Starting phenix.real_space_refine on Wed Apr 10 16:12:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8san_40274/04_2024/8san_40274_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8san_40274/04_2024/8san_40274.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8san_40274/04_2024/8san_40274.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8san_40274/04_2024/8san_40274.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8san_40274/04_2024/8san_40274_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8san_40274/04_2024/8san_40274_neut.pdb" } resolution = 4.6 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 12486 2.51 5 N 3402 2.21 5 O 3885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "B ASP 632": "OD1" <-> "OD2" Residue "B GLU 634": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "C ASP 31": "OD1" <-> "OD2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C ASP 76": "OD1" <-> "OD2" Residue "C TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 370": "OE1" <-> "OE2" Residue "E ASP 474": "OD1" <-> "OD2" Residue "F TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 654": "OE1" <-> "OE2" Residue "G GLU 28": "OE1" <-> "OE2" Residue "G TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 76": "OD1" <-> "OD2" Residue "G ASP 99": "OD1" <-> "OD2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 169": "OE1" <-> "OE2" Residue "I GLU 187": "OE1" <-> "OE2" Residue "J GLU 634": "OE1" <-> "OE2" Residue "J GLU 654": "OE1" <-> "OE2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "L TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 58": "OD1" <-> "OD2" Residue "L GLU 94": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 19908 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3538 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 24, 'TRANS': 426} Chain breaks: 1 Chain: "B" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1154 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 141} Chain: "C" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "D" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 783 Classifications: {'peptide': 101} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain: "E" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3538 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 24, 'TRANS': 426} Chain breaks: 1 Chain: "F" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1154 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 141} Chain: "G" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "H" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 783 Classifications: {'peptide': 101} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain: "I" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3538 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 24, 'TRANS': 426} Chain breaks: 1 Chain: "J" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1154 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 141} Chain: "K" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "L" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 783 Classifications: {'peptide': 101} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain: "M" 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: "N" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "O" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "P" 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: "Q" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "S" 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: "T" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "U" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 11.41, per 1000 atoms: 0.57 Number of scatterers: 19908 At special positions: 0 Unit cell: (140.712, 148.174, 121.524, 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 135 16.00 O 3885 8.00 N 3402 7.00 C 12486 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " 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 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 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 B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 32 " - pdb=" SG CYS C 98 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 86 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.05 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 32 " - pdb=" SG CYS G 98 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 86 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.04 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.04 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.03 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.04 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 32 " - pdb=" SG CYS K 98 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 86 " 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 N 3 " - " MAN N 7 " " MAN N 4 " - " MAN N 5 " " MAN O 4 " - " MAN O 5 " " BMA Q 3 " - " MAN Q 7 " " MAN Q 4 " - " MAN Q 5 " " MAN R 4 " - " MAN R 5 " " BMA T 3 " - " MAN T 7 " " MAN T 4 " - " MAN T 5 " " MAN U 4 " - " MAN U 5 " ALPHA1-6 " BMA N 3 " - " MAN N 4 " " MAN N 4 " - " MAN N 6 " " BMA O 3 " - " MAN O 4 " " MAN O 4 " - " MAN O 6 " " BMA Q 3 " - " MAN Q 4 " " MAN Q 4 " - " MAN Q 6 " " BMA R 3 " - " MAN R 4 " " MAN R 4 " - " MAN R 6 " " BMA T 3 " - " MAN T 4 " " MAN T 4 " - " MAN T 6 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 6 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG M 1 " - " ASN A 197 " " NAG N 1 " - " ASN A 262 " " NAG O 1 " - " ASN A 276 " " NAG P 1 " - " ASN E 197 " " NAG Q 1 " - " ASN E 262 " " NAG R 1 " - " ASN E 276 " " NAG S 1 " - " ASN I 197 " " NAG T 1 " - " ASN I 262 " " NAG U 1 " - " ASN I 276 " Time building additional restraints: 8.93 Conformation dependent library (CDL) restraints added in 3.6 seconds 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4542 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 52 sheets defined 21.7% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 31 through 36 removed outlier: 3.714A pdb=" N TRP A 35 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL A 36 " --> pdb=" O ASN A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 64 removed outlier: 4.262A pdb=" N LYS A 62 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS A 63 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.799A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 392 removed outlier: 4.171A pdb=" N ASN A 392 " --> pdb=" O LYS A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 480 removed outlier: 3.952A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 removed outlier: 3.996A pdb=" N ALA B 525 " --> pdb=" O GLY B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 535 removed outlier: 4.127A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 538 No H-bonds generated for 'chain 'B' and resid 536 through 538' Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 561 through 567 Processing helix chain 'B' and resid 569 through 595 removed outlier: 3.968A pdb=" N ILE B 573 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 removed outlier: 4.381A pdb=" N ILE B 622 " --> pdb=" O ASN B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 631 Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.748A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.564A pdb=" N ASP C 31 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 28 through 32' Processing helix chain 'C' and resid 60 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'E' and resid 59 through 64 removed outlier: 3.906A pdb=" N LYS E 62 " --> pdb=" O LYS E 59 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS E 63 " --> pdb=" O ALA E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.873A pdb=" N ILE E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 351 through 353 No H-bonds generated for 'chain 'E' and resid 351 through 353' Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 392 removed outlier: 4.129A pdb=" N ASN E 392 " --> pdb=" O LYS E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 479 Processing helix chain 'F' and resid 521 through 526 Processing helix chain 'F' and resid 529 through 535 Processing helix chain 'F' and resid 536 through 538 No H-bonds generated for 'chain 'F' and resid 536 through 538' Processing helix chain 'F' and resid 539 through 546 removed outlier: 3.560A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 567 Processing helix chain 'F' and resid 569 through 595 Processing helix chain 'F' and resid 619 through 625 removed outlier: 3.593A pdb=" N ASN F 625 " --> pdb=" O GLU F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 631 removed outlier: 3.526A pdb=" N GLN F 630 " --> pdb=" O THR F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 662 removed outlier: 3.687A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'I' and resid 31 through 35 Processing helix chain 'I' and resid 59 through 64 removed outlier: 4.038A pdb=" N LYS I 62 " --> pdb=" O LYS I 59 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS I 63 " --> pdb=" O ALA I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 116 removed outlier: 3.584A pdb=" N GLN I 103 " --> pdb=" O ASP I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 181 Processing helix chain 'I' and resid 335 through 351 removed outlier: 3.598A pdb=" N LYS I 351 " --> pdb=" O LYS I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 387 through 392 removed outlier: 4.201A pdb=" N ASN I 392 " --> pdb=" O LYS I 389 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 480 removed outlier: 3.950A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) Processing helix chain 'J' and resid 520 through 525 Processing helix chain 'J' and resid 529 through 535 removed outlier: 3.644A pdb=" N MET J 535 " --> pdb=" O GLY J 531 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 538 No H-bonds generated for 'chain 'J' and resid 536 through 538' Processing helix chain 'J' and resid 539 through 544 removed outlier: 3.521A pdb=" N ASN J 543 " --> pdb=" O VAL J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 561 through 567 removed outlier: 3.565A pdb=" N LEU J 565 " --> pdb=" O ALA J 561 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 595 Processing helix chain 'J' and resid 619 through 625 Processing helix chain 'J' and resid 627 through 630 Processing helix chain 'J' and resid 631 through 636 removed outlier: 4.336A pdb=" N ILE J 635 " --> pdb=" O TRP J 631 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 662 Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.726A pdb=" N ASP K 31 " --> pdb=" O GLU K 28 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N CYS K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 32' Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.939A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.882A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 93 " --> pdb=" O GLY A 237 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 160 through 162 removed outlier: 3.529A pdb=" N LYS A 170 " --> pdb=" O THR A 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.823A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A 434 " --> pdb=" O ILE A 424 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.489A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 11.599A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.567A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.475A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.108A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.192A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS A 385 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 270 through 271 removed outlier: 11.192A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.108A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.475A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.567A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.599A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 304 removed outlier: 7.301A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AA9, first strand: chain 'A' and resid 358 through 360 removed outlier: 6.434A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6 removed outlier: 4.541A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP C 72 " --> pdb=" O THR C 77 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.595A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TRP C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN C 35 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 37 " --> pdb=" O PHE C 91 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE C 91 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.595A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TRP C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN C 35 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 37 " --> pdb=" O PHE C 91 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE C 91 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.523A pdb=" N THR D 5 " --> pdb=" O ARG D 24 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR D 69 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR D 72 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER D 61 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.810A pdb=" N LEU D 11 " --> pdb=" O GLN D 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 32 through 34 Processing sheet with id=AB7, first strand: chain 'D' and resid 46 through 47 Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.955A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=AC1, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.804A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 129 through 131 removed outlier: 3.887A pdb=" N ILE E 130 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.767A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.625A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.524A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.547A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 12.815A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.060A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.990A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N SER E 334 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL E 295 " --> pdb=" O ASN E 332 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS E 385 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 270 through 274 removed outlier: 3.591A pdb=" N ARG E 273 " --> pdb=" O ILE E 285 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE E 285 " --> pdb=" O ARG E 273 " (cutoff:3.500A) removed outlier: 10.990A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.060A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.815A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 12.547A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.524A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL E 292 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 301 through 304 removed outlier: 7.247A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 307 through 308 Processing sheet with id=AC8, first strand: chain 'E' and resid 358 through 360 removed outlier: 6.202A pdb=" N THR E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'G' and resid 3 through 6 removed outlier: 4.545A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP G 72 " --> pdb=" O THR G 77 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 56 through 57 removed outlier: 3.540A pdb=" N ALA G 56 " --> pdb=" O LYS G 52 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS G 52 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN G 35 " --> pdb=" O THR G 93 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE G 37 " --> pdb=" O PHE G 91 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 56 through 57 removed outlier: 3.540A pdb=" N ALA G 56 " --> pdb=" O LYS G 52 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS G 52 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN G 35 " --> pdb=" O THR G 93 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE G 37 " --> pdb=" O PHE G 91 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 5 through 7 removed outlier: 4.394A pdb=" N TYR H 69 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER H 61 " --> pdb=" O THR H 72 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.021A pdb=" N LEU H 11 " --> pdb=" O GLN H 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'H' and resid 32 through 34 Processing sheet with id=AD6, first strand: chain 'H' and resid 46 through 47 Processing sheet with id=AD7, first strand: chain 'I' and resid 38 through 39 removed outlier: 3.907A pdb=" N VAL I 38 " --> pdb=" O CYS J 604 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 45 through 47 removed outlier: 3.542A pdb=" N LEU I 226 " --> pdb=" O LYS I 487 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE I 225 " --> pdb=" O VAL I 245 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 54 through 55 removed outlier: 5.913A pdb=" N ILE I 215 " --> pdb=" O GLY I 250 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY I 250 " --> pdb=" O ILE I 215 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR I 217 " --> pdb=" O THR I 248 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 91 through 92 removed outlier: 3.793A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 158 through 162 Processing sheet with id=AE3, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.966A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.564A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) removed outlier: 11.660A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 9.732A pdb=" N LYS I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 10.928A pdb=" N VAL I 292 " --> pdb=" O LYS I 446 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N GLU I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N SER I 334 " --> pdb=" O GLU I 293 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS I 330 " --> pdb=" O THR I 297 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU I 381 " --> pdb=" O CYS I 378 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS I 378 " --> pdb=" O GLU I 381 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE I 376 " --> pdb=" O PHE I 383 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS I 385 " --> pdb=" O HIS I 374 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 270 through 271 removed outlier: 6.585A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N THR I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N ASN I 448 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 10.928A pdb=" N VAL I 292 " --> pdb=" O LYS I 446 " (cutoff:3.500A) removed outlier: 9.732A pdb=" N LYS I 446 " --> pdb=" O VAL I 292 " (cutoff:3.500A) removed outlier: 11.660A pdb=" N ILE I 294 " --> pdb=" O THR I 444 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N THR I 444 " --> pdb=" O ILE I 294 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 301 through 304 removed outlier: 7.267A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 307 through 308 Processing sheet with id=AE8, first strand: chain 'I' and resid 358 through 360 removed outlier: 6.338A pdb=" N THR I 358 " --> pdb=" O GLU I 466 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'K' and resid 5 through 6 Processing sheet with id=AF1, first strand: chain 'K' and resid 18 through 20 Processing sheet with id=AF2, first strand: chain 'K' and resid 57 through 59 removed outlier: 4.203A pdb=" N ASN K 58 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TRP K 50 " --> pdb=" O ASN K 58 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU K 46 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG K 38 " --> pdb=" O GLU K 46 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TRP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE K 37 " --> pdb=" O PHE K 91 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 57 through 59 removed outlier: 4.203A pdb=" N ASN K 58 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TRP K 50 " --> pdb=" O ASN K 58 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU K 46 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG K 38 " --> pdb=" O GLU K 46 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TRP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE K 37 " --> pdb=" O PHE K 91 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.527A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR L 69 " --> pdb=" O CYS L 23 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.962A pdb=" N LEU L 11 " --> pdb=" O GLN L 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'L' and resid 32 through 34 Processing sheet with id=AF7, first strand: chain 'L' and resid 46 through 47 577 hydrogen bonds defined for protein. 1458 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: 6.57 Time building geometry restraints manager: 9.44 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: 6386 1.35 - 1.47: 5097 1.47 - 1.60: 8668 1.60 - 1.73: 3 1.73 - 1.86: 180 Bond restraints: 20334 Sorted by residual: bond pdb=" C1 BMA O 3 " pdb=" C2 BMA O 3 " ideal model delta sigma weight residual 1.519 1.621 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C1 BMA R 3 " pdb=" C2 BMA R 3 " ideal model delta sigma weight residual 1.519 1.619 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C1 BMA U 3 " pdb=" C2 BMA U 3 " ideal model delta sigma weight residual 1.519 1.613 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C LYS E 117 " pdb=" N PRO E 118 " ideal model delta sigma weight residual 1.328 1.365 -0.037 1.25e-02 6.40e+03 8.68e+00 bond pdb=" C3 MAN U 4 " pdb=" O3 MAN U 4 " ideal model delta sigma weight residual 1.408 1.466 -0.058 2.00e-02 2.50e+03 8.53e+00 ... (remaining 20329 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.70: 432 105.70 - 112.83: 10724 112.83 - 119.96: 7157 119.96 - 127.09: 8978 127.09 - 134.22: 312 Bond angle restraints: 27603 Sorted by residual: angle pdb=" C SER J 613 " pdb=" N TRP J 614 " pdb=" CA TRP J 614 " ideal model delta sigma weight residual 121.70 132.32 -10.62 1.80e+00 3.09e-01 3.48e+01 angle pdb=" C SER F 613 " pdb=" N TRP F 614 " pdb=" CA TRP F 614 " ideal model delta sigma weight residual 121.70 132.28 -10.58 1.80e+00 3.09e-01 3.45e+01 angle pdb=" C SER B 613 " pdb=" N TRP B 614 " pdb=" CA TRP B 614 " ideal model delta sigma weight residual 121.70 132.17 -10.47 1.80e+00 3.09e-01 3.39e+01 angle pdb=" C ARG D 24 " pdb=" N THR D 25 " pdb=" CA THR D 25 " ideal model delta sigma weight residual 121.70 131.07 -9.37 1.80e+00 3.09e-01 2.71e+01 angle pdb=" C ARG H 24 " pdb=" N THR H 25 " pdb=" CA THR H 25 " ideal model delta sigma weight residual 121.70 130.91 -9.21 1.80e+00 3.09e-01 2.62e+01 ... (remaining 27598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.68: 12040 23.68 - 47.35: 628 47.35 - 71.03: 110 71.03 - 94.71: 56 94.71 - 118.38: 42 Dihedral angle restraints: 12876 sinusoidal: 5805 harmonic: 7071 Sorted by residual: dihedral pdb=" CA LEU A 34 " pdb=" C LEU A 34 " pdb=" N TRP A 35 " pdb=" CA TRP A 35 " ideal model delta harmonic sigma weight residual 180.00 141.34 38.66 0 5.00e+00 4.00e-02 5.98e+01 dihedral pdb=" CA CYS A 196 " pdb=" C CYS A 196 " pdb=" N ASN A 197 " pdb=" CA ASN A 197 " ideal model delta harmonic sigma weight residual 180.00 142.55 37.45 0 5.00e+00 4.00e-02 5.61e+01 dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -148.17 62.17 1 1.00e+01 1.00e-02 5.12e+01 ... (remaining 12873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2910 0.095 - 0.190: 259 0.190 - 0.284: 23 0.284 - 0.379: 5 0.379 - 0.474: 1 Chirality restraints: 3198 Sorted by residual: chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN I 197 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN A 197 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 3195 not shown) Planarity restraints: 3480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 608 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.34e+00 pdb=" N PRO B 609 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 609 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 609 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 503 " 0.151 9.50e-02 1.11e+02 7.04e-02 7.19e+00 pdb=" NE ARG I 503 " 0.003 2.00e-02 2.50e+03 pdb=" CZ ARG I 503 " -0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG I 503 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG I 503 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 608 " 0.044 5.00e-02 4.00e+02 6.63e-02 7.04e+00 pdb=" N PRO F 609 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO F 609 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 609 " 0.036 5.00e-02 4.00e+02 ... (remaining 3477 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 346 2.63 - 3.20: 19019 3.20 - 3.77: 28682 3.77 - 4.33: 37728 4.33 - 4.90: 60982 Nonbonded interactions: 146757 Sorted by model distance: nonbonded pdb=" OG SER I 447 " pdb=" O7 NAG T 1 " model vdw 2.064 2.440 nonbonded pdb=" OG SER E 447 " pdb=" O7 NAG Q 1 " model vdw 2.102 2.440 nonbonded pdb=" OG SER A 447 " pdb=" O7 NAG N 1 " model vdw 2.102 2.440 nonbonded pdb=" O VAL E 68 " pdb=" OG1 THR E 71 " model vdw 2.116 2.440 nonbonded pdb=" OE1 GLN B 591 " pdb=" OH TYR J 586 " model vdw 2.121 2.440 ... (remaining 146752 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' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'S' } ncs_group { reference = (chain 'N' and (resid 2 or resid 5 through 7)) selection = (chain 'O' and (resid 1 or resid 4 through 6)) selection = (chain 'Q' and (resid 2 or resid 5 through 7)) selection = (chain 'R' and (resid 1 or resid 4 through 6)) selection = (chain 'T' and (resid 2 or resid 5 through 7)) selection = (chain 'U' and (resid 1 or resid 4 through 6)) } 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.830 Check model and map are aligned: 0.350 Set scattering table: 0.190 Process input model: 54.750 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 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 : 0.006 0.102 20334 Z= 0.376 Angle : 0.967 10.621 27603 Z= 0.480 Chirality : 0.056 0.474 3198 Planarity : 0.006 0.092 3471 Dihedral : 16.779 118.383 8208 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.86 % Favored : 89.89 % Rotamer: Outliers : 0.09 % Allowed : 0.28 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.24 (0.16), residues: 2424 helix: -0.28 (0.27), residues: 351 sheet: -1.40 (0.22), residues: 519 loop : -1.89 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP I 45 HIS 0.008 0.001 HIS E 249 PHE 0.034 0.003 PHE G 100D TYR 0.037 0.003 TYR B 643 ARG 0.036 0.001 ARG I 503 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 557 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.8432 (m-80) cc_final: 0.8077 (m-10) REVERT: A 102 ASP cc_start: 0.8874 (m-30) cc_final: 0.8506 (m-30) REVERT: A 177 TYR cc_start: 0.4691 (m-80) cc_final: 0.4354 (m-80) REVERT: A 180 ASP cc_start: 0.9002 (m-30) cc_final: 0.8767 (m-30) REVERT: A 192 ARG cc_start: 0.8005 (ptm160) cc_final: 0.7589 (ptt90) REVERT: A 216 HIS cc_start: 0.8241 (m-70) cc_final: 0.7821 (m-70) REVERT: A 217 TYR cc_start: 0.7266 (m-80) cc_final: 0.7013 (m-80) REVERT: A 351 LYS cc_start: 0.9000 (tmtt) cc_final: 0.8744 (tptt) REVERT: A 369 MET cc_start: 0.7344 (mtt) cc_final: 0.7102 (mtt) REVERT: A 465 GLU cc_start: 0.8618 (pm20) cc_final: 0.8405 (mm-30) REVERT: B 571 TRP cc_start: 0.7082 (m-10) cc_final: 0.6710 (m-10) REVERT: B 591 GLN cc_start: 0.9392 (tp40) cc_final: 0.9153 (tp40) REVERT: C 39 LEU cc_start: 0.9225 (mm) cc_final: 0.8944 (mm) REVERT: C 52 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8359 (mtmt) REVERT: D 81 PHE cc_start: 0.6798 (p90) cc_final: 0.6310 (p90) REVERT: D 95 PHE cc_start: 0.7295 (m-10) cc_final: 0.7093 (m-10) REVERT: D 103 GLN cc_start: 0.7566 (pt0) cc_final: 0.6936 (pp30) REVERT: E 35 TRP cc_start: 0.5005 (m100) cc_final: 0.4762 (m100) REVERT: E 102 ASP cc_start: 0.9026 (m-30) cc_final: 0.8699 (m-30) REVERT: E 348 GLU cc_start: 0.7751 (tt0) cc_final: 0.7193 (tt0) REVERT: E 363 GLN cc_start: 0.8157 (pp30) cc_final: 0.7836 (pp30) REVERT: E 369 MET cc_start: 0.7360 (mtt) cc_final: 0.7020 (mtt) REVERT: E 383 PHE cc_start: 0.7506 (m-10) cc_final: 0.7254 (m-10) REVERT: E 426 MET cc_start: 0.8791 (ptp) cc_final: 0.7640 (tpt) REVERT: E 434 MET cc_start: 0.8455 (ptm) cc_final: 0.8224 (ppp) REVERT: E 460 THR cc_start: 0.8093 (p) cc_final: 0.7865 (p) REVERT: F 651 ASN cc_start: 0.8647 (m-40) cc_final: 0.8427 (m-40) REVERT: G 36 TRP cc_start: 0.8227 (m100) cc_final: 0.7667 (m100) REVERT: G 39 LEU cc_start: 0.9300 (mm) cc_final: 0.9033 (mm) REVERT: H 73 ILE cc_start: 0.9476 (mm) cc_final: 0.9100 (mm) REVERT: H 81 PHE cc_start: 0.7142 (p90) cc_final: 0.6682 (p90) REVERT: H 84 TYR cc_start: 0.7279 (p90) cc_final: 0.7068 (p90) REVERT: I 95 MET cc_start: 0.8699 (ppp) cc_final: 0.8454 (ppp) REVERT: I 159 PHE cc_start: 0.8507 (t80) cc_final: 0.8025 (t80) REVERT: I 180 ASP cc_start: 0.8953 (m-30) cc_final: 0.8448 (m-30) REVERT: I 252 ARG cc_start: 0.9027 (mpp80) cc_final: 0.8675 (mpt-90) REVERT: I 351 LYS cc_start: 0.9137 (tmtt) cc_final: 0.8892 (tptt) REVERT: I 423 ILE cc_start: 0.9435 (mm) cc_final: 0.9110 (mm) REVERT: J 571 TRP cc_start: 0.6469 (m-10) cc_final: 0.6223 (m-10) REVERT: J 574 LYS cc_start: 0.9135 (mmtm) cc_final: 0.8704 (mmtp) REVERT: J 607 ASN cc_start: 0.7902 (t0) cc_final: 0.7530 (t0) REVERT: J 651 ASN cc_start: 0.8810 (m-40) cc_final: 0.8502 (m-40) REVERT: K 28 GLU cc_start: 0.7865 (pm20) cc_final: 0.7596 (pm20) REVERT: K 36 TRP cc_start: 0.8267 (m100) cc_final: 0.7867 (m100) REVERT: K 89 VAL cc_start: 0.8706 (t) cc_final: 0.8396 (p) REVERT: K 96 LYS cc_start: 0.8227 (ptpt) cc_final: 0.8010 (ptpt) REVERT: L 80 ASP cc_start: 0.8388 (m-30) cc_final: 0.7902 (m-30) REVERT: L 81 PHE cc_start: 0.6766 (p90) cc_final: 0.5987 (p90) outliers start: 2 outliers final: 0 residues processed: 559 average time/residue: 0.3246 time to fit residues: 274.9073 Evaluate side-chains 433 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 2.9990 chunk 184 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 73 optimal weight: 20.0000 chunk 115 optimal weight: 9.9990 chunk 141 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN G 58 ASN G 100AASN H 103 GLN I 156 ASN K 100AASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20334 Z= 0.210 Angle : 0.736 9.747 27603 Z= 0.366 Chirality : 0.052 0.396 3198 Planarity : 0.005 0.069 3471 Dihedral : 14.743 104.101 3603 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.16 % Favored : 90.59 % Rotamer: Outliers : 0.14 % Allowed : 3.94 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.00 (0.16), residues: 2424 helix: 0.27 (0.29), residues: 333 sheet: -1.18 (0.23), residues: 492 loop : -1.83 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 36 HIS 0.003 0.001 HIS E 330 PHE 0.022 0.002 PHE L 60 TYR 0.032 0.002 TYR L 47 ARG 0.009 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 545 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8882 (m-30) cc_final: 0.8515 (m-30) REVERT: A 177 TYR cc_start: 0.4917 (m-80) cc_final: 0.4227 (m-80) REVERT: A 180 ASP cc_start: 0.8850 (m-30) cc_final: 0.8611 (m-30) REVERT: A 216 HIS cc_start: 0.8205 (m-70) cc_final: 0.7928 (m90) REVERT: A 351 LYS cc_start: 0.8972 (tmtt) cc_final: 0.8757 (tptt) REVERT: A 370 GLU cc_start: 0.8025 (tp30) cc_final: 0.7521 (tp30) REVERT: A 383 PHE cc_start: 0.7223 (m-10) cc_final: 0.7011 (m-10) REVERT: B 631 TRP cc_start: 0.8439 (t-100) cc_final: 0.8203 (t-100) REVERT: C 39 LEU cc_start: 0.9431 (mm) cc_final: 0.9052 (mm) REVERT: C 51 LEU cc_start: 0.8268 (tt) cc_final: 0.7828 (mp) REVERT: C 52 LYS cc_start: 0.8887 (mtpp) cc_final: 0.8075 (mtmt) REVERT: C 68 THR cc_start: 0.8342 (m) cc_final: 0.8089 (p) REVERT: C 69 MET cc_start: 0.8676 (ptm) cc_final: 0.8220 (ptm) REVERT: C 82 LEU cc_start: 0.8346 (pp) cc_final: 0.7939 (tp) REVERT: D 34 TYR cc_start: 0.7882 (m-10) cc_final: 0.7658 (m-10) REVERT: D 81 PHE cc_start: 0.7028 (p90) cc_final: 0.6453 (p90) REVERT: D 103 GLN cc_start: 0.7577 (pt0) cc_final: 0.7162 (pp30) REVERT: E 49 LYS cc_start: 0.8844 (tmtt) cc_final: 0.8278 (tmtt) REVERT: E 102 ASP cc_start: 0.8987 (m-30) cc_final: 0.8590 (m-30) REVERT: E 426 MET cc_start: 0.8761 (ptp) cc_final: 0.8427 (tpt) REVERT: E 434 MET cc_start: 0.8532 (ptm) cc_final: 0.8205 (ppp) REVERT: E 460 THR cc_start: 0.8138 (p) cc_final: 0.7889 (p) REVERT: E 479 TRP cc_start: 0.9089 (m100) cc_final: 0.8588 (m-10) REVERT: F 591 GLN cc_start: 0.9454 (tp40) cc_final: 0.9242 (tp40) REVERT: G 36 TRP cc_start: 0.8297 (m100) cc_final: 0.7666 (m100) REVERT: G 46 GLU cc_start: 0.8306 (tp30) cc_final: 0.8083 (tp30) REVERT: G 100 TYR cc_start: 0.8279 (t80) cc_final: 0.7925 (t80) REVERT: H 73 ILE cc_start: 0.9451 (mm) cc_final: 0.9239 (mm) REVERT: H 84 TYR cc_start: 0.7454 (p90) cc_final: 0.6779 (p90) REVERT: I 159 PHE cc_start: 0.8487 (t80) cc_final: 0.8071 (t80) REVERT: I 180 ASP cc_start: 0.8807 (m-30) cc_final: 0.8457 (m-30) REVERT: I 252 ARG cc_start: 0.8978 (mpp80) cc_final: 0.8686 (mpt-90) REVERT: I 351 LYS cc_start: 0.9130 (tmtt) cc_final: 0.8893 (tptt) REVERT: I 427 TRP cc_start: 0.7565 (m100) cc_final: 0.7015 (m100) REVERT: J 603 ILE cc_start: 0.8508 (mm) cc_final: 0.8292 (mm) REVERT: J 651 ASN cc_start: 0.8894 (m-40) cc_final: 0.8621 (m-40) REVERT: K 18 MET cc_start: 0.8443 (ppp) cc_final: 0.8215 (ppp) REVERT: K 28 GLU cc_start: 0.8079 (pm20) cc_final: 0.7820 (pm20) REVERT: K 35 ASN cc_start: 0.8784 (m-40) cc_final: 0.8577 (p0) REVERT: K 36 TRP cc_start: 0.8533 (m100) cc_final: 0.8167 (m100) REVERT: K 48 MET cc_start: 0.8873 (tpp) cc_final: 0.8384 (tpp) REVERT: K 82 LEU cc_start: 0.8519 (tp) cc_final: 0.8250 (tp) REVERT: K 96 LYS cc_start: 0.8428 (ptpt) cc_final: 0.7927 (ptpt) REVERT: K 100 ASP cc_start: 0.7476 (p0) cc_final: 0.7252 (p0) outliers start: 3 outliers final: 1 residues processed: 545 average time/residue: 0.3447 time to fit residues: 291.5457 Evaluate side-chains 411 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 410 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 183 optimal weight: 0.4980 chunk 150 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 221 optimal weight: 10.0000 chunk 238 optimal weight: 0.0970 chunk 196 optimal weight: 10.0000 chunk 219 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 177 optimal weight: 0.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 ASN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 HIS G 58 ASN ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 575 GLN ** J 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20334 Z= 0.185 Angle : 0.695 9.284 27603 Z= 0.343 Chirality : 0.051 0.347 3198 Planarity : 0.004 0.061 3471 Dihedral : 13.602 100.049 3603 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.50 % Favored : 91.25 % Rotamer: Outliers : 0.05 % Allowed : 2.77 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.87 (0.16), residues: 2424 helix: 0.32 (0.29), residues: 333 sheet: -0.97 (0.24), residues: 441 loop : -1.76 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 33 HIS 0.004 0.001 HIS K 102 PHE 0.023 0.002 PHE A 53 TYR 0.026 0.002 TYR L 47 ARG 0.006 0.000 ARG I 503 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 536 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8784 (m-30) cc_final: 0.8386 (m-30) REVERT: A 177 TYR cc_start: 0.4836 (m-80) cc_final: 0.4074 (m-80) REVERT: A 180 ASP cc_start: 0.8806 (m-30) cc_final: 0.8514 (m-30) REVERT: A 216 HIS cc_start: 0.7921 (m-70) cc_final: 0.7554 (m-70) REVERT: A 351 LYS cc_start: 0.8939 (tmtt) cc_final: 0.8709 (tptt) REVERT: B 591 GLN cc_start: 0.9378 (tp40) cc_final: 0.8810 (tp40) REVERT: B 631 TRP cc_start: 0.8376 (t-100) cc_final: 0.8116 (t-100) REVERT: B 634 GLU cc_start: 0.8506 (mp0) cc_final: 0.8193 (mp0) REVERT: C 51 LEU cc_start: 0.8105 (tt) cc_final: 0.7830 (mp) REVERT: C 82 LEU cc_start: 0.8309 (pp) cc_final: 0.7960 (tp) REVERT: D 34 TYR cc_start: 0.8077 (m-10) cc_final: 0.7740 (m-10) REVERT: D 81 PHE cc_start: 0.6916 (p90) cc_final: 0.6539 (p90) REVERT: D 98 GLN cc_start: 0.7639 (tp40) cc_final: 0.7216 (pm20) REVERT: D 103 GLN cc_start: 0.7579 (pt0) cc_final: 0.7254 (pp30) REVERT: E 49 LYS cc_start: 0.8849 (tmtt) cc_final: 0.8093 (tmtt) REVERT: E 93 PHE cc_start: 0.7610 (m-10) cc_final: 0.7369 (m-10) REVERT: E 102 ASP cc_start: 0.8977 (m-30) cc_final: 0.8465 (m-30) REVERT: E 104 MET cc_start: 0.8475 (tpp) cc_final: 0.8256 (mmt) REVERT: E 348 GLU cc_start: 0.7545 (tt0) cc_final: 0.7166 (tt0) REVERT: E 383 PHE cc_start: 0.7415 (m-10) cc_final: 0.7180 (m-10) REVERT: E 426 MET cc_start: 0.8756 (ptp) cc_final: 0.8241 (tpt) REVERT: E 434 MET cc_start: 0.8489 (ptm) cc_final: 0.8163 (ppp) REVERT: E 460 THR cc_start: 0.8095 (p) cc_final: 0.7693 (p) REVERT: E 479 TRP cc_start: 0.9062 (m100) cc_final: 0.8619 (m-10) REVERT: G 36 TRP cc_start: 0.8214 (m100) cc_final: 0.7547 (m100) REVERT: G 46 GLU cc_start: 0.8309 (tp30) cc_final: 0.7995 (tp30) REVERT: G 100 ASN cc_start: 0.8913 (p0) cc_final: 0.8610 (p0) REVERT: H 84 TYR cc_start: 0.7424 (p90) cc_final: 0.6810 (p90) REVERT: I 95 MET cc_start: 0.8701 (ppp) cc_final: 0.8182 (ppp) REVERT: I 159 PHE cc_start: 0.8490 (t80) cc_final: 0.8039 (t80) REVERT: I 252 ARG cc_start: 0.8997 (mpp80) cc_final: 0.8774 (mpt-90) REVERT: I 351 LYS cc_start: 0.9104 (tmtt) cc_final: 0.8851 (tptt) REVERT: I 427 TRP cc_start: 0.7405 (m100) cc_final: 0.6934 (m100) REVERT: I 494 LEU cc_start: 0.9339 (tp) cc_final: 0.8960 (tt) REVERT: J 539 VAL cc_start: 0.8331 (m) cc_final: 0.8078 (p) REVERT: J 574 LYS cc_start: 0.9326 (mmtm) cc_final: 0.9031 (mmtm) REVERT: J 585 ARG cc_start: 0.9291 (tpp80) cc_final: 0.8939 (tpp80) REVERT: J 589 ASP cc_start: 0.8498 (m-30) cc_final: 0.7979 (m-30) REVERT: J 651 ASN cc_start: 0.8815 (m-40) cc_final: 0.8554 (m-40) REVERT: K 18 MET cc_start: 0.8624 (ppp) cc_final: 0.8367 (ppp) REVERT: K 28 GLU cc_start: 0.7920 (pm20) cc_final: 0.7689 (pm20) REVERT: K 31 ASP cc_start: 0.8868 (m-30) cc_final: 0.8450 (m-30) REVERT: K 36 TRP cc_start: 0.8436 (m100) cc_final: 0.7978 (m100) REVERT: K 39 LEU cc_start: 0.9232 (mm) cc_final: 0.8750 (mm) REVERT: K 44 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7415 (mmm-85) REVERT: K 82 LEU cc_start: 0.8432 (tp) cc_final: 0.8213 (mp) REVERT: K 96 LYS cc_start: 0.8462 (ptpt) cc_final: 0.8154 (ptpt) outliers start: 1 outliers final: 0 residues processed: 537 average time/residue: 0.3143 time to fit residues: 258.5616 Evaluate side-chains 421 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 421 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 8.9990 chunk 166 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 0.0870 chunk 148 optimal weight: 20.0000 chunk 221 optimal weight: 6.9990 chunk 234 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 ASN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 575 GLN ** J 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100AASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20334 Z= 0.178 Angle : 0.665 9.635 27603 Z= 0.328 Chirality : 0.049 0.342 3198 Planarity : 0.004 0.064 3471 Dihedral : 12.675 93.981 3603 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.75 % Favored : 91.01 % Rotamer: Outliers : 0.09 % Allowed : 2.63 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.74 (0.16), residues: 2424 helix: 0.48 (0.30), residues: 333 sheet: -0.85 (0.24), residues: 441 loop : -1.69 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 33 HIS 0.005 0.001 HIS E 216 PHE 0.020 0.002 PHE C 100D TYR 0.016 0.001 TYR F 586 ARG 0.004 0.000 ARG I 503 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 535 time to evaluate : 2.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8849 (m-30) cc_final: 0.8486 (m-30) REVERT: A 104 MET cc_start: 0.8858 (mmp) cc_final: 0.8643 (tpp) REVERT: A 177 TYR cc_start: 0.5322 (m-80) cc_final: 0.4117 (m-80) REVERT: A 180 ASP cc_start: 0.8800 (m-30) cc_final: 0.8537 (m-30) REVERT: A 198 THR cc_start: 0.8475 (p) cc_final: 0.8251 (p) REVERT: A 216 HIS cc_start: 0.8067 (m-70) cc_final: 0.7587 (m-70) REVERT: A 217 TYR cc_start: 0.7522 (m-80) cc_final: 0.7310 (m-80) REVERT: A 351 LYS cc_start: 0.8885 (tmtt) cc_final: 0.8658 (tptt) REVERT: A 494 LEU cc_start: 0.9429 (tp) cc_final: 0.8972 (tt) REVERT: B 571 TRP cc_start: 0.6866 (m-10) cc_final: 0.6261 (m-10) REVERT: B 591 GLN cc_start: 0.9364 (tp40) cc_final: 0.8704 (tp40) REVERT: B 631 TRP cc_start: 0.8363 (t-100) cc_final: 0.8129 (t-100) REVERT: C 51 LEU cc_start: 0.8241 (tt) cc_final: 0.7858 (mp) REVERT: C 82 LEU cc_start: 0.8328 (pp) cc_final: 0.8081 (tp) REVERT: D 81 PHE cc_start: 0.6860 (p90) cc_final: 0.6365 (p90) REVERT: E 102 ASP cc_start: 0.8928 (m-30) cc_final: 0.8592 (m-30) REVERT: E 308 ARG cc_start: 0.9273 (ttm-80) cc_final: 0.8893 (mmt90) REVERT: E 348 GLU cc_start: 0.7446 (tt0) cc_final: 0.7074 (tt0) REVERT: E 426 MET cc_start: 0.8749 (ptp) cc_final: 0.8167 (tpt) REVERT: E 434 MET cc_start: 0.8469 (ptm) cc_final: 0.8158 (ppp) REVERT: E 460 THR cc_start: 0.8079 (p) cc_final: 0.7870 (p) REVERT: E 485 LYS cc_start: 0.8738 (mttt) cc_final: 0.8528 (mttt) REVERT: F 530 MET cc_start: 0.8124 (ptm) cc_final: 0.7754 (ptt) REVERT: F 574 LYS cc_start: 0.9083 (mmtp) cc_final: 0.8694 (mptt) REVERT: F 575 GLN cc_start: 0.8987 (mt0) cc_final: 0.8723 (mp10) REVERT: G 36 TRP cc_start: 0.8324 (m100) cc_final: 0.7617 (m100) REVERT: G 37 ILE cc_start: 0.9301 (tp) cc_final: 0.9078 (tp) REVERT: G 39 LEU cc_start: 0.9018 (mm) cc_final: 0.8748 (mm) REVERT: G 96 LYS cc_start: 0.8748 (ptpt) cc_final: 0.8483 (ptpt) REVERT: G 100 ASN cc_start: 0.9039 (p0) cc_final: 0.8761 (p0) REVERT: H 84 TYR cc_start: 0.7375 (p90) cc_final: 0.6900 (p90) REVERT: I 159 PHE cc_start: 0.8503 (t80) cc_final: 0.8218 (t80) REVERT: I 252 ARG cc_start: 0.9002 (mpp80) cc_final: 0.8746 (mpt-90) REVERT: I 351 LYS cc_start: 0.9091 (tmtt) cc_final: 0.8866 (tptt) REVERT: I 494 LEU cc_start: 0.9365 (tp) cc_final: 0.8886 (tt) REVERT: J 539 VAL cc_start: 0.8407 (m) cc_final: 0.8115 (p) REVERT: J 574 LYS cc_start: 0.9149 (mmtp) cc_final: 0.8907 (mptt) REVERT: J 585 ARG cc_start: 0.9274 (tpp80) cc_final: 0.8887 (tpp80) REVERT: J 589 ASP cc_start: 0.8530 (m-30) cc_final: 0.8045 (m-30) REVERT: J 603 ILE cc_start: 0.8649 (mm) cc_final: 0.8400 (mm) REVERT: J 651 ASN cc_start: 0.8911 (m-40) cc_final: 0.8602 (m-40) REVERT: K 36 TRP cc_start: 0.8279 (m100) cc_final: 0.8056 (m100) REVERT: K 39 LEU cc_start: 0.9350 (mm) cc_final: 0.8900 (mm) REVERT: K 82 LEU cc_start: 0.8545 (tp) cc_final: 0.8271 (mp) REVERT: L 13 LEU cc_start: 0.9080 (pp) cc_final: 0.8599 (mm) outliers start: 2 outliers final: 0 residues processed: 536 average time/residue: 0.3465 time to fit residues: 287.3057 Evaluate side-chains 419 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 200 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 119 optimal weight: 10.0000 chunk 210 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN D 103 GLN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN G 58 ASN J 575 GLN ** J 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100AASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20334 Z= 0.209 Angle : 0.683 9.444 27603 Z= 0.337 Chirality : 0.050 0.377 3198 Planarity : 0.004 0.063 3471 Dihedral : 11.768 83.752 3603 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.69 % Favored : 90.10 % Rotamer: Outliers : 0.09 % Allowed : 3.05 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.16), residues: 2424 helix: 0.42 (0.30), residues: 333 sheet: -0.72 (0.24), residues: 441 loop : -1.69 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 50 HIS 0.004 0.001 HIS I 249 PHE 0.022 0.002 PHE C 100D TYR 0.026 0.002 TYR L 47 ARG 0.011 0.000 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 515 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ASP cc_start: 0.8874 (m-30) cc_final: 0.8537 (m-30) REVERT: A 154 MET cc_start: 0.2568 (tpt) cc_final: 0.1681 (mmm) REVERT: A 180 ASP cc_start: 0.8829 (m-30) cc_final: 0.8626 (m-30) REVERT: A 217 TYR cc_start: 0.7595 (m-80) cc_final: 0.7350 (m-80) REVERT: A 351 LYS cc_start: 0.8924 (tmtt) cc_final: 0.8628 (tptt) REVERT: A 383 PHE cc_start: 0.7202 (m-10) cc_final: 0.6847 (m-10) REVERT: A 434 MET cc_start: 0.8108 (ppp) cc_final: 0.7875 (ppp) REVERT: A 494 LEU cc_start: 0.9490 (tp) cc_final: 0.9040 (tt) REVERT: B 538 THR cc_start: 0.9173 (p) cc_final: 0.8830 (t) REVERT: B 571 TRP cc_start: 0.7068 (m-10) cc_final: 0.6424 (m-10) REVERT: B 591 GLN cc_start: 0.9350 (tp40) cc_final: 0.8702 (tp40) REVERT: C 82 LEU cc_start: 0.8343 (pp) cc_final: 0.7955 (tp) REVERT: C 89 VAL cc_start: 0.8540 (t) cc_final: 0.8193 (p) REVERT: D 34 TYR cc_start: 0.7927 (m-10) cc_final: 0.7518 (m-10) REVERT: D 81 PHE cc_start: 0.6988 (p90) cc_final: 0.6577 (p90) REVERT: E 93 PHE cc_start: 0.8016 (m-10) cc_final: 0.7747 (m-10) REVERT: E 102 ASP cc_start: 0.8873 (m-30) cc_final: 0.8516 (m-30) REVERT: E 279 ASN cc_start: 0.7982 (t0) cc_final: 0.7666 (p0) REVERT: E 348 GLU cc_start: 0.7544 (tt0) cc_final: 0.7216 (tt0) REVERT: E 383 PHE cc_start: 0.7417 (m-10) cc_final: 0.7156 (m-10) REVERT: E 434 MET cc_start: 0.8623 (ptm) cc_final: 0.8209 (ppp) REVERT: E 460 THR cc_start: 0.8143 (p) cc_final: 0.7906 (p) REVERT: E 485 LYS cc_start: 0.8765 (mttt) cc_final: 0.8534 (mttt) REVERT: F 574 LYS cc_start: 0.9103 (mmtp) cc_final: 0.8751 (mptt) REVERT: G 36 TRP cc_start: 0.8288 (m100) cc_final: 0.7528 (m100) REVERT: G 37 ILE cc_start: 0.9281 (tp) cc_final: 0.9054 (tp) REVERT: G 39 LEU cc_start: 0.9226 (mm) cc_final: 0.8848 (mm) REVERT: G 76 ASP cc_start: 0.6940 (t0) cc_final: 0.6419 (m-30) REVERT: G 100 TYR cc_start: 0.8133 (t80) cc_final: 0.7518 (t80) REVERT: G 100 ASN cc_start: 0.9013 (p0) cc_final: 0.8813 (p0) REVERT: H 4 LEU cc_start: 0.6999 (tp) cc_final: 0.6784 (tp) REVERT: H 84 TYR cc_start: 0.7426 (p90) cc_final: 0.7059 (p90) REVERT: H 98 GLN cc_start: 0.8679 (tp-100) cc_final: 0.8434 (tp40) REVERT: I 95 MET cc_start: 0.8815 (ppp) cc_final: 0.8249 (ppp) REVERT: I 180 ASP cc_start: 0.8864 (m-30) cc_final: 0.8604 (m-30) REVERT: I 252 ARG cc_start: 0.9032 (mpp80) cc_final: 0.8772 (mpt-90) REVERT: I 270 ILE cc_start: 0.8283 (mm) cc_final: 0.8072 (mm) REVERT: I 327 ARG cc_start: 0.6405 (tpt170) cc_final: 0.6093 (tpp-160) REVERT: I 351 LYS cc_start: 0.9071 (tmtt) cc_final: 0.8843 (tptt) REVERT: I 369 MET cc_start: 0.7240 (mtt) cc_final: 0.7024 (mtt) REVERT: I 494 LEU cc_start: 0.9425 (tp) cc_final: 0.8972 (tt) REVERT: J 539 VAL cc_start: 0.8493 (m) cc_final: 0.8163 (p) REVERT: J 574 LYS cc_start: 0.9112 (mmtp) cc_final: 0.8885 (mptt) REVERT: J 585 ARG cc_start: 0.9254 (tpp80) cc_final: 0.8883 (tpp80) REVERT: J 589 ASP cc_start: 0.8485 (m-30) cc_final: 0.8006 (m-30) REVERT: J 603 ILE cc_start: 0.8661 (mm) cc_final: 0.8382 (mm) REVERT: J 651 ASN cc_start: 0.8957 (m-40) cc_final: 0.8624 (m-40) REVERT: K 36 TRP cc_start: 0.8216 (m100) cc_final: 0.7930 (m100) REVERT: K 39 LEU cc_start: 0.9465 (mm) cc_final: 0.9263 (mm) REVERT: K 82 LEU cc_start: 0.8607 (tp) cc_final: 0.8335 (mp) REVERT: K 96 LYS cc_start: 0.8429 (ptpt) cc_final: 0.7744 (ptpt) REVERT: L 13 LEU cc_start: 0.9014 (pp) cc_final: 0.8472 (mm) outliers start: 2 outliers final: 0 residues processed: 516 average time/residue: 0.3274 time to fit residues: 261.6047 Evaluate side-chains 415 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 57 optimal weight: 0.0870 chunk 235 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 108 optimal weight: 0.4980 chunk 19 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 overall best weight: 2.5164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 ASN E 478 ASN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 ASN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 575 GLN K 100AASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20334 Z= 0.203 Angle : 0.683 9.155 27603 Z= 0.335 Chirality : 0.051 0.374 3198 Planarity : 0.004 0.063 3471 Dihedral : 10.907 79.823 3603 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.20 % Favored : 90.59 % Rotamer: Outliers : 0.09 % Allowed : 1.88 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.67 (0.16), residues: 2424 helix: 0.50 (0.30), residues: 333 sheet: -0.64 (0.24), residues: 447 loop : -1.70 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 36 HIS 0.004 0.001 HIS E 72 PHE 0.025 0.002 PHE C 100D TYR 0.016 0.001 TYR H 47 ARG 0.006 0.000 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 516 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8710 (ppp) cc_final: 0.8425 (ppp) REVERT: A 102 ASP cc_start: 0.8838 (m-30) cc_final: 0.8460 (m-30) REVERT: A 154 MET cc_start: 0.2371 (tpt) cc_final: 0.1496 (mmm) REVERT: A 270 ILE cc_start: 0.8398 (mm) cc_final: 0.8174 (mm) REVERT: A 351 LYS cc_start: 0.8897 (tmtt) cc_final: 0.8680 (tptt) REVERT: A 383 PHE cc_start: 0.7258 (m-10) cc_final: 0.6899 (m-10) REVERT: A 494 LEU cc_start: 0.9470 (tp) cc_final: 0.9029 (tt) REVERT: B 538 THR cc_start: 0.9174 (p) cc_final: 0.8806 (t) REVERT: B 571 TRP cc_start: 0.7184 (m-10) cc_final: 0.6285 (m-10) REVERT: B 591 GLN cc_start: 0.9356 (tp40) cc_final: 0.8790 (tp40) REVERT: B 624 ASP cc_start: 0.7532 (m-30) cc_final: 0.7327 (m-30) REVERT: C 39 LEU cc_start: 0.9395 (mm) cc_final: 0.9154 (mm) REVERT: C 51 LEU cc_start: 0.8498 (tt) cc_final: 0.8164 (mp) REVERT: C 82 LEU cc_start: 0.8132 (pp) cc_final: 0.7913 (tp) REVERT: C 100 ASN cc_start: 0.8306 (p0) cc_final: 0.8089 (p0) REVERT: D 34 TYR cc_start: 0.7844 (m-10) cc_final: 0.7501 (m-10) REVERT: D 81 PHE cc_start: 0.6943 (p90) cc_final: 0.6458 (p90) REVERT: E 93 PHE cc_start: 0.8123 (m-10) cc_final: 0.7872 (m-10) REVERT: E 102 ASP cc_start: 0.8805 (m-30) cc_final: 0.8405 (m-30) REVERT: E 121 LYS cc_start: 0.9425 (mppt) cc_final: 0.8991 (mmtm) REVERT: E 279 ASN cc_start: 0.7923 (t0) cc_final: 0.7636 (p0) REVERT: E 348 GLU cc_start: 0.7473 (tt0) cc_final: 0.7147 (tt0) REVERT: E 383 PHE cc_start: 0.7422 (m-10) cc_final: 0.7149 (m-10) REVERT: E 426 MET cc_start: 0.8824 (ptp) cc_final: 0.8050 (tpt) REVERT: E 434 MET cc_start: 0.8492 (ptm) cc_final: 0.8151 (ppp) REVERT: E 460 THR cc_start: 0.8115 (p) cc_final: 0.7862 (p) REVERT: E 485 LYS cc_start: 0.8746 (mttt) cc_final: 0.8507 (mttt) REVERT: F 574 LYS cc_start: 0.9144 (mmtp) cc_final: 0.8707 (mptt) REVERT: F 575 GLN cc_start: 0.8991 (mt0) cc_final: 0.8682 (mp10) REVERT: F 603 ILE cc_start: 0.8631 (mm) cc_final: 0.8329 (mm) REVERT: G 36 TRP cc_start: 0.8310 (m100) cc_final: 0.7507 (m100) REVERT: G 37 ILE cc_start: 0.9268 (tp) cc_final: 0.9045 (tp) REVERT: G 39 LEU cc_start: 0.9213 (mm) cc_final: 0.8838 (mm) REVERT: G 76 ASP cc_start: 0.6939 (t0) cc_final: 0.6408 (m-30) REVERT: G 100 ASN cc_start: 0.9114 (p0) cc_final: 0.8731 (p0) REVERT: H 56 ILE cc_start: 0.8006 (mm) cc_final: 0.7783 (mm) REVERT: H 84 TYR cc_start: 0.7377 (p90) cc_final: 0.7109 (p90) REVERT: I 95 MET cc_start: 0.8859 (ppp) cc_final: 0.8274 (ppp) REVERT: I 154 MET cc_start: 0.3018 (tpt) cc_final: 0.2080 (mmm) REVERT: I 180 ASP cc_start: 0.8881 (m-30) cc_final: 0.8584 (m-30) REVERT: I 203 GLN cc_start: 0.8630 (tp40) cc_final: 0.8420 (tp40) REVERT: I 308 ARG cc_start: 0.9138 (ttm-80) cc_final: 0.8869 (mmt90) REVERT: I 327 ARG cc_start: 0.6663 (tpt170) cc_final: 0.6179 (tpp-160) REVERT: I 351 LYS cc_start: 0.9039 (tmtt) cc_final: 0.8795 (tptt) REVERT: I 369 MET cc_start: 0.7258 (mtt) cc_final: 0.7042 (mtt) REVERT: I 494 LEU cc_start: 0.9426 (tp) cc_final: 0.8998 (tt) REVERT: J 539 VAL cc_start: 0.8522 (m) cc_final: 0.8188 (p) REVERT: J 651 ASN cc_start: 0.8935 (m-40) cc_final: 0.8604 (m-40) REVERT: K 39 LEU cc_start: 0.9499 (mm) cc_final: 0.9143 (mm) REVERT: K 82 LEU cc_start: 0.8637 (tp) cc_final: 0.8354 (mp) REVERT: K 96 LYS cc_start: 0.8708 (ptpt) cc_final: 0.8181 (ptpt) REVERT: L 13 LEU cc_start: 0.8985 (pp) cc_final: 0.8656 (pp) outliers start: 2 outliers final: 0 residues processed: 516 average time/residue: 0.3064 time to fit residues: 244.0085 Evaluate side-chains 406 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 234 optimal weight: 7.9990 chunk 146 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 144 optimal weight: 0.6980 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN D 103 GLN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 ASN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100AASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 20334 Z= 0.295 Angle : 0.749 9.419 27603 Z= 0.374 Chirality : 0.052 0.397 3198 Planarity : 0.005 0.068 3471 Dihedral : 10.016 76.543 3603 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.63 % Favored : 88.16 % Rotamer: Outliers : 0.14 % Allowed : 2.25 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.89 (0.16), residues: 2424 helix: 0.28 (0.29), residues: 333 sheet: -0.80 (0.24), residues: 480 loop : -1.84 (0.14), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP I 338 HIS 0.007 0.001 HIS K 102 PHE 0.021 0.002 PHE C 100D TYR 0.020 0.002 TYR A 191 ARG 0.008 0.001 ARG K 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 502 time to evaluate : 2.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ILE cc_start: 0.9506 (mm) cc_final: 0.9223 (mm) REVERT: A 154 MET cc_start: 0.2500 (tpt) cc_final: 0.2153 (tpt) REVERT: A 351 LYS cc_start: 0.8981 (tmtt) cc_final: 0.8747 (tptt) REVERT: A 383 PHE cc_start: 0.7304 (m-10) cc_final: 0.6995 (m-10) REVERT: A 434 MET cc_start: 0.8372 (ppp) cc_final: 0.7760 (ppp) REVERT: A 494 LEU cc_start: 0.9521 (tp) cc_final: 0.9130 (tt) REVERT: B 574 LYS cc_start: 0.8681 (mtmm) cc_final: 0.8223 (mttp) REVERT: B 591 GLN cc_start: 0.9389 (tp40) cc_final: 0.8890 (tp40) REVERT: B 624 ASP cc_start: 0.7637 (m-30) cc_final: 0.7426 (m-30) REVERT: C 89 VAL cc_start: 0.8364 (t) cc_final: 0.8145 (t) REVERT: C 100 ASN cc_start: 0.8222 (p0) cc_final: 0.7959 (p0) REVERT: D 81 PHE cc_start: 0.7212 (p90) cc_final: 0.6654 (p90) REVERT: E 121 LYS cc_start: 0.9382 (mppt) cc_final: 0.9044 (mmtm) REVERT: E 279 ASN cc_start: 0.7980 (t0) cc_final: 0.7731 (p0) REVERT: E 369 MET cc_start: 0.7497 (mtt) cc_final: 0.7235 (mtt) REVERT: E 426 MET cc_start: 0.8881 (ptp) cc_final: 0.8165 (tpt) REVERT: E 434 MET cc_start: 0.8457 (ptm) cc_final: 0.8119 (ppp) REVERT: E 460 THR cc_start: 0.7905 (p) cc_final: 0.7544 (p) REVERT: F 574 LYS cc_start: 0.9105 (mmtp) cc_final: 0.8679 (mptt) REVERT: F 648 GLU cc_start: 0.9408 (pt0) cc_final: 0.9141 (pt0) REVERT: G 36 TRP cc_start: 0.8426 (m100) cc_final: 0.7645 (m100) REVERT: G 39 LEU cc_start: 0.9251 (mm) cc_final: 0.8948 (mm) REVERT: G 44 ARG cc_start: 0.8220 (ttm-80) cc_final: 0.7966 (mmm-85) REVERT: G 100 TYR cc_start: 0.8457 (t80) cc_final: 0.7924 (t80) REVERT: G 100 ASN cc_start: 0.9117 (p0) cc_final: 0.8742 (p0) REVERT: H 56 ILE cc_start: 0.7938 (mm) cc_final: 0.7672 (mm) REVERT: H 84 TYR cc_start: 0.7673 (p90) cc_final: 0.7395 (p90) REVERT: I 159 PHE cc_start: 0.8485 (t80) cc_final: 0.8191 (t80) REVERT: I 180 ASP cc_start: 0.9011 (m-30) cc_final: 0.8775 (m-30) REVERT: I 270 ILE cc_start: 0.8449 (mm) cc_final: 0.8193 (mm) REVERT: I 351 LYS cc_start: 0.9119 (tmtt) cc_final: 0.8881 (tptt) REVERT: I 426 MET cc_start: 0.8936 (ptp) cc_final: 0.8260 (tpt) REVERT: I 494 LEU cc_start: 0.9482 (tp) cc_final: 0.9098 (tt) REVERT: J 538 THR cc_start: 0.9331 (p) cc_final: 0.9034 (t) REVERT: J 589 ASP cc_start: 0.8538 (m-30) cc_final: 0.8219 (m-30) REVERT: J 624 ASP cc_start: 0.7729 (m-30) cc_final: 0.7517 (m-30) REVERT: J 651 ASN cc_start: 0.9019 (m-40) cc_final: 0.8696 (m-40) REVERT: K 18 MET cc_start: 0.8501 (ppp) cc_final: 0.8284 (ppp) REVERT: K 36 TRP cc_start: 0.8424 (m100) cc_final: 0.8200 (m100) REVERT: K 39 LEU cc_start: 0.9538 (mm) cc_final: 0.9164 (mm) REVERT: K 82 LEU cc_start: 0.8704 (tp) cc_final: 0.8485 (tp) REVERT: K 96 LYS cc_start: 0.8521 (ptpt) cc_final: 0.8035 (ptpt) outliers start: 3 outliers final: 0 residues processed: 504 average time/residue: 0.3020 time to fit residues: 237.0717 Evaluate side-chains 411 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 159 optimal weight: 30.0000 chunk 115 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 184 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 HIS B 543 ASN C 58 ASN D 103 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 ASN G 64 GLN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100AASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 20334 Z= 0.379 Angle : 0.837 9.753 27603 Z= 0.424 Chirality : 0.054 0.425 3198 Planarity : 0.005 0.071 3471 Dihedral : 9.920 73.004 3603 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.75 % Favored : 87.05 % Rotamer: Outliers : 0.09 % Allowed : 1.64 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.20 (0.16), residues: 2424 helix: -0.13 (0.28), residues: 333 sheet: -0.96 (0.25), residues: 444 loop : -2.01 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 50 HIS 0.011 0.002 HIS A 72 PHE 0.040 0.003 PHE C 100D TYR 0.029 0.003 TYR H 47 ARG 0.009 0.001 ARG K 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 479 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8802 (ppp) cc_final: 0.8248 (ppp) REVERT: A 100 MET cc_start: 0.8388 (ppp) cc_final: 0.8035 (ppp) REVERT: A 108 ILE cc_start: 0.9461 (mm) cc_final: 0.9224 (mm) REVERT: A 351 LYS cc_start: 0.9018 (tmtt) cc_final: 0.8790 (tptt) REVERT: A 371 ILE cc_start: 0.9369 (tt) cc_final: 0.9119 (tp) REVERT: A 383 PHE cc_start: 0.7425 (m-10) cc_final: 0.7077 (m-10) REVERT: A 434 MET cc_start: 0.8354 (ppp) cc_final: 0.7723 (ppp) REVERT: A 494 LEU cc_start: 0.9530 (tp) cc_final: 0.9148 (tt) REVERT: B 571 TRP cc_start: 0.7114 (m-10) cc_final: 0.6748 (m-10) REVERT: B 624 ASP cc_start: 0.7792 (m-30) cc_final: 0.7509 (m-30) REVERT: C 89 VAL cc_start: 0.8412 (t) cc_final: 0.8210 (t) REVERT: C 100 TYR cc_start: 0.8136 (t80) cc_final: 0.7788 (t80) REVERT: C 100 ASN cc_start: 0.8404 (p0) cc_final: 0.7989 (p0) REVERT: D 98 GLN cc_start: 0.8433 (tp40) cc_final: 0.7838 (tp40) REVERT: E 270 ILE cc_start: 0.8622 (mm) cc_final: 0.8240 (mm) REVERT: E 279 ASN cc_start: 0.7943 (t0) cc_final: 0.7732 (p0) REVERT: E 348 GLU cc_start: 0.7451 (tt0) cc_final: 0.6975 (tt0) REVERT: E 369 MET cc_start: 0.7594 (mtt) cc_final: 0.7233 (mtt) REVERT: E 426 MET cc_start: 0.8841 (ptp) cc_final: 0.8144 (tpt) REVERT: E 434 MET cc_start: 0.8490 (ptm) cc_final: 0.8128 (ppp) REVERT: E 460 THR cc_start: 0.7824 (p) cc_final: 0.7498 (p) REVERT: F 574 LYS cc_start: 0.9068 (mmtp) cc_final: 0.8526 (mttp) REVERT: F 575 GLN cc_start: 0.9008 (mt0) cc_final: 0.8505 (tm-30) REVERT: F 648 GLU cc_start: 0.9346 (pt0) cc_final: 0.9139 (pt0) REVERT: G 36 TRP cc_start: 0.8557 (m100) cc_final: 0.7395 (m100) REVERT: G 76 ASP cc_start: 0.7186 (t0) cc_final: 0.6667 (m-30) REVERT: G 97 ASN cc_start: 0.9372 (p0) cc_final: 0.9171 (p0) REVERT: G 100 TYR cc_start: 0.8424 (t80) cc_final: 0.8130 (t80) REVERT: G 100 ASN cc_start: 0.9109 (p0) cc_final: 0.8641 (p0) REVERT: H 56 ILE cc_start: 0.7733 (mm) cc_final: 0.7462 (mm) REVERT: H 84 TYR cc_start: 0.7942 (p90) cc_final: 0.7516 (p90) REVERT: I 159 PHE cc_start: 0.8505 (t80) cc_final: 0.8272 (t80) REVERT: I 180 ASP cc_start: 0.9003 (m-30) cc_final: 0.8800 (m-30) REVERT: I 270 ILE cc_start: 0.8518 (mm) cc_final: 0.8270 (mm) REVERT: I 308 ARG cc_start: 0.9241 (ttm-80) cc_final: 0.8936 (mmt90) REVERT: I 351 LYS cc_start: 0.9156 (tmtt) cc_final: 0.8913 (tptt) REVERT: I 434 MET cc_start: 0.8343 (ppp) cc_final: 0.8072 (ptp) REVERT: I 474 ASP cc_start: 0.8228 (t0) cc_final: 0.8000 (t0) REVERT: I 494 LEU cc_start: 0.9518 (tp) cc_final: 0.9206 (tt) REVERT: J 603 ILE cc_start: 0.8576 (mm) cc_final: 0.8364 (mm) REVERT: J 651 ASN cc_start: 0.9101 (m-40) cc_final: 0.8734 (m-40) REVERT: K 18 MET cc_start: 0.8523 (ppp) cc_final: 0.8283 (ppp) REVERT: K 36 TRP cc_start: 0.8484 (m100) cc_final: 0.8100 (m100) REVERT: K 39 LEU cc_start: 0.9538 (mm) cc_final: 0.9106 (mm) REVERT: K 82 LEU cc_start: 0.8822 (tp) cc_final: 0.8582 (tp) outliers start: 2 outliers final: 0 residues processed: 480 average time/residue: 0.3075 time to fit residues: 227.6409 Evaluate side-chains 405 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 218 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 95 optimal weight: 0.0670 chunk 171 optimal weight: 0.0270 chunk 66 optimal weight: 9.9990 chunk 197 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 chunk 217 optimal weight: 7.9990 chunk 143 optimal weight: 6.9990 overall best weight: 1.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN D 103 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN F 543 ASN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 ASN I 98 ASN ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100AASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20334 Z= 0.196 Angle : 0.725 9.578 27603 Z= 0.358 Chirality : 0.052 0.411 3198 Planarity : 0.004 0.066 3471 Dihedral : 9.365 72.208 3603 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.87 % Favored : 90.92 % Rotamer: Outliers : 0.05 % Allowed : 0.75 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.92 (0.16), residues: 2424 helix: 0.42 (0.30), residues: 312 sheet: -0.85 (0.23), residues: 480 loop : -1.86 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP I 338 HIS 0.004 0.001 HIS E 249 PHE 0.033 0.002 PHE C 100D TYR 0.030 0.002 TYR A 217 ARG 0.005 0.000 ARG I 503 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 518 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 93 PHE cc_start: 0.8187 (m-10) cc_final: 0.7835 (m-10) REVERT: A 95 MET cc_start: 0.8628 (ppp) cc_final: 0.8325 (ppp) REVERT: A 104 MET cc_start: 0.9030 (mmm) cc_final: 0.8593 (mmp) REVERT: A 108 ILE cc_start: 0.9345 (mm) cc_final: 0.9108 (mm) REVERT: A 121 LYS cc_start: 0.9336 (mppt) cc_final: 0.9118 (mmtm) REVERT: A 154 MET cc_start: 0.2537 (tpt) cc_final: 0.1690 (mmm) REVERT: A 180 ASP cc_start: 0.8863 (m-30) cc_final: 0.8587 (m-30) REVERT: A 216 HIS cc_start: 0.8465 (m-70) cc_final: 0.7952 (m-70) REVERT: A 351 LYS cc_start: 0.8997 (tmtt) cc_final: 0.8777 (tptt) REVERT: A 423 ILE cc_start: 0.9560 (mm) cc_final: 0.9354 (mm) REVERT: A 434 MET cc_start: 0.8257 (ppp) cc_final: 0.7688 (ppp) REVERT: A 494 LEU cc_start: 0.9483 (tp) cc_final: 0.9131 (tt) REVERT: B 571 TRP cc_start: 0.6749 (m-10) cc_final: 0.6172 (m-10) REVERT: B 591 GLN cc_start: 0.9381 (tp40) cc_final: 0.8925 (tp-100) REVERT: B 624 ASP cc_start: 0.7749 (m-30) cc_final: 0.7465 (m-30) REVERT: C 51 LEU cc_start: 0.8516 (tt) cc_final: 0.8225 (mt) REVERT: C 82 LEU cc_start: 0.8280 (pp) cc_final: 0.7956 (tp) REVERT: C 100 ASN cc_start: 0.8615 (p0) cc_final: 0.7992 (p0) REVERT: D 98 GLN cc_start: 0.8400 (tp40) cc_final: 0.8017 (tp40) REVERT: E 102 ASP cc_start: 0.8764 (m-30) cc_final: 0.8429 (m-30) REVERT: E 279 ASN cc_start: 0.7806 (t0) cc_final: 0.7605 (p0) REVERT: E 369 MET cc_start: 0.7240 (mtt) cc_final: 0.6901 (mtt) REVERT: E 383 PHE cc_start: 0.7310 (m-10) cc_final: 0.6976 (m-10) REVERT: E 426 MET cc_start: 0.8612 (ptp) cc_final: 0.7433 (tpt) REVERT: E 434 MET cc_start: 0.8576 (ptm) cc_final: 0.8185 (ppp) REVERT: E 460 THR cc_start: 0.7717 (p) cc_final: 0.7426 (p) REVERT: E 482 GLU cc_start: 0.8333 (mp0) cc_final: 0.7972 (mp0) REVERT: F 574 LYS cc_start: 0.9139 (mmtp) cc_final: 0.8683 (mptt) REVERT: F 575 GLN cc_start: 0.8931 (mt0) cc_final: 0.8717 (pp30) REVERT: F 648 GLU cc_start: 0.9350 (pt0) cc_final: 0.8917 (pp20) REVERT: F 651 ASN cc_start: 0.8610 (m-40) cc_final: 0.8392 (m-40) REVERT: G 36 TRP cc_start: 0.8384 (m100) cc_final: 0.7863 (m100) REVERT: G 39 LEU cc_start: 0.8985 (mm) cc_final: 0.8765 (mm) REVERT: G 71 ARG cc_start: 0.8798 (ptt-90) cc_final: 0.8196 (ptt-90) REVERT: G 76 ASP cc_start: 0.7026 (t0) cc_final: 0.6643 (m-30) REVERT: G 100 ASN cc_start: 0.9113 (p0) cc_final: 0.8643 (p0) REVERT: H 37 ARG cc_start: 0.8495 (tpt-90) cc_final: 0.8226 (tpt-90) REVERT: H 56 ILE cc_start: 0.7735 (mm) cc_final: 0.7495 (mm) REVERT: I 95 MET cc_start: 0.8750 (ppp) cc_final: 0.8352 (ppp) REVERT: I 159 PHE cc_start: 0.8433 (t80) cc_final: 0.8023 (t80) REVERT: I 180 ASP cc_start: 0.8859 (m-30) cc_final: 0.8609 (m-30) REVERT: I 308 ARG cc_start: 0.9152 (ttm-80) cc_final: 0.8846 (mmt90) REVERT: I 351 LYS cc_start: 0.9065 (tmtt) cc_final: 0.8820 (tptt) REVERT: I 383 PHE cc_start: 0.7648 (m-10) cc_final: 0.7436 (m-10) REVERT: I 494 LEU cc_start: 0.9449 (tp) cc_final: 0.9207 (tt) REVERT: J 539 VAL cc_start: 0.8670 (m) cc_final: 0.8320 (p) REVERT: J 603 ILE cc_start: 0.8399 (mm) cc_final: 0.8192 (mm) REVERT: J 651 ASN cc_start: 0.8901 (m-40) cc_final: 0.8558 (m-40) REVERT: K 36 TRP cc_start: 0.8306 (m100) cc_final: 0.7922 (m100) REVERT: K 39 LEU cc_start: 0.9643 (mm) cc_final: 0.9437 (mm) outliers start: 1 outliers final: 1 residues processed: 518 average time/residue: 0.3051 time to fit residues: 244.6750 Evaluate side-chains 420 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 419 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 chunk 109 optimal weight: 20.0000 chunk 160 optimal weight: 20.0000 chunk 242 optimal weight: 9.9990 chunk 222 optimal weight: 0.0050 chunk 192 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 overall best weight: 4.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN C 64 GLN D 103 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN F 543 ASN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 ASN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 577 GLN ** K 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20334 Z= 0.268 Angle : 0.744 8.990 27603 Z= 0.372 Chirality : 0.052 0.396 3198 Planarity : 0.005 0.068 3471 Dihedral : 9.265 70.748 3603 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.26 % Favored : 88.53 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.97 (0.16), residues: 2424 helix: 0.09 (0.29), residues: 330 sheet: -0.95 (0.24), residues: 474 loop : -1.82 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP I 338 HIS 0.004 0.001 HIS C 102 PHE 0.031 0.002 PHE K 100D TYR 0.025 0.002 TYR L 89 ARG 0.007 0.000 ARG K 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4848 Ramachandran restraints generated. 2424 Oldfield, 0 Emsley, 2424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 492 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.8417 (m-10) cc_final: 0.8057 (m-10) REVERT: A 104 MET cc_start: 0.9110 (mmm) cc_final: 0.8693 (mmp) REVERT: A 121 LYS cc_start: 0.9313 (mppt) cc_final: 0.9012 (mmtm) REVERT: A 180 ASP cc_start: 0.8917 (m-30) cc_final: 0.8641 (m-30) REVERT: A 216 HIS cc_start: 0.8568 (m-70) cc_final: 0.8088 (m-70) REVERT: A 270 ILE cc_start: 0.8369 (mm) cc_final: 0.8166 (mm) REVERT: A 351 LYS cc_start: 0.9014 (tmtt) cc_final: 0.8752 (tptt) REVERT: A 371 ILE cc_start: 0.9415 (tt) cc_final: 0.9181 (tp) REVERT: A 434 MET cc_start: 0.8248 (ppp) cc_final: 0.7663 (ppp) REVERT: A 494 LEU cc_start: 0.9494 (tp) cc_final: 0.9124 (tt) REVERT: B 591 GLN cc_start: 0.9368 (tp40) cc_final: 0.9146 (tp-100) REVERT: B 624 ASP cc_start: 0.7799 (m-30) cc_final: 0.7527 (m-30) REVERT: B 634 GLU cc_start: 0.8394 (mp0) cc_final: 0.8090 (mp0) REVERT: C 89 VAL cc_start: 0.8393 (t) cc_final: 0.8116 (p) REVERT: C 100 TYR cc_start: 0.8486 (t80) cc_final: 0.7614 (t80) REVERT: C 100 ASN cc_start: 0.8519 (p0) cc_final: 0.7942 (p0) REVERT: D 37 ARG cc_start: 0.8481 (tpt-90) cc_final: 0.7997 (tpt-90) REVERT: D 81 PHE cc_start: 0.7320 (p90) cc_final: 0.6623 (p90) REVERT: D 103 GLN cc_start: 0.7764 (pt0) cc_final: 0.7334 (pp30) REVERT: E 102 ASP cc_start: 0.8844 (m-30) cc_final: 0.8493 (m-30) REVERT: E 270 ILE cc_start: 0.8617 (mm) cc_final: 0.8382 (mm) REVERT: E 279 ASN cc_start: 0.7923 (t0) cc_final: 0.7689 (p0) REVERT: E 348 GLU cc_start: 0.7397 (tt0) cc_final: 0.7093 (tt0) REVERT: E 369 MET cc_start: 0.7413 (mtt) cc_final: 0.7178 (mtt) REVERT: E 426 MET cc_start: 0.8629 (ptp) cc_final: 0.7352 (tpt) REVERT: E 434 MET cc_start: 0.8520 (ptm) cc_final: 0.8141 (ppp) REVERT: E 460 THR cc_start: 0.7642 (p) cc_final: 0.7348 (p) REVERT: F 574 LYS cc_start: 0.9114 (mmtp) cc_final: 0.8696 (mptt) REVERT: F 575 GLN cc_start: 0.9075 (mt0) cc_final: 0.8705 (pp30) REVERT: G 36 TRP cc_start: 0.8447 (m100) cc_final: 0.7871 (m100) REVERT: G 76 ASP cc_start: 0.7113 (t0) cc_final: 0.6667 (m-30) REVERT: G 100 ASN cc_start: 0.9196 (p0) cc_final: 0.8670 (p0) REVERT: G 101 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8288 (mt-10) REVERT: H 37 ARG cc_start: 0.8518 (tpt-90) cc_final: 0.8243 (tpt-90) REVERT: H 56 ILE cc_start: 0.7731 (mm) cc_final: 0.7436 (mm) REVERT: H 84 TYR cc_start: 0.7883 (p90) cc_final: 0.7490 (p90) REVERT: I 159 PHE cc_start: 0.8487 (t80) cc_final: 0.8176 (t80) REVERT: I 180 ASP cc_start: 0.8955 (m-30) cc_final: 0.8727 (m-30) REVERT: I 270 ILE cc_start: 0.8370 (mm) cc_final: 0.8104 (mm) REVERT: I 308 ARG cc_start: 0.9193 (ttm-80) cc_final: 0.8878 (mmt90) REVERT: I 351 LYS cc_start: 0.9088 (tmtt) cc_final: 0.8838 (tptt) REVERT: I 494 LEU cc_start: 0.9486 (tp) cc_final: 0.9065 (tt) REVERT: J 538 THR cc_start: 0.9370 (p) cc_final: 0.9109 (t) REVERT: J 589 ASP cc_start: 0.8410 (m-30) cc_final: 0.8068 (m-30) REVERT: J 651 ASN cc_start: 0.8974 (m-40) cc_final: 0.8653 (m-40) REVERT: K 36 TRP cc_start: 0.8433 (m100) cc_final: 0.8036 (m100) REVERT: K 43 LYS cc_start: 0.8936 (mppt) cc_final: 0.8572 (mmmm) REVERT: K 96 LYS cc_start: 0.7731 (ptpt) cc_final: 0.7343 (mmmm) outliers start: 0 outliers final: 0 residues processed: 492 average time/residue: 0.3091 time to fit residues: 235.6541 Evaluate side-chains 411 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 7.9990 chunk 59 optimal weight: 0.0020 chunk 177 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 193 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 198 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 0.0050 chunk 169 optimal weight: 8.9990 overall best weight: 1.5206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 ASN ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100AASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.140973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.118022 restraints weight = 50109.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.121356 restraints weight = 32266.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.123698 restraints weight = 23429.924| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20334 Z= 0.192 Angle : 0.707 9.214 27603 Z= 0.348 Chirality : 0.051 0.428 3198 Planarity : 0.004 0.064 3471 Dihedral : 8.924 69.633 3603 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.25 % Favored : 91.54 % Rotamer: Outliers : 0.05 % Allowed : 0.42 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.82 (0.16), residues: 2424 helix: 0.44 (0.30), residues: 312 sheet: -0.87 (0.24), residues: 474 loop : -1.75 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP I 338 HIS 0.004 0.001 HIS K 102 PHE 0.028 0.002 PHE K 100D TYR 0.025 0.002 TYR L 89 ARG 0.004 0.000 ARG E 308 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4710.96 seconds wall clock time: 86 minutes 58.69 seconds (5218.69 seconds total)