_start: 0.7591 (mtm) cc_final: 0.7284 (mtm) REVERT: F 626 MET cc_start: 0.7988 (mmm) cc_final: 0.7626 (tpp) outliers start: 79 outliers final: 51 residues processed: 282 average time/residue: 0.2210 time to fit residues: 97.8329 Evaluate side-chains 247 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 193 time to evaluate : 1.710 ------------------------------------------------------------------------------- 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 333 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 116 LEU 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 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 448 ASN Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 562 GLN Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 610 TRP Chi-restraints excluded: chain D residue 629 LEU Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain Y residue 11 THR 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 53 ASP Chi-restraints excluded: chain Z residue 73 ASN Chi-restraints excluded: chain Z residue 78 ASP 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 162 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 156 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 HIS C 352 HIS E 625 ASN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 15314 Z= 0.334 Angle : 0.729 11.644 20757 Z= 0.356 Chirality : 0.049 0.467 2457 Planarity : 0.004 0.049 2585 Dihedral : 9.848 93.030 2640 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 6.83 % Allowed : 25.90 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.19), residues: 1798 helix: 0.42 (0.24), residues: 449 sheet: -0.88 (0.27), residues: 370 loop : -1.89 (0.18), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 623 HIS 0.007 0.001 HIS A 66 PHE 0.021 0.002 PHE C 382 TYR 0.018 0.002 TYR D 586 ARG 0.006 0.000 ARG Z 131 *********************** 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 310 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 198 time to evaluate : 1.835 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: 0.9069 (OUTLIER) cc_final: 0.8626 (m110) REVERT: A 479 TRP cc_start: 0.8249 (m-90) cc_final: 0.7701 (m-90) REVERT: B 57 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.7767 (p0) REVERT: B 80 ASN cc_start: 0.8837 (t0) cc_final: 0.8630 (t0) REVERT: C 95 MET cc_start: 0.8821 (ppp) cc_final: 0.8276 (ppp) REVERT: C 96 TRP cc_start: 0.8880 (m100) cc_final: 0.8473 (m100) REVERT: C 318 TYR cc_start: 0.7546 (t80) cc_final: 0.6935 (t80) REVERT: C 479 TRP cc_start: 0.7500 (m-90) cc_final: 0.6871 (m-90) REVERT: C 483 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7586 (pp) REVERT: E 530 MET cc_start: 0.7710 (mtm) cc_final: 0.7423 (mtm) outliers start: 112 outliers final: 79 residues processed: 284 average time/residue: 0.2220 time to fit residues: 100.0301 Evaluate side-chains 267 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 185 time to evaluate : 1.593 ------------------------------------------------------------------------------- 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 80 ASN 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 342 LEU Chi-restraints excluded: chain A residue 373 THR 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 47 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 57 ASP 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 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 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 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 198 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 272 ILE 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 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 570 VAL Chi-restraints excluded: chain D residue 604 CYS 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 523 LEU 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 625 ASN Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 637 ASN 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 610 TRP Chi-restraints excluded: chain F residue 625 ASN 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 88 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 11 THR Chi-restraints excluded: chain Z residue 44 LEU Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 73 ASN Chi-restraints excluded: chain Z residue 78 ASP 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 145 optimal weight: 0.0970 chunk 99 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 149 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 157 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS C 440 GLN E 575 GLN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 652 GLN F 653 GLN Z 25 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15314 Z= 0.230 Angle : 0.678 12.007 20757 Z= 0.330 Chirality : 0.048 0.465 2457 Planarity : 0.004 0.050 2585 Dihedral : 9.128 94.281 2640 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 6.70 % Allowed : 26.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.19), residues: 1798 helix: 0.43 (0.25), residues: 449 sheet: -0.81 (0.27), residues: 370 loop : -1.86 (0.18), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 316 HIS 0.007 0.001 HIS A 66 PHE 0.017 0.002 PHE C 382 TYR 0.012 0.002 TYR A 217 ARG 0.005 0.000 ARG C 476 *********************** 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 312 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 202 time to evaluate : 1.786 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: A 67 ASN cc_start: 0.9082 (OUTLIER) cc_final: 0.8609 (m110) REVERT: A 479 TRP cc_start: 0.8195 (m-90) cc_final: 0.7659 (m-90) REVERT: B 57 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.7823 (p0) REVERT: B 80 ASN cc_start: 0.8834 (t0) cc_final: 0.8611 (t0) REVERT: C 96 TRP cc_start: 0.8801 (m100) cc_final: 0.8323 (m100) REVERT: C 479 TRP cc_start: 0.7458 (m-90) cc_final: 0.6977 (m-90) REVERT: C 483 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7652 (pp) REVERT: E 530 MET cc_start: 0.7628 (mtm) cc_final: 0.7380 (mtm) outliers start: 110 outliers final: 81 residues processed: 283 average time/residue: 0.2133 time to fit residues: 96.3419 Evaluate side-chains 276 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 192 time to evaluate : 1.733 ------------------------------------------------------------------------------- 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 80 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 373 THR 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 47 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 57 ASP 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 215 ILE Chi-restraints excluded: chain B residue 245 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 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 198 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 449 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 604 CYS 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 523 LEU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 577 GLN Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 610 TRP 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 88 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 11 THR Chi-restraints excluded: chain Z residue 25 GLN Chi-restraints excluded: chain Z residue 45 THR Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 78 ASP Chi-restraints excluded: chain Z residue 98 PHE Chi-restraints excluded: chain Z residue 158 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 102 optimal weight: 0.0470 chunk 43 optimal weight: 3.9990 chunk 175 optimal weight: 20.0000 chunk 145 optimal weight: 0.9990 chunk 81 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS E 625 ASN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15314 Z= 0.239 Angle : 0.671 11.987 20757 Z= 0.324 Chirality : 0.047 0.465 2457 Planarity : 0.004 0.048 2585 Dihedral : 8.714 96.092 2640 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 6.95 % Allowed : 26.87 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.19), residues: 1798 helix: 0.50 (0.25), residues: 449 sheet: -0.86 (0.26), residues: 389 loop : -1.84 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 316 HIS 0.006 0.001 HIS A 66 PHE 0.017 0.002 PHE C 382 TYR 0.014 0.002 TYR A 217 ARG 0.003 0.000 ARG Z 131 *********************** 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 311 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 197 time to evaluate : 1.927 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: A 67 ASN cc_start: 0.9077 (OUTLIER) cc_final: 0.8602 (m110) REVERT: A 479 TRP cc_start: 0.8185 (m-10) cc_final: 0.7693 (m-90) REVERT: B 57 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.7805 (p0) REVERT: B 80 ASN cc_start: 0.8811 (t0) cc_final: 0.8601 (t0) REVERT: C 96 TRP cc_start: 0.8824 (m100) cc_final: 0.8333 (m100) REVERT: C 424 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7084 (mm) REVERT: C 453 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9073 (tt) REVERT: C 479 TRP cc_start: 0.7508 (m-90) cc_final: 0.6924 (m-90) REVERT: C 483 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7689 (pp) REVERT: E 530 MET cc_start: 0.7701 (mtm) cc_final: 0.7439 (mtm) outliers start: 114 outliers final: 86 residues processed: 284 average time/residue: 0.2434 time to fit residues: 110.1911 Evaluate side-chains 278 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 187 time to evaluate : 1.677 ------------------------------------------------------------------------------- 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 64 GLU Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 373 THR 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 47 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 57 ASP 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 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 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 198 THR 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 396 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 562 GLN Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 604 CYS 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 E residue 519 PHE Chi-restraints excluded: chain E residue 523 LEU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 610 TRP 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 51 LEU Chi-restraints excluded: chain Y residue 74 LEU Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 88 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 11 THR Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 45 THR Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 78 ASP Chi-restraints excluded: chain Z residue 98 PHE Chi-restraints excluded: chain Z residue 158 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 20.0000 chunk 97 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 15314 Z= 0.431 Angle : 0.780 12.735 20757 Z= 0.385 Chirality : 0.050 0.462 2457 Planarity : 0.005 0.047 2585 Dihedral : 8.862 98.903 2640 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 20.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 7.13 % Allowed : 26.81 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.19), residues: 1798 helix: 0.32 (0.25), residues: 443 sheet: -1.09 (0.27), residues: 374 loop : -1.89 (0.18), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C 316 HIS 0.006 0.001 HIS C 216 PHE 0.025 0.002 PHE B 53 TYR 0.024 0.002 TYR A 217 ARG 0.004 0.000 ARG Z 134 *********************** 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 299 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 182 time to evaluate : 1.695 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: 0.9111 (OUTLIER) cc_final: 0.8660 (m110) REVERT: A 434 MET cc_start: 0.5250 (mmt) cc_final: 0.5030 (mmt) REVERT: A 479 TRP cc_start: 0.8424 (m-10) cc_final: 0.7884 (m-90) REVERT: B 57 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.7823 (p0) REVERT: B 210 PHE cc_start: 0.8371 (t80) cc_final: 0.7852 (t80) REVERT: B 446 VAL cc_start: 0.8632 (OUTLIER) cc_final: 0.8251 (p) REVERT: C 96 TRP cc_start: 0.8933 (m100) cc_final: 0.8524 (m100) REVERT: C 479 TRP cc_start: 0.7643 (m-90) cc_final: 0.7097 (m-90) REVERT: C 483 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7685 (pp) REVERT: D 631 TRP cc_start: 0.7887 (OUTLIER) cc_final: 0.6259 (t60) REVERT: E 530 MET cc_start: 0.7812 (mtm) cc_final: 0.7558 (mtm) REVERT: E 625 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7863 (p0) outliers start: 117 outliers final: 89 residues processed: 275 average time/residue: 0.2055 time to fit residues: 90.7022 Evaluate side-chains 266 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 171 time to evaluate : 1.770 ------------------------------------------------------------------------------- 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 80 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 THR 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 57 ASP 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 119 CYS 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 261 LEU Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 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 198 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 449 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 C residue 499 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 604 CYS 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 631 TRP Chi-restraints excluded: chain E residue 519 PHE Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 625 ASN Chi-restraints excluded: chain E residue 629 LEU 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 610 TRP Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain Y residue 11 THR Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Y residue 74 LEU Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 88 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 11 THR Chi-restraints excluded: chain Z residue 45 THR Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 78 ASP Chi-restraints excluded: chain Z residue 98 PHE Chi-restraints excluded: chain Z residue 158 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 86 optimal weight: 0.0670 chunk 16 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 158 optimal weight: 20.0000 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 352 HIS E 625 ASN ** E 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15314 Z= 0.227 Angle : 0.688 12.540 20757 Z= 0.333 Chirality : 0.047 0.449 2457 Planarity : 0.004 0.047 2585 Dihedral : 8.302 97.438 2638 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 6.03 % Allowed : 28.15 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.19), residues: 1798 helix: 0.38 (0.25), residues: 443 sheet: -0.95 (0.27), residues: 370 loop : -1.79 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 316 HIS 0.005 0.001 HIS A 66 PHE 0.015 0.001 PHE C 382 TYR 0.014 0.002 TYR A 217 ARG 0.004 0.000 ARG Z 131 *********************** 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 285 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 186 time to evaluate : 1.837 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: 0.9091 (OUTLIER) cc_final: 0.8650 (m110) REVERT: A 102 GLU cc_start: 0.7525 (tm-30) cc_final: 0.6842 (tm-30) REVERT: A 252 LYS cc_start: 0.8282 (mmtp) cc_final: 0.7877 (mmtm) REVERT: A 479 TRP cc_start: 0.8304 (m-10) cc_final: 0.7827 (m-90) REVERT: B 57 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.7822 (p0) REVERT: B 210 PHE cc_start: 0.8289 (t80) cc_final: 0.7682 (t80) REVERT: B 211 GLU cc_start: 0.7902 (tp30) cc_final: 0.7567 (tp30) REVERT: B 446 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8233 (p) REVERT: C 96 TRP cc_start: 0.8916 (m100) cc_final: 0.8451 (m100) REVERT: C 300 ASN cc_start: 0.5614 (OUTLIER) cc_final: 0.5122 (t0) REVERT: C 479 TRP cc_start: 0.7529 (m-90) cc_final: 0.7045 (m-90) REVERT: C 483 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7739 (pp) REVERT: Y 39 ASN cc_start: 0.7726 (p0) cc_final: 0.7506 (p0) outliers start: 99 outliers final: 85 residues processed: 265 average time/residue: 0.2102 time to fit residues: 89.8190 Evaluate side-chains 267 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 177 time to evaluate : 1.651 ------------------------------------------------------------------------------- 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 80 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 373 THR 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 57 ASP 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 119 CYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 217 TYR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 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 198 THR 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 300 ASN Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 449 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 C residue 499 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 604 CYS 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 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 534 SER Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain Y residue 11 THR Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Y residue 74 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 88 ASP Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain Y residue 93 VAL Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Y residue 160 THR Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 162 optimal weight: 30.0000 chunk 97 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 106 optimal weight: 0.0870 chunk 171 optimal weight: 0.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS ** E 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15314 Z= 0.196 Angle : 0.680 12.125 20757 Z= 0.326 Chirality : 0.048 0.434 2457 Planarity : 0.004 0.047 2585 Dihedral : 8.005 95.570 2638 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 5.36 % Allowed : 29.43 % Favored : 65.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.19), residues: 1798 helix: 0.47 (0.25), residues: 440 sheet: -0.84 (0.27), residues: 370 loop : -1.75 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP C 338 HIS 0.006 0.001 HIS A 66 PHE 0.014 0.001 PHE C 382 TYR 0.010 0.002 TYR A 217 ARG 0.010 0.000 ARG Z 131 *********************** 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 285 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 197 time to evaluate : 1.674 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: 0.9117 (OUTLIER) cc_final: 0.8634 (m110) REVERT: A 102 GLU cc_start: 0.7528 (tm-30) cc_final: 0.6963 (tm-30) REVERT: A 107 ASP cc_start: 0.8390 (t0) cc_final: 0.8123 (t0) REVERT: A 252 LYS cc_start: 0.8247 (mmtp) cc_final: 0.7892 (mmtm) REVERT: A 478 ASN cc_start: 0.8599 (m-40) cc_final: 0.8131 (t0) REVERT: A 479 TRP cc_start: 0.8177 (m-10) cc_final: 0.7410 (m-90) REVERT: B 57 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.7825 (p0) REVERT: B 210 PHE cc_start: 0.8221 (t80) cc_final: 0.7701 (t80) REVERT: B 211 GLU cc_start: 0.7891 (tp30) cc_final: 0.7599 (tp30) REVERT: C 342 LEU cc_start: 0.8790 (mp) cc_final: 0.8502 (tt) REVERT: C 479 TRP cc_start: 0.7468 (m-90) cc_final: 0.6961 (m-90) REVERT: C 483 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7701 (pp) REVERT: D 595 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9166 (tp) REVERT: E 654 GLU cc_start: 0.8217 (pp20) cc_final: 0.7510 (pp20) REVERT: Y 39 ASN cc_start: 0.7682 (p0) cc_final: 0.7482 (p0) REVERT: Z 20 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7307 (mp10) REVERT: Z 131 ARG cc_start: 0.7619 (tpt90) cc_final: 0.6960 (tpt90) outliers start: 88 outliers final: 76 residues processed: 265 average time/residue: 0.2108 time to fit residues: 89.0635 Evaluate side-chains 269 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 188 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 109 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 373 THR 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 47 ASP Chi-restraints excluded: chain B residue 57 ASP 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 119 CYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 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 396 ILE Chi-restraints excluded: chain C residue 449 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 566 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 604 CYS 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 E residue 519 PHE Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain Y residue 11 THR Chi-restraints excluded: chain Y residue 19 SER Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Y residue 74 LEU Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain Y residue 93 VAL Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Y residue 160 THR Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 20 GLN Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 78 ASP Chi-restraints excluded: chain Z residue 98 PHE Chi-restraints excluded: chain Z residue 158 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 180 optimal weight: 0.0170 chunk 165 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 110 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 overall best weight: 1.6824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 300 ASN C 352 HIS ** E 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15314 Z= 0.249 Angle : 0.691 11.832 20757 Z= 0.332 Chirality : 0.047 0.413 2457 Planarity : 0.004 0.045 2585 Dihedral : 7.951 93.717 2638 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 5.42 % Allowed : 29.43 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.19), residues: 1798 helix: 0.41 (0.25), residues: 442 sheet: -0.83 (0.27), residues: 370 loop : -1.74 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 338 HIS 0.005 0.001 HIS A 66 PHE 0.019 0.002 PHE Y 43 TYR 0.034 0.002 TYR A 217 ARG 0.009 0.000 ARG Z 131 ********************** 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 276 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 187 time to evaluate : 1.728 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: 0.9122 (OUTLIER) cc_final: 0.8643 (m110) REVERT: A 102 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7068 (tm-30) REVERT: A 479 TRP cc_start: 0.8289 (m-10) cc_final: 0.7798 (m-90) REVERT: B 57 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.7812 (p0) REVERT: B 104 MET cc_start: 0.9007 (ttm) cc_final: 0.7788 (tpp) REVERT: B 210 PHE cc_start: 0.8263 (t80) cc_final: 0.7789 (t80) REVERT: C 113 ASP cc_start: 0.7980 (m-30) cc_final: 0.7693 (t0) REVERT: C 300 ASN cc_start: 0.5580 (OUTLIER) cc_final: 0.4791 (t0) REVERT: C 342 LEU cc_start: 0.8750 (mp) cc_final: 0.8412 (tt) REVERT: C 453 ILE cc_start: 0.9541 (OUTLIER) cc_final: 0.9111 (tt) REVERT: C 479 TRP cc_start: 0.7571 (m-90) cc_final: 0.7043 (m-90) REVERT: C 483 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7653 (pp) REVERT: E 654 GLU cc_start: 0.8213 (pp20) cc_final: 0.7515 (pp20) REVERT: Y 39 ASN cc_start: 0.7732 (p0) cc_final: 0.7514 (p0) REVERT: Z 20 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7331 (mp10) REVERT: Z 131 ARG cc_start: 0.7669 (tpt90) cc_final: 0.7023 (tpt90) outliers start: 89 outliers final: 74 residues processed: 258 average time/residue: 0.2155 time to fit residues: 89.1254 Evaluate side-chains 261 residues out of total 1641 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 181 time to evaluate : 1.740 ------------------------------------------------------------------------------- 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 80 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 THR 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 47 ASP Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 PHE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 439 ILE Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain C residue 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 300 ASN Chi-restraints excluded: chain C residue 396 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 566 LEU Chi-restraints excluded: chain D residue 604 CYS 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 E residue 519 PHE Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain F residue 534 SER Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 610 TRP Chi-restraints excluded: chain F residue 619 LEU Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain Y residue 11 THR Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Y residue 80 ASP Chi-restraints excluded: chain Y residue 81 THR Chi-restraints excluded: chain Y residue 89 GLN Chi-restraints excluded: chain Y residue 93 VAL Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Y residue 160 THR Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 20 GLN Chi-restraints excluded: chain Z residue 45 THR Chi-restraints excluded: chain Z residue 49 SER Chi-restraints excluded: chain Z residue 53 ASP Chi-restraints excluded: chain Z residue 98 PHE Chi-restraints excluded: chain Z residue 158 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 39 optimal weight: 0.0370 chunk 143 optimal weight: 8.9990 chunk 60 optimal weight: 0.5980 chunk 147 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 126 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 overall best weight: 1.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 352 HIS ** E 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.124779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.093739 restraints weight = 41309.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.091828 restraints weight = 28780.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.092940 restraints weight = 32092.939| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.219 15314 Z= 0.304 Angle : 0.905 59.189 20757 Z= 0.493 Chirality : 0.053 1.068 2457 Planarity : 0.004 0.045 2585 Dihedral : 7.985 93.696 2638 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 5.24 % Allowed : 29.80 % Favored : 64.96 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.19), residues: 1798 helix: 0.41 (0.25), residues: 442 sheet: -0.83 (0.27), residues: 370 loop : -1.73 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 338 HIS 0.005 0.001 HIS A 66 PHE 0.014 0.002 PHE B 53 TYR 0.031 0.002 TYR A 217 ARG 0.007 0.000 ARG Z 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2950.68 seconds wall clock time: 55 minutes 10.67 seconds (3310.67 seconds total)