Starting phenix.real_space_refine on Sat Sep 28 22:54:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um7_20819/09_2024/6um7_20819.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um7_20819/09_2024/6um7_20819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um7_20819/09_2024/6um7_20819.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um7_20819/09_2024/6um7_20819.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um7_20819/09_2024/6um7_20819.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6um7_20819/09_2024/6um7_20819.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.141 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 12687 2.51 5 N 3375 2.21 5 O 4137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 20334 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3613 Classifications: {'peptide': 462} Link IDs: {'CIS': 4, 'PTRANS': 23, 'TRANS': 434} Chain: "H" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "J" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "K" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "E" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3613 Classifications: {'peptide': 462} Link IDs: {'CIS': 4, 'PTRANS': 23, 'TRANS': 434} Chain: "F" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "G" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "1" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "B" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "C" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "I" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3613 Classifications: {'peptide': 462} Link IDs: {'CIS': 4, 'PTRANS': 23, 'TRANS': 434} Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "I" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 12.68, per 1000 atoms: 0.62 Number of scatterers: 20334 At special positions: 0 Unit cell: (160.5, 161.57, 140.17, 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 4137 8.00 N 3375 7.00 C 12687 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.27 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.20 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.00 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=1.98 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.08 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.20 Simple disulfide: pdb=" SG CYS H 598 " - pdb=" SG CYS H 604 " distance=2.07 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.09 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.07 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.27 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.20 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.00 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.02 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=1.98 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.08 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.19 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.08 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.02 Simple disulfide: pdb=" SG CYS 1 598 " - pdb=" SG CYS 1 604 " distance=2.07 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.08 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 90 " distance=2.02 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.27 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.20 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.00 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=1.98 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.08 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.19 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN S 4 " - " MAN S 5 " " MAN X 4 " - " MAN X 5 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA S 3 " - " MAN S 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA N 3 " - " MAN N 6 " " BMA S 3 " - " MAN S 6 " " BMA X 3 " - " MAN X 6 " BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " 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 V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " NAG-ASN " NAG A 619 " - " ASN A 386 " " NAG A 620 " - " ASN A 362 " " NAG A 621 " - " ASN A 197 " " NAG A 622 " - " ASN A 158 " " NAG A 623 " - " ASN A 234 " " NAG A 624 " - " ASN A 88 " " NAG A 625 " - " ASN A 241 " " NAG A 626 " - " ASN A 339 " " NAG E 619 " - " ASN E 386 " " NAG E 620 " - " ASN E 362 " " NAG E 621 " - " ASN E 197 " " NAG E 622 " - " ASN E 158 " " NAG E 623 " - " ASN E 234 " " NAG E 624 " - " ASN E 88 " " NAG E 625 " - " ASN E 241 " " NAG E 626 " - " ASN E 339 " " NAG I 619 " - " ASN I 386 " " NAG I 620 " - " ASN I 362 " " NAG I 621 " - " ASN I 197 " " NAG I 622 " - " ASN I 158 " " NAG I 623 " - " ASN I 234 " " NAG I 624 " - " ASN I 88 " " NAG I 625 " - " ASN I 241 " " NAG I 626 " - " ASN I 339 " " NAG L 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 301 " " NAG N 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 154 " " NAG P 1 " - " ASN A 392 " " NAG Q 1 " - " ASN E 262 " " NAG R 1 " - " ASN E 301 " " NAG S 1 " - " ASN E 332 " " NAG T 1 " - " ASN E 154 " " NAG U 1 " - " ASN E 392 " " NAG V 1 " - " ASN I 262 " " NAG W 1 " - " ASN I 301 " " NAG X 1 " - " ASN I 332 " " NAG Y 1 " - " ASN I 154 " " NAG Z 1 " - " ASN I 392 " Time building additional restraints: 5.45 Conformation dependent library (CDL) restraints added in 2.6 seconds 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4590 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 42 sheets defined 25.5% alpha, 33.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... Processing helix chain 'A' and resid 62 through 68 removed outlier: 3.711A pdb=" N HIS A 66 " --> pdb=" O LYS A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.550A pdb=" N GLN A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 138 through 151 removed outlier: 3.915A pdb=" N GLU A 151 " --> pdb=" O GLY A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 389 through 392 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.669A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 513 through 520 Processing helix chain 'H' and resid 523 through 528 removed outlier: 4.062A pdb=" N GLY H 527 " --> pdb=" O GLY H 524 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 536 Processing helix chain 'H' and resid 538 through 543 removed outlier: 3.562A pdb=" N ARG H 542 " --> pdb=" O THR H 538 " (cutoff:3.500A) Processing helix chain 'H' and resid 570 through 597 removed outlier: 3.593A pdb=" N LYS H 574 " --> pdb=" O VAL H 570 " (cutoff:3.500A) Processing helix chain 'H' and resid 611 through 615 Processing helix chain 'H' and resid 618 through 625 Processing helix chain 'H' and resid 627 through 635 removed outlier: 3.545A pdb=" N LYS H 633 " --> pdb=" O LEU H 629 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU H 634 " --> pdb=" O GLN H 630 " (cutoff:3.500A) Processing helix chain 'H' and resid 638 through 664 Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'J' and resid 74 through 76 No H-bonds generated for 'chain 'J' and resid 74 through 76' Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 25 through 30 Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'D' and resid 513 through 520 Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.061A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 536 Processing helix chain 'D' and resid 538 through 543 removed outlier: 3.561A pdb=" N ARG D 542 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 597 removed outlier: 3.592A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.546A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 664 Processing helix chain 'E' and resid 62 through 68 removed outlier: 3.710A pdb=" N HIS E 66 " --> pdb=" O LYS E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 116 removed outlier: 3.552A pdb=" N GLN E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 138 through 151 removed outlier: 3.915A pdb=" N GLU E 151 " --> pdb=" O GLY E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 377 through 381 Processing helix chain 'E' and resid 389 through 392 Processing helix chain 'E' and resid 474 through 484 removed outlier: 3.671A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 74 through 76 No H-bonds generated for 'chain 'F' and resid 74 through 76' Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 25 through 30 Processing helix chain 'G' and resid 81 through 85 Processing helix chain '1' and resid 513 through 520 Processing helix chain '1' and resid 523 through 528 removed outlier: 4.061A pdb=" N GLY 1 527 " --> pdb=" O GLY 1 524 " (cutoff:3.500A) Processing helix chain '1' and resid 529 through 536 Processing helix chain '1' and resid 538 through 543 removed outlier: 3.561A pdb=" N ARG 1 542 " --> pdb=" O THR 1 538 " (cutoff:3.500A) Processing helix chain '1' and resid 570 through 597 removed outlier: 3.591A pdb=" N LYS 1 574 " --> pdb=" O VAL 1 570 " (cutoff:3.500A) Processing helix chain '1' and resid 611 through 615 Processing helix chain '1' and resid 618 through 625 Processing helix chain '1' and resid 627 through 635 removed outlier: 3.547A pdb=" N LYS 1 633 " --> pdb=" O LEU 1 629 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU 1 634 " --> pdb=" O GLN 1 630 " (cutoff:3.500A) Processing helix chain '1' and resid 638 through 664 Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'I' and resid 62 through 68 removed outlier: 3.710A pdb=" N HIS I 66 " --> pdb=" O LYS I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 98 No H-bonds generated for 'chain 'I' and resid 96 through 98' Processing helix chain 'I' and resid 99 through 116 removed outlier: 3.552A pdb=" N GLN I 103 " --> pdb=" O ASP I 99 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU I 116 " --> pdb=" O TRP I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 138 through 151 removed outlier: 3.914A pdb=" N GLU I 151 " --> pdb=" O GLY I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 198 Processing helix chain 'I' and resid 335 through 350 Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 377 through 381 Processing helix chain 'I' and resid 389 through 392 Processing helix chain 'I' and resid 474 through 484 removed outlier: 3.670A pdb=" N ASN I 478 " --> pdb=" O ASP I 474 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 498 removed outlier: 5.009A pdb=" N VAL H 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N VAL A 38 " --> pdb=" O THR H 606 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N THR H 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 175 Processing sheet with id=AA5, first strand: chain 'A' and resid 260 through 261 removed outlier: 8.030A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 11.716A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.023A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.326A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.604A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.610A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 12.254A pdb=" N ILE A 284 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 11.610A pdb=" N ASP A 457 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 10.604A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.326A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.023A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.716A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LYS A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 358 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 302 through 308 removed outlier: 7.085A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 423 through 426 removed outlier: 4.866A pdb=" N MET A 426 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG A 432 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AB1, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.847A pdb=" N TYR J 33 " --> pdb=" O GLY J 99 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N TRP J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.217A pdb=" N TYR J 116 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 9 through 10 removed outlier: 6.364A pdb=" N TRP K 37 " --> pdb=" O MET K 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 9 through 10 removed outlier: 6.249A pdb=" N THR K 98 " --> pdb=" O ALA K 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AB6, first strand: chain 'D' and resid 603 through 609 removed outlier: 7.842A pdb=" N THR D 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N VAL E 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL D 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB8, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB9, first strand: chain 'E' and resid 167 through 175 Processing sheet with id=AC1, first strand: chain 'E' and resid 260 through 261 removed outlier: 8.032A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 11.716A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 12.021A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.610A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 12.253A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER E 334 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 271 through 273 removed outlier: 12.253A pdb=" N ILE E 284 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 11.610A pdb=" N ASP E 457 " --> pdb=" O ILE E 284 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.327A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 12.021A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 12.000A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.716A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR E 357 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE E 468 " --> pdb=" O THR E 357 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE E 358 " --> pdb=" O TYR E 395 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 302 through 308 removed outlier: 7.085A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 423 through 426 removed outlier: 4.868A pdb=" N MET E 426 " --> pdb=" O ARG E 432 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG E 432 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.847A pdb=" N TYR F 33 " --> pdb=" O GLY F 99 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TRP F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.215A pdb=" N TYR F 116 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 9 through 10 removed outlier: 6.364A pdb=" N TRP G 37 " --> pdb=" O MET G 49 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 9 through 10 removed outlier: 6.251A pdb=" N THR G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 18 through 23 Processing sheet with id=AD2, first strand: chain '1' and resid 603 through 609 removed outlier: 7.842A pdb=" N THR 1 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N VAL I 38 " --> pdb=" O THR 1 606 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL 1 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AD4, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.847A pdb=" N TYR B 33 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE B 34 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TRP B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.216A pdb=" N TYR B 116 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 9 through 10 removed outlier: 6.363A pdb=" N TRP C 37 " --> pdb=" O MET C 49 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 9 through 10 removed outlier: 6.249A pdb=" N THR C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 18 through 23 Processing sheet with id=AD9, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AE1, first strand: chain 'I' and resid 91 through 94 Processing sheet with id=AE2, first strand: chain 'I' and resid 167 through 175 Processing sheet with id=AE3, first strand: chain 'I' and resid 260 through 261 removed outlier: 8.031A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 11.717A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 12.002A pdb=" N LEU I 453 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 12.025A pdb=" N LEU I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 11.326A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 11.610A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLU I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER I 334 " --> pdb=" O GLU I 293 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 271 through 273 removed outlier: 12.254A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 11.610A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 11.326A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 12.025A pdb=" N LEU I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 12.002A pdb=" N LEU I 453 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 11.717A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR I 357 " --> pdb=" O GLU I 466 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE I 468 " --> pdb=" O THR I 357 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS I 360 " --> pdb=" O PHE I 468 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE I 358 " --> pdb=" O TYR I 395 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR I 395 " --> pdb=" O ILE I 358 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 302 through 308 removed outlier: 7.085A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 423 through 426 removed outlier: 4.867A pdb=" N MET I 426 " --> pdb=" O ARG I 432 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARG I 432 " --> pdb=" O MET I 426 " (cutoff:3.500A) 810 hydrogen bonds defined for protein. 2025 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: 7.28 Time building geometry restraints manager: 6.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 5203 1.33 - 1.47: 6467 1.47 - 1.62: 8892 1.62 - 1.76: 21 1.76 - 1.90: 165 Bond restraints: 20748 Sorted by residual: bond pdb=" N PRO I 177 " pdb=" CD PRO I 177 " ideal model delta sigma weight residual 1.473 1.689 -0.216 1.40e-02 5.10e+03 2.38e+02 bond pdb=" N PRO A 177 " pdb=" CD PRO A 177 " ideal model delta sigma weight residual 1.473 1.689 -0.216 1.40e-02 5.10e+03 2.38e+02 bond pdb=" N PRO E 177 " pdb=" CD PRO E 177 " ideal model delta sigma weight residual 1.473 1.689 -0.216 1.40e-02 5.10e+03 2.38e+02 bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.384 0.113 1.40e-02 5.10e+03 6.50e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.386 0.111 1.40e-02 5.10e+03 6.29e+01 ... (remaining 20743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.69: 27911 6.69 - 13.38: 271 13.38 - 20.07: 9 20.07 - 26.76: 0 26.76 - 33.44: 9 Bond angle restraints: 28200 Sorted by residual: angle pdb=" C SER F 84 " pdb=" N ARG F 85 " pdb=" CA ARG F 85 " ideal model delta sigma weight residual 122.68 152.73 -30.05 1.47e+00 4.63e-01 4.18e+02 angle pdb=" C SER B 84 " pdb=" N ARG B 85 " pdb=" CA ARG B 85 " ideal model delta sigma weight residual 122.68 152.62 -29.94 1.47e+00 4.63e-01 4.15e+02 angle pdb=" C SER J 84 " pdb=" N ARG J 85 " pdb=" CA ARG J 85 " ideal model delta sigma weight residual 122.68 152.62 -29.94 1.47e+00 4.63e-01 4.15e+02 angle pdb=" C SER 1 546 " pdb=" N GLY 1 547 " pdb=" CA GLY 1 547 " ideal model delta sigma weight residual 121.70 155.14 -33.44 1.80e+00 3.09e-01 3.45e+02 angle pdb=" C SER D 546 " pdb=" N GLY D 547 " pdb=" CA GLY D 547 " ideal model delta sigma weight residual 121.70 155.07 -33.37 1.80e+00 3.09e-01 3.44e+02 ... (remaining 28195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.43: 12770 23.43 - 46.85: 355 46.85 - 70.28: 100 70.28 - 93.70: 98 93.70 - 117.13: 63 Dihedral angle restraints: 13386 sinusoidal: 6216 harmonic: 7170 Sorted by residual: dihedral pdb=" CA ARG I 446 " pdb=" C ARG I 446 " pdb=" N SER I 447 " pdb=" CA SER I 447 " ideal model delta harmonic sigma weight residual 180.00 62.87 117.13 0 5.00e+00 4.00e-02 5.49e+02 dihedral pdb=" CA ARG A 446 " pdb=" C ARG A 446 " pdb=" N SER A 447 " pdb=" CA SER A 447 " ideal model delta harmonic sigma weight residual 180.00 62.93 117.07 0 5.00e+00 4.00e-02 5.48e+02 dihedral pdb=" CA ARG E 446 " pdb=" C ARG E 446 " pdb=" N SER E 447 " pdb=" CA SER E 447 " ideal model delta harmonic sigma weight residual 180.00 63.16 116.84 0 5.00e+00 4.00e-02 5.46e+02 ... (remaining 13383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.940: 3393 0.940 - 1.879: 0 1.879 - 2.819: 0 2.819 - 3.759: 0 3.759 - 4.699: 3 Chirality restraints: 3396 Sorted by residual: chirality pdb=" C1 MAN S 4 " pdb=" O3 BMA S 3 " pdb=" C2 MAN S 4 " pdb=" O5 MAN S 4 " both_signs ideal model delta sigma weight residual False 2.40 1.70 0.70 2.00e-02 2.50e+03 1.22e+03 chirality pdb=" C1 MAN N 4 " pdb=" O3 BMA N 3 " pdb=" C2 MAN N 4 " pdb=" O5 MAN N 4 " both_signs ideal model delta sigma weight residual False 2.40 1.70 0.70 2.00e-02 2.50e+03 1.22e+03 chirality pdb=" C1 MAN X 4 " pdb=" O3 BMA X 3 " pdb=" C2 MAN X 4 " pdb=" O5 MAN X 4 " both_signs ideal model delta sigma weight residual False 2.40 1.71 0.69 2.00e-02 2.50e+03 1.19e+03 ... (remaining 3393 not shown) Planarity restraints: 3528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " -0.344 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG R 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " -0.057 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " 0.522 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " -0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.344 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG M 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.057 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.521 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 2 " 0.344 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG W 2 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG W 2 " 0.057 2.00e-02 2.50e+03 pdb=" N2 NAG W 2 " -0.521 2.00e-02 2.50e+03 pdb=" O7 NAG W 2 " 0.201 2.00e-02 2.50e+03 ... (remaining 3525 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 1321 2.69 - 3.24: 20028 3.24 - 3.79: 32047 3.79 - 4.35: 41984 4.35 - 4.90: 66859 Nonbonded interactions: 162239 Sorted by model distance: nonbonded pdb=" OG1 THR E 297 " pdb=" O ILE E 443 " model vdw 2.132 3.040 nonbonded pdb=" OG1 THR I 297 " pdb=" O ILE I 443 " model vdw 2.132 3.040 nonbonded pdb=" OG1 THR A 297 " pdb=" O ILE A 443 " model vdw 2.133 3.040 nonbonded pdb=" OD1 ASN E 339 " pdb=" C1 NAG E 626 " model vdw 2.165 2.776 nonbonded pdb=" OD1 ASN I 339 " pdb=" C1 NAG I 626 " model vdw 2.165 2.776 ... (remaining 162234 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '1' selection = chain 'D' selection = chain 'H' } 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 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'N' selection = chain 'S' selection = chain 'X' } 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: 10.530 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: 0.000 Extract box with map and model: 0.660 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 47.700 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 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 : 0.018 0.216 20748 Z= 1.192 Angle : 2.068 33.444 28200 Z= 1.359 Chirality : 0.177 4.699 3396 Planarity : 0.027 0.297 3489 Dihedral : 16.468 117.128 8697 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.96 % Favored : 94.19 % Rotamer: Outliers : 0.89 % Allowed : 1.26 % Favored : 97.86 % Cbeta Deviations : 0.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % 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: 0.01 (0.17), residues: 2460 helix: -0.60 (0.23), residues: 399 sheet: 0.62 (0.21), residues: 546 loop : 0.05 (0.17), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.010 TRP C 37 HIS 0.008 0.003 HIS J 35 PHE 0.033 0.007 PHE G 101 TYR 0.079 0.009 TYR F 105 ARG 0.013 0.001 ARG J 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 2.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 518 VAL cc_start: 0.4024 (t) cc_final: 0.3691 (p) REVERT: J 89 ASP cc_start: 0.8254 (m-30) cc_final: 0.8003 (m-30) REVERT: E 125 LEU cc_start: 0.7985 (mm) cc_final: 0.7611 (mt) REVERT: 1 535 MET cc_start: 0.4424 (mmp) cc_final: 0.4210 (mpp) REVERT: B 70 MET cc_start: 0.5300 (mtm) cc_final: 0.4998 (mtm) outliers start: 19 outliers final: 4 residues processed: 203 average time/residue: 0.3896 time to fit residues: 114.3706 Evaluate side-chains 78 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain I residue 234 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 40.0000 chunk 192 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 223 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS A 363 GLN H 575 GLN J 3 GLN D 575 GLN D 591 GLN E 203 GLN E 300 ASN E 363 GLN F 1 GLN F 113 ASN 1 658 GLN B 65 GLN I 203 GLN I 287 HIS I 363 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 20748 Z= 0.347 Angle : 0.964 12.854 28200 Z= 0.492 Chirality : 0.056 0.379 3396 Planarity : 0.006 0.075 3489 Dihedral : 12.645 90.843 4275 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.73 % Allowed : 3.58 % Favored : 95.69 % Rotamer: Outliers : 1.17 % Allowed : 4.90 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 3.03 % 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: -0.17 (0.17), residues: 2460 helix: 0.94 (0.27), residues: 402 sheet: 0.17 (0.18), residues: 714 loop : -0.55 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP F 101 HIS 0.009 0.002 HIS I 105 PHE 0.030 0.003 PHE H 522 TYR 0.028 0.002 TYR K 51 ARG 0.007 0.001 ARG I 446 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 83 time to evaluate : 2.374 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.8377 (mm) cc_final: 0.7956 (mt) REVERT: E 369 MET cc_start: 0.5036 (OUTLIER) cc_final: 0.4792 (ptm) REVERT: 1 545 LEU cc_start: 0.6886 (tp) cc_final: 0.6443 (mt) outliers start: 25 outliers final: 7 residues processed: 103 average time/residue: 0.2869 time to fit residues: 49.2076 Evaluate side-chains 76 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 369 MET Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 234 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 124 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 185 optimal weight: 10.0000 chunk 152 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 223 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 221 optimal weight: 0.2980 chunk 76 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 658 GLN J 115 ASN E 203 GLN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN 1 543 ASN B 65 GLN B 115 ASN I 422 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 20748 Z= 0.375 Angle : 0.909 13.304 28200 Z= 0.470 Chirality : 0.053 0.337 3396 Planarity : 0.006 0.071 3489 Dihedral : 10.452 89.322 4268 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.04 % Favored : 94.39 % Rotamer: Outliers : 1.49 % Allowed : 6.62 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.43 (0.17), residues: 2460 helix: 0.92 (0.26), residues: 417 sheet: 0.03 (0.19), residues: 678 loop : -0.82 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP I 479 HIS 0.009 0.002 HIS E 105 PHE 0.027 0.003 PHE I 382 TYR 0.026 0.002 TYR K 51 ARG 0.011 0.001 ARG A 504 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 76 time to evaluate : 2.459 Fit side-chains revert: symmetry clash REVERT: E 125 LEU cc_start: 0.8818 (mm) cc_final: 0.8387 (mt) REVERT: G 100 ILE cc_start: 0.7231 (OUTLIER) cc_final: 0.6919 (mt) REVERT: 1 545 LEU cc_start: 0.8008 (tp) cc_final: 0.7584 (mt) REVERT: I 434 MET cc_start: 0.8989 (ptm) cc_final: 0.8212 (ptt) outliers start: 32 outliers final: 16 residues processed: 96 average time/residue: 0.2873 time to fit residues: 46.3576 Evaluate side-chains 84 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 67 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain 1 residue 573 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain I residue 503 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 0.4980 chunk 168 optimal weight: 5.9990 chunk 116 optimal weight: 0.0370 chunk 24 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 212 optimal weight: 8.9990 chunk 64 optimal weight: 0.0370 overall best weight: 1.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN 1 575 GLN B 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.6549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20748 Z= 0.217 Angle : 0.732 12.847 28200 Z= 0.376 Chirality : 0.048 0.318 3396 Planarity : 0.004 0.068 3489 Dihedral : 9.437 77.227 4266 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.61 % Allowed : 4.27 % Favored : 95.12 % Rotamer: Outliers : 1.21 % Allowed : 7.69 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.17), residues: 2460 helix: 1.85 (0.28), residues: 399 sheet: 0.02 (0.19), residues: 684 loop : -0.61 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 112 HIS 0.004 0.001 HIS E 105 PHE 0.014 0.001 PHE I 383 TYR 0.020 0.001 TYR K 51 ARG 0.004 0.001 ARG D 585 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 68 time to evaluate : 2.306 Fit side-chains REVERT: A 152 MET cc_start: 0.8211 (mmt) cc_final: 0.7880 (mmt) REVERT: J 1 GLN cc_start: 0.8189 (pm20) cc_final: 0.7975 (pm20) REVERT: D 626 MET cc_start: 0.7792 (ttm) cc_final: 0.7395 (ttm) REVERT: G 107 MET cc_start: 0.7639 (tpp) cc_final: 0.7022 (tpp) REVERT: 1 626 MET cc_start: 0.6736 (tpp) cc_final: 0.6334 (tpp) REVERT: B 63 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7973 (ptpt) REVERT: C 49 MET cc_start: 0.7828 (mmp) cc_final: 0.7617 (mmp) REVERT: C 100 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7032 (pt) REVERT: I 434 MET cc_start: 0.9019 (ptm) cc_final: 0.8626 (ptt) outliers start: 26 outliers final: 12 residues processed: 83 average time/residue: 0.2801 time to fit residues: 39.5726 Evaluate side-chains 78 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 369 MET Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 475 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 177 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 chunk 164 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 213 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 GLN D 658 GLN F 39 GLN C 1 GLN I 300 ASN I 417 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.8028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 20748 Z= 0.336 Angle : 0.803 12.752 28200 Z= 0.412 Chirality : 0.050 0.336 3396 Planarity : 0.005 0.067 3489 Dihedral : 9.592 80.581 4266 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.26 % Favored : 93.09 % Rotamer: Outliers : 1.91 % Allowed : 8.62 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % 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: -0.46 (0.17), residues: 2460 helix: 1.28 (0.27), residues: 423 sheet: -0.11 (0.19), residues: 681 loop : -0.91 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 427 HIS 0.007 0.001 HIS F 35 PHE 0.019 0.002 PHE I 383 TYR 0.023 0.002 TYR I 217 ARG 0.006 0.001 ARG E 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 68 time to evaluate : 2.186 Fit side-chains REVERT: A 152 MET cc_start: 0.8472 (mmt) cc_final: 0.8037 (mmt) REVERT: J 1 GLN cc_start: 0.8339 (pm20) cc_final: 0.8009 (pm20) REVERT: D 626 MET cc_start: 0.8030 (ttm) cc_final: 0.7675 (ttm) REVERT: E 175 TYR cc_start: 0.6913 (OUTLIER) cc_final: 0.5260 (p90) REVERT: G 100 ILE cc_start: 0.7350 (OUTLIER) cc_final: 0.7010 (mt) REVERT: 1 626 MET cc_start: 0.7855 (tpp) cc_final: 0.7527 (tpp) REVERT: B 63 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8121 (ptpt) REVERT: C 100 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.6808 (pt) REVERT: I 95 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7412 (ttp) REVERT: I 434 MET cc_start: 0.9093 (ptm) cc_final: 0.8480 (ptt) outliers start: 41 outliers final: 20 residues processed: 95 average time/residue: 0.2774 time to fit residues: 44.6752 Evaluate side-chains 87 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 62 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 175 TYR Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 369 MET Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 475 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 2.9990 chunk 214 optimal weight: 0.0570 chunk 47 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 238 optimal weight: 4.9990 chunk 197 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 422 GLN ** 1 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 1 GLN I 229 ASN I 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.8441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20748 Z= 0.246 Angle : 0.729 12.622 28200 Z= 0.371 Chirality : 0.048 0.319 3396 Planarity : 0.004 0.062 3489 Dihedral : 9.035 75.450 4266 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.63 % Favored : 94.72 % Rotamer: Outliers : 1.35 % Allowed : 9.74 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % 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: -0.35 (0.17), residues: 2460 helix: 1.71 (0.27), residues: 405 sheet: -0.13 (0.19), residues: 696 loop : -0.89 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 631 HIS 0.005 0.001 HIS A 249 PHE 0.014 0.002 PHE A 382 TYR 0.019 0.001 TYR I 175 ARG 0.004 0.001 ARG E 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 62 time to evaluate : 2.152 Fit side-chains revert: symmetry clash REVERT: H 626 MET cc_start: 0.7362 (mtp) cc_final: 0.7067 (ttm) REVERT: J 1 GLN cc_start: 0.8310 (pm20) cc_final: 0.8043 (pm20) REVERT: K 83 GLU cc_start: 0.8220 (mp0) cc_final: 0.7760 (tm-30) REVERT: D 626 MET cc_start: 0.7935 (ttm) cc_final: 0.7608 (ttm) REVERT: F 102 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8563 (pt) REVERT: G 107 MET cc_start: 0.7517 (tpp) cc_final: 0.7003 (tpp) REVERT: 1 626 MET cc_start: 0.7839 (tpp) cc_final: 0.7438 (tpp) REVERT: B 63 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8087 (ptpt) REVERT: C 100 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.6933 (pt) REVERT: I 434 MET cc_start: 0.8901 (ptm) cc_final: 0.8570 (ptm) outliers start: 29 outliers final: 18 residues processed: 82 average time/residue: 0.3085 time to fit residues: 42.6147 Evaluate side-chains 83 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 62 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 369 MET Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain I residue 503 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 200 optimal weight: 0.5980 chunk 132 optimal weight: 6.9990 chunk 237 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 144 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 39 GLN J 113 ASN C 40 GLN I 287 HIS I 300 ASN I 350 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.8913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20748 Z= 0.255 Angle : 0.715 12.616 28200 Z= 0.364 Chirality : 0.048 0.332 3396 Planarity : 0.004 0.059 3489 Dihedral : 8.766 74.022 4266 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.65 % Allowed : 5.65 % Favored : 93.70 % Rotamer: Outliers : 1.86 % Allowed : 9.88 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % 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: -0.37 (0.17), residues: 2460 helix: 1.81 (0.27), residues: 405 sheet: -0.11 (0.19), residues: 702 loop : -0.96 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 96 HIS 0.006 0.001 HIS A 249 PHE 0.015 0.002 PHE I 382 TYR 0.017 0.001 TYR I 175 ARG 0.003 0.000 ARG 1 542 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 64 time to evaluate : 2.250 Fit side-chains REVERT: A 175 TYR cc_start: 0.7070 (OUTLIER) cc_final: 0.4998 (p90) REVERT: H 626 MET cc_start: 0.7293 (mtp) cc_final: 0.6724 (ttp) REVERT: J 29 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.7070 (p90) REVERT: K 83 GLU cc_start: 0.8254 (mp0) cc_final: 0.7798 (tm-30) REVERT: D 626 MET cc_start: 0.7897 (ttm) cc_final: 0.7589 (ttm) REVERT: F 102 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8506 (pt) REVERT: G 100 ILE cc_start: 0.7430 (OUTLIER) cc_final: 0.7066 (mt) REVERT: B 29 PHE cc_start: 0.6868 (OUTLIER) cc_final: 0.5876 (p90) REVERT: C 39 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7793 (tt0) REVERT: C 100 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.6962 (pt) REVERT: I 175 TYR cc_start: 0.6881 (OUTLIER) cc_final: 0.5309 (p90) REVERT: I 503 ARG cc_start: 0.6503 (OUTLIER) cc_final: 0.5019 (ptp-170) outliers start: 40 outliers final: 17 residues processed: 95 average time/residue: 0.2809 time to fit residues: 45.0686 Evaluate side-chains 89 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 63 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain J residue 29 PHE Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain I residue 503 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 141 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 overall best weight: 4.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 115 ASN D 658 GLN I 82 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 300 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.9527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20748 Z= 0.357 Angle : 0.790 12.517 28200 Z= 0.399 Chirality : 0.049 0.341 3396 Planarity : 0.004 0.058 3489 Dihedral : 9.259 77.291 4266 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.42 % Favored : 92.89 % Rotamer: Outliers : 1.68 % Allowed : 10.07 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % 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: -0.51 (0.17), residues: 2460 helix: 1.52 (0.27), residues: 408 sheet: -0.23 (0.19), residues: 687 loop : -0.96 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 1 631 HIS 0.007 0.002 HIS I 287 PHE 0.019 0.002 PHE 1 519 TYR 0.020 0.002 TYR E 175 ARG 0.010 0.001 ARG I 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 64 time to evaluate : 2.248 Fit side-chains REVERT: A 175 TYR cc_start: 0.6775 (OUTLIER) cc_final: 0.4978 (p90) REVERT: A 475 MET cc_start: 0.8226 (mmm) cc_final: 0.7900 (mmm) REVERT: K 83 GLU cc_start: 0.8271 (mp0) cc_final: 0.7724 (tm-30) REVERT: K 107 MET cc_start: 0.7871 (tpp) cc_final: 0.7513 (tpp) REVERT: D 626 MET cc_start: 0.8027 (ttm) cc_final: 0.7769 (ttm) REVERT: E 175 TYR cc_start: 0.7007 (OUTLIER) cc_final: 0.5068 (p90) REVERT: F 102 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8609 (pt) REVERT: G 107 MET cc_start: 0.7616 (tpp) cc_final: 0.7046 (tpp) REVERT: 1 614 TRP cc_start: 0.5709 (OUTLIER) cc_final: 0.4907 (m-10) REVERT: 1 626 MET cc_start: 0.8236 (tpp) cc_final: 0.7868 (tpp) REVERT: B 29 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.6262 (p90) REVERT: C 100 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7544 (mt) REVERT: I 175 TYR cc_start: 0.6949 (OUTLIER) cc_final: 0.5215 (p90) REVERT: I 434 MET cc_start: 0.8926 (ptm) cc_final: 0.8522 (ptm) REVERT: I 503 ARG cc_start: 0.6360 (OUTLIER) cc_final: 0.4865 (ptp-170) outliers start: 36 outliers final: 22 residues processed: 89 average time/residue: 0.2733 time to fit residues: 41.7048 Evaluate side-chains 92 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 62 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 175 TYR Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain 1 residue 530 MET Chi-restraints excluded: chain 1 residue 614 TRP Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 152 MET Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 300 ASN Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain I residue 503 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 215 optimal weight: 8.9990 chunk 227 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 220 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 199 optimal weight: 6.9990 chunk 208 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 GLN J 39 GLN E 229 ASN E 350 GLN B 115 ASN C 40 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 300 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 1.0032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 20748 Z= 0.429 Angle : 0.843 12.374 28200 Z= 0.426 Chirality : 0.051 0.355 3396 Planarity : 0.005 0.057 3489 Dihedral : 9.926 82.665 4266 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.73 % Allowed : 7.32 % Favored : 91.95 % Rotamer: Outliers : 1.59 % Allowed : 10.16 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % 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: -0.77 (0.17), residues: 2460 helix: 1.43 (0.26), residues: 399 sheet: -0.35 (0.20), residues: 687 loop : -1.19 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 96 HIS 0.009 0.002 HIS I 287 PHE 0.020 0.002 PHE A 376 TYR 0.020 0.002 TYR E 400 ARG 0.013 0.001 ARG I 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 61 time to evaluate : 2.446 Fit side-chains REVERT: A 175 TYR cc_start: 0.6911 (OUTLIER) cc_final: 0.4983 (p90) REVERT: A 475 MET cc_start: 0.8210 (mmm) cc_final: 0.7923 (mmm) REVERT: K 83 GLU cc_start: 0.8328 (mp0) cc_final: 0.7782 (tm-30) REVERT: D 626 MET cc_start: 0.8120 (ttm) cc_final: 0.7917 (ttm) REVERT: F 29 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7043 (p90) REVERT: F 102 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8564 (pt) REVERT: 1 614 TRP cc_start: 0.5670 (OUTLIER) cc_final: 0.4692 (m-10) REVERT: 1 626 MET cc_start: 0.8286 (tpp) cc_final: 0.7817 (tpp) REVERT: B 29 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.6474 (p90) REVERT: C 100 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7492 (mt) REVERT: I 175 TYR cc_start: 0.6985 (OUTLIER) cc_final: 0.5189 (p90) REVERT: I 434 MET cc_start: 0.8908 (ptm) cc_final: 0.8582 (ptm) outliers start: 34 outliers final: 21 residues processed: 88 average time/residue: 0.2688 time to fit residues: 41.7789 Evaluate side-chains 84 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 56 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 175 TYR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 89 ASP Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 315 GLN Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain F residue 29 PHE Chi-restraints excluded: chain F residue 66 ASP Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain 1 residue 614 TRP Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 175 TYR Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 475 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 233 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 245 optimal weight: 0.0370 chunk 225 optimal weight: 0.8980 chunk 195 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 1.0044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20748 Z= 0.195 Angle : 0.728 12.285 28200 Z= 0.366 Chirality : 0.048 0.344 3396 Planarity : 0.004 0.052 3489 Dihedral : 8.999 72.870 4266 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.69 % Allowed : 4.55 % Favored : 94.76 % Rotamer: Outliers : 0.84 % Allowed : 10.86 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % 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: -0.43 (0.17), residues: 2460 helix: 1.91 (0.27), residues: 396 sheet: -0.17 (0.21), residues: 627 loop : -0.99 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 96 HIS 0.012 0.001 HIS I 105 PHE 0.013 0.001 PHE I 382 TYR 0.017 0.001 TYR A 191 ARG 0.005 0.000 ARG I 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 61 time to evaluate : 2.246 Fit side-chains REVERT: A 475 MET cc_start: 0.8039 (mmm) cc_final: 0.7668 (mmm) REVERT: H 626 MET cc_start: 0.8039 (ttm) cc_final: 0.7661 (ttp) REVERT: K 83 GLU cc_start: 0.8352 (mp0) cc_final: 0.7869 (tm-30) REVERT: D 626 MET cc_start: 0.8009 (ttm) cc_final: 0.7809 (ttm) REVERT: E 175 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.5178 (p90) REVERT: F 102 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8522 (pt) REVERT: 1 614 TRP cc_start: 0.5702 (OUTLIER) cc_final: 0.5173 (m-90) REVERT: 1 626 MET cc_start: 0.8113 (tpp) cc_final: 0.7729 (tpp) REVERT: I 434 MET cc_start: 0.8899 (ptm) cc_final: 0.8474 (ptm) outliers start: 18 outliers final: 14 residues processed: 76 average time/residue: 0.2714 time to fit residues: 36.4200 Evaluate side-chains 75 residues out of total 2145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 58 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain J residue 70 MET Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain E residue 175 TYR Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 403 THR Chi-restraints excluded: chain E residue 475 MET Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain 1 residue 614 TRP Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain I residue 184 GLU Chi-restraints excluded: chain I residue 403 THR Chi-restraints excluded: chain I residue 414 ILE Chi-restraints excluded: chain I residue 475 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 195 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 200 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 36 optimal weight: 30.0000 chunk 171 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.040209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.033189 restraints weight = 186108.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.034061 restraints weight = 110031.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.034639 restraints weight = 80585.183| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 1.0211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20748 Z= 0.285 Angle : 0.747 12.260 28200 Z= 0.376 Chirality : 0.048 0.349 3396 Planarity : 0.004 0.051 3489 Dihedral : 9.102 74.552 4266 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.02 % Favored : 93.29 % Rotamer: Outliers : 1.12 % Allowed : 10.58 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % 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: -0.47 (0.17), residues: 2460 helix: 1.86 (0.27), residues: 396 sheet: -0.20 (0.20), residues: 657 loop : -1.01 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 96 HIS 0.006 0.001 HIS A 249 PHE 0.016 0.002 PHE A 376 TYR 0.015 0.002 TYR G 51 ARG 0.005 0.000 ARG I 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2981.09 seconds wall clock time: 56 minutes 14.27 seconds (3374.27 seconds total)