Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 8 17:30:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8san_40274/05_2023/8san_40274_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8san_40274/05_2023/8san_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_40274/05_2023/8san_40274.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8san_40274/05_2023/8san_40274.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8san_40274/05_2023/8san_40274_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8san_40274/05_2023/8san_40274_neut.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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 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 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 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 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 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 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 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 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 chiralities: 6 Time building chain proxies: 10.49, per 1000 atoms: 0.53 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: 9.09 Conformation dependent library (CDL) restraints added in 2.7 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: 1.46 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: 6.39 Time building geometry restraints manager: 9.68 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 - 16.99: 10734 16.99 - 33.98: 953 33.98 - 50.97: 182 50.97 - 67.97: 41 67.97 - 84.96: 18 Dihedral angle restraints: 11928 sinusoidal: 4857 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 11925 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: 0.340 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: 3.540 Check model and map are aligned: 0.350 Set scattering table: 0.170 Process input model: 51.560 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.050 ------------------------------------------------------------------------------- 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 : 13.484 84.958 7260 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 % 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 *********************** 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 : 2.163 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 outliers start: 2 outliers final: 0 residues processed: 559 average time/residue: 0.3150 time to fit residues: 268.3520 Evaluate side-chains 415 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 2.414 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9482 ------------------------------------------------------------------------------- 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: 0.9990 chunk 102 optimal weight: 20.0000 chunk 62 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 190 optimal weight: 0.9990 chunk 73 optimal weight: 20.0000 chunk 115 optimal weight: 0.9980 chunk 141 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** G 58 ASN G 100AASN H 103 GLN ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100AASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 20334 Z= 0.200 Angle : 0.741 9.636 27603 Z= 0.366 Chirality : 0.051 0.391 3198 Planarity : 0.005 0.073 3471 Dihedral : 6.414 83.382 2655 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.58 % Favored : 91.17 % Rotamer Outliers : 0.19 % 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: -1.95 (0.16), residues: 2424 helix: 0.34 (0.29), residues: 333 sheet: -1.13 (0.23), residues: 492 loop : -1.81 (0.14), residues: 1599 *********************** 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 547 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 543 time to evaluate : 2.364 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 outliers start: 4 outliers final: 0 residues processed: 544 average time/residue: 0.3115 time to fit residues: 261.1182 Evaluate side-chains 407 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 407 time to evaluate : 2.394 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3222 ------------------------------------------------------------------------------- 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: 20.0000 chunk 68 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 221 optimal weight: 9.9990 chunk 238 optimal weight: 0.2980 chunk 196 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 177 optimal weight: 0.9980 overall best weight: 3.4586 ------------------------------------------------------------------------------- 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 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 F 577 GLN G 58 ASN H 103 GLN I 156 ASN J 651 ASN ** J 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 20334 Z= 0.234 Angle : 0.719 10.588 27603 Z= 0.358 Chirality : 0.050 0.355 3198 Planarity : 0.005 0.061 3471 Dihedral : 6.219 82.337 2655 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.82 % Favored : 89.93 % Rotamer Outliers : 0.19 % 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: -1.92 (0.16), residues: 2424 helix: 0.35 (0.30), residues: 333 sheet: -1.03 (0.24), residues: 459 loop : -1.81 (0.14), residues: 1632 *********************** 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 522 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 518 time to evaluate : 2.374 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 outliers start: 4 outliers final: 0 residues processed: 520 average time/residue: 0.3778 time to fit residues: 309.8223 Evaluate side-chains 393 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 2.150 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9113 ------------------------------------------------------------------------------- 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: 10.0000 chunk 166 optimal weight: 0.7980 chunk 114 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 234 optimal weight: 9.9990 chunk 115 optimal weight: 0.9980 chunk 210 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 300 ASN ** I 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 651 ASN ** J 652 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: 0.7474 moved from start: 0.2343 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= 0.181 Angle : 0.685 9.352 27603 Z= 0.335 Chirality : 0.049 0.371 3198 Planarity : 0.004 0.065 3471 Dihedral : 5.959 81.945 2655 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.54 % Favored : 91.21 % Rotamer Outliers : 0.05 % 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: -1.79 (0.16), residues: 2424 helix: 0.38 (0.29), residues: 333 sheet: -0.86 (0.23), residues: 459 loop : -1.72 (0.14), residues: 1632 *********************** 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 528 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 527 time to evaluate : 2.370 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 outliers start: 1 outliers final: 0 residues processed: 527 average time/residue: 0.3098 time to fit residues: 252.8906 Evaluate side-chains 401 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 2.326 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0932 ------------------------------------------------------------------------------- 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: 8.9990 chunk 133 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 119 optimal weight: 4.9990 chunk 210 optimal weight: 0.0000 chunk 59 optimal weight: 8.9990 overall best weight: 5.3992 ------------------------------------------------------------------------------- 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 543 ASN B 577 GLN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 229 ASN G 58 ASN G 100AASN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 575 GLN J 651 ASN K 100AASN K 102 HIS ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 20334 Z= 0.308 Angle : 0.761 9.150 27603 Z= 0.380 Chirality : 0.051 0.388 3198 Planarity : 0.005 0.068 3471 Dihedral : 6.215 78.992 2655 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.26 % Favored : 88.53 % Rotamer Outliers : 0.19 % 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: -1.88 (0.16), residues: 2424 helix: 0.28 (0.30), residues: 333 sheet: -0.89 (0.23), residues: 492 loop : -1.81 (0.15), residues: 1599 *********************** 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 507 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 503 time to evaluate : 2.162 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 outliers start: 4 outliers final: 0 residues processed: 505 average time/residue: 0.3074 time to fit residues: 241.6628 Evaluate side-chains 386 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 2.184 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9374 ------------------------------------------------------------------------------- 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: 8.9990 chunk 211 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 235 optimal weight: 8.9990 chunk 195 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 77 optimal weight: 20.0000 chunk 123 optimal weight: 8.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- 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 591 GLN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 ASN G 100AASN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 575 GLN J 651 ASN K 100AASN ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 20334 Z= 0.282 Angle : 0.759 12.871 27603 Z= 0.376 Chirality : 0.051 0.398 3198 Planarity : 0.005 0.068 3471 Dihedral : 6.248 77.016 2655 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.40 % Favored : 89.40 % Rotamer Outliers : 0.14 % 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: -2.00 (0.16), residues: 2424 helix: 0.17 (0.29), residues: 333 sheet: -1.04 (0.23), residues: 498 loop : -1.85 (0.15), residues: 1593 *********************** 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 498 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 495 time to evaluate : 2.334 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 outliers start: 3 outliers final: 0 residues processed: 496 average time/residue: 0.3035 time to fit residues: 234.6217 Evaluate side-chains 388 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 2.253 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1676 ------------------------------------------------------------------------------- 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: 6.9990 chunk 26 optimal weight: 0.0170 chunk 133 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 197 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 234 optimal weight: 0.0370 chunk 146 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 overall best weight: 2.0100 ------------------------------------------------------------------------------- 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** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 ASN G 100AASN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 ASN ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 651 ASN K 100AASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2995 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= 0.200 Angle : 0.715 8.982 27603 Z= 0.351 Chirality : 0.050 0.394 3198 Planarity : 0.004 0.064 3471 Dihedral : 5.983 76.205 2655 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.86 % Favored : 89.93 % Rotamer Outliers : 0.09 % 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: -1.87 (0.16), residues: 2424 helix: 0.52 (0.30), residues: 315 sheet: -0.96 (0.23), residues: 489 loop : -1.79 (0.15), residues: 1620 *********************** 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 512 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 510 time to evaluate : 2.450 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 outliers start: 2 outliers final: 0 residues processed: 510 average time/residue: 0.3146 time to fit residues: 251.6636 Evaluate side-chains 403 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 2.301 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2936 ------------------------------------------------------------------------------- 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: 8.9990 chunk 139 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 159 optimal weight: 30.0000 chunk 115 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 184 optimal weight: 0.9980 chunk 213 optimal weight: 10.0000 overall best weight: 7.1988 ------------------------------------------------------------------------------- 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 330 HIS A 478 ASN C 58 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** 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 100AASN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 651 ASN K 100AASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.063 20334 Z= 0.383 Angle : 0.846 9.403 27603 Z= 0.427 Chirality : 0.053 0.389 3198 Planarity : 0.006 0.073 3471 Dihedral : 6.551 72.583 2655 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.21 % Allowed : 13.28 % Favored : 86.51 % Rotamer Outliers : 0.23 % 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: -2.21 (0.16), residues: 2424 helix: -0.03 (0.29), residues: 333 sheet: -1.09 (0.24), residues: 468 loop : -2.01 (0.14), residues: 1623 *********************** 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 477 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 472 time to evaluate : 2.271 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 outliers start: 5 outliers final: 0 residues processed: 475 average time/residue: 0.3030 time to fit residues: 225.2182 Evaluate side-chains 384 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 2.283 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0214 ------------------------------------------------------------------------------- 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: 5.9990 chunk 204 optimal weight: 0.9990 chunk 218 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 66 optimal weight: 0.0050 chunk 197 optimal weight: 3.9990 chunk 206 optimal weight: 2.9990 chunk 217 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- 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** A 478 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN G 58 ASN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 577 GLN J 651 ASN ** J 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100AASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3292 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= 0.203 Angle : 0.745 9.177 27603 Z= 0.367 Chirality : 0.051 0.401 3198 Planarity : 0.004 0.070 3471 Dihedral : 6.135 71.924 2655 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.95 % Favored : 90.84 % Rotamer Outliers : 0.14 % 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: -2.00 (0.16), residues: 2424 helix: 0.33 (0.30), residues: 312 sheet: -1.05 (0.25), residues: 438 loop : -1.85 (0.14), residues: 1674 *********************** 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 516 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 513 time to evaluate : 2.212 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 outliers start: 3 outliers final: 1 residues processed: 515 average time/residue: 0.2965 time to fit residues: 239.1373 Evaluate side-chains 403 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 402 time to evaluate : 2.332 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1796 time to fit residues: 3.5413 ------------------------------------------------------------------------------- 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: 7.9990 chunk 140 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 chunk 160 optimal weight: 7.9990 chunk 242 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 chunk 20 optimal weight: 20.0000 chunk 148 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 ** 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 G 58 ASN G 100AASN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 478 ASN ** J 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 651 ASN ** J 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 20334 Z= 0.309 Angle : 0.789 8.826 27603 Z= 0.394 Chirality : 0.052 0.410 3198 Planarity : 0.005 0.116 3471 Dihedral : 6.278 70.315 2655 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.76 % Favored : 88.04 % Rotamer Outliers : 0.09 % 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: -2.13 (0.16), residues: 2424 helix: 0.15 (0.30), residues: 312 sheet: -1.20 (0.25), residues: 444 loop : -1.90 (0.14), residues: 1668 ********************** 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 487 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 485 time to evaluate : 2.290 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 outliers start: 2 outliers final: 0 residues processed: 486 average time/residue: 0.3079 time to fit residues: 236.1469 Evaluate side-chains 383 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 2.169 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0523 ------------------------------------------------------------------------------- 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: 1.9990 chunk 59 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 169 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** A 428 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN ** D 103 GLN ** 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 G 58 ASN ** H 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 478 ASN J 651 ASN ** J 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.139390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.117185 restraints weight = 48848.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.120365 restraints weight = 31531.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.122643 restraints weight = 23057.375| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3594 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= 0.214 Angle : 0.750 10.018 27603 Z= 0.368 Chirality : 0.051 0.407 3198 Planarity : 0.005 0.068 3471 Dihedral : 6.054 69.219 2655 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.28 % Favored : 90.51 % Rotamer Outliers : 0.05 % 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: -2.04 (0.16), residues: 2424 helix: 0.13 (0.30), residues: 312 sheet: -1.13 (0.25), residues: 450 loop : -1.82 (0.14), residues: 1662 =============================================================================== Job complete usr+sys time: 4439.28 seconds wall clock time: 81 minutes 49.05 seconds (4909.05 seconds total)