Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 8 16:58:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sau_40280/05_2023/8sau_40280_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sau_40280/05_2023/8sau_40280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sau_40280/05_2023/8sau_40280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sau_40280/05_2023/8sau_40280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sau_40280/05_2023/8sau_40280_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sau_40280/05_2023/8sau_40280_neut.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 138 5.16 5 C 12429 2.51 5 N 3321 2.21 5 O 3996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 589": "OD1" <-> "OD2" Residue "C PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 28": "OD1" <-> "OD2" Residue "D PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "F TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 466": "OE1" <-> "OE2" Residue "F PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 474": "OD1" <-> "OD2" Residue "G ASP 632": "OD1" <-> "OD2" Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 73": "OD1" <-> "OD2" Residue "H PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 102": "OD1" <-> "OD2" Residue "K GLU 211": "OE1" <-> "OE2" Residue "L ASP 632": "OD1" <-> "OD2" Residue "L GLU 634": "OE1" <-> "OE2" Residue "L ASP 659": "OD1" <-> "OD2" Residue "M ASP 63": "OD1" <-> "OD2" Residue "M TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 28": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 19884 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "B" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "C" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 992 Classifications: {'peptide': 126} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "D" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "G" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "H" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 992 Classifications: {'peptide': 126} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "I" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 3615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3615 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 436} Chain: "L" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 983 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain: "M" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 992 Classifications: {'peptide': 126} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 805 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 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 chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 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 chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 10.62, per 1000 atoms: 0.53 Number of scatterers: 19884 At special positions: 0 Unit cell: (157.768, 158.834, 137.514, 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 138 16.00 O 3996 8.00 N 3321 7.00 C 12429 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.06 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 91 " - pdb=" SG CYS D 101 " distance=2.04 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.04 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.02 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.05 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.04 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS G 605 " distance=2.04 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 91 " - pdb=" SG CYS I 101 " distance=2.04 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.05 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.04 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS L 605 " distance=2.04 Simple disulfide: pdb=" SG CYS L 598 " - pdb=" SG CYS L 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.02 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 91 " - pdb=" SG CYS N 101 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN J 8 " - " MAN J 9 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN R 8 " - " MAN R 9 " " MAN R 10 " - " MAN R 11 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " " MAN V 8 " - " MAN V 9 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA J 3 " - " MAN J 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 8 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " ALPHA1-6 " BMA J 3 " - " MAN J 7 " " MAN J 7 " - " MAN J 8 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 10 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 8 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " 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-ASN " NAG E 1 " - " ASN A 301 " " NAG J 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 442 " " NAG Q 1 " - " ASN F 301 " " NAG R 1 " - " ASN F 332 " " NAG S 1 " - " ASN F 156 " " NAG T 1 " - " ASN F 442 " " NAG U 1 " - " ASN K 301 " " NAG V 1 " - " ASN K 332 " " NAG W 1 " - " ASN K 156 " " NAG X 1 " - " ASN K 442 " Time building additional restraints: 9.46 Conformation dependent library (CDL) restraints added in 3.0 seconds 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4542 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 41 sheets defined 20.3% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 57 through 61 Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.535A pdb=" N ALA A 73 " --> pdb=" O TRP A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 350 removed outlier: 3.575A pdb=" N GLU A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.670A pdb=" N THR A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.696A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 571 through 596 removed outlier: 4.015A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.055A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 4.365A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'F' and resid 57 through 61 removed outlier: 3.630A pdb=" N ALA F 60 " --> pdb=" O ASP F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 73 Processing helix chain 'F' and resid 99 through 116 Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 335 through 350 removed outlier: 3.607A pdb=" N GLU F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.665A pdb=" N THR F 373 " --> pdb=" O MET F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 481 removed outlier: 3.654A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 537 through 542 Processing helix chain 'G' and resid 543 through 545 No H-bonds generated for 'chain 'G' and resid 543 through 545' Processing helix chain 'G' and resid 572 through 596 removed outlier: 3.674A pdb=" N LEU G 576 " --> pdb=" O GLY G 572 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA G 578 " --> pdb=" O LYS G 574 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 615 Processing helix chain 'G' and resid 618 through 624 Processing helix chain 'G' and resid 627 through 636 removed outlier: 4.128A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 664 removed outlier: 4.346A pdb=" N GLY G 644 " --> pdb=" O GLN G 640 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU G 645 " --> pdb=" O ILE G 641 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN G 650 " --> pdb=" O LEU G 646 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN G 656 " --> pdb=" O GLN G 652 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU G 661 " --> pdb=" O GLU G 657 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'K' and resid 57 through 61 removed outlier: 3.568A pdb=" N ALA K 60 " --> pdb=" O ASP K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 73 removed outlier: 3.511A pdb=" N ALA K 73 " --> pdb=" O TRP K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 116 Processing helix chain 'K' and resid 122 through 126 Processing helix chain 'K' and resid 177 through 179 No H-bonds generated for 'chain 'K' and resid 177 through 179' Processing helix chain 'K' and resid 335 through 350 removed outlier: 3.556A pdb=" N GLU K 348 " --> pdb=" O LYS K 344 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 373 removed outlier: 3.609A pdb=" N THR K 373 " --> pdb=" O MET K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 474 through 481 removed outlier: 3.614A pdb=" N ASN K 478 " --> pdb=" O ASP K 474 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER K 481 " --> pdb=" O ASP K 477 " (cutoff:3.500A) Processing helix chain 'K' and resid 482 through 484 No H-bonds generated for 'chain 'K' and resid 482 through 484' Processing helix chain 'L' and resid 529 through 534 Processing helix chain 'L' and resid 537 through 542 Processing helix chain 'L' and resid 543 through 545 No H-bonds generated for 'chain 'L' and resid 543 through 545' Processing helix chain 'L' and resid 571 through 596 removed outlier: 3.864A pdb=" N GLN L 575 " --> pdb=" O TRP L 571 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU L 576 " --> pdb=" O GLY L 572 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 615 Processing helix chain 'L' and resid 618 through 624 Processing helix chain 'L' and resid 627 through 636 removed outlier: 4.013A pdb=" N LYS L 633 " --> pdb=" O LEU L 629 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU L 634 " --> pdb=" O GLN L 630 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 664 removed outlier: 4.477A pdb=" N GLY L 644 " --> pdb=" O GLN L 640 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU L 645 " --> pdb=" O ILE L 641 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLN L 650 " --> pdb=" O LEU L 646 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN L 656 " --> pdb=" O GLN L 652 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU L 661 " --> pdb=" O GLU L 657 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 65 Processing helix chain 'M' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 3.729A pdb=" N THR A 499 " --> pdb=" O TRP A 35 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP A 35 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.017A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.738A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 176 removed outlier: 3.653A pdb=" N GLU A 172 " --> pdb=" O PHE A 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 260 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 260 current: chain 'A' and resid 284 through 302 removed outlier: 7.716A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 330 through 334 current: chain 'A' and resid 382 through 385 removed outlier: 4.518A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 413 through 421 current: chain 'A' and resid 468 through 470 Processing sheet with id=AA7, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AA8, first strand: chain 'A' and resid 423 through 425 Processing sheet with id=AA9, first strand: chain 'C' and resid 2 through 3 Processing sheet with id=AB1, first strand: chain 'C' and resid 18 through 22 removed outlier: 3.510A pdb=" N LEU C 83 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU C 82 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR C 69 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 32 through 39 removed outlier: 6.634A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 58 through 60 current: chain 'C' and resid 116 through 117 Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.906A pdb=" N GLY D 12 " --> pdb=" O THR D 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 23 Processing sheet with id=AB5, first strand: chain 'D' and resid 46 through 50 removed outlier: 5.948A pdb=" N TYR D 48 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLN D 39 " --> pdb=" O TYR D 48 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE D 38 " --> pdb=" O TYR D 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 494 through 499 removed outlier: 3.551A pdb=" N THR F 499 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP F 35 " --> pdb=" O THR F 499 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL F 36 " --> pdb=" O THR G 606 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 45 through 46 removed outlier: 3.624A pdb=" N LYS F 46 " --> pdb=" O LYS F 490 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE F 225 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AB9, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.692A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 173 through 176 Processing sheet with id=AC2, first strand: chain 'F' and resid 161 through 162 Processing sheet with id=AC3, first strand: chain 'F' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 261 current: chain 'F' and resid 284 through 308 removed outlier: 6.623A pdb=" N ASN F 301 " --> pdb=" O ILE F 322 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ILE F 322 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 316 through 323 current: chain 'F' and resid 382 through 385 removed outlier: 4.539A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 413 through 421 current: chain 'F' and resid 468 through 470 Processing sheet with id=AC4, first strand: chain 'F' and resid 423 through 425 Processing sheet with id=AC5, first strand: chain 'H' and resid 2 through 3 Processing sheet with id=AC6, first strand: chain 'H' and resid 18 through 22 removed outlier: 4.023A pdb=" N GLU H 82 " --> pdb=" O THR H 69 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR H 69 " --> pdb=" O GLU H 82 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 32 through 39 removed outlier: 6.618A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 60 current: chain 'H' and resid 116 through 117 Processing sheet with id=AC8, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.661A pdb=" N GLY I 12 " --> pdb=" O THR I 108 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 19 through 23 Processing sheet with id=AD1, first strand: chain 'I' and resid 46 through 50 removed outlier: 6.026A pdb=" N TYR I 48 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLN I 39 " --> pdb=" O TYR I 48 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE I 38 " --> pdb=" O TYR I 89 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 494 through 499 removed outlier: 3.875A pdb=" N THR K 499 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TRP K 35 " --> pdb=" O THR K 499 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL K 36 " --> pdb=" O THR L 606 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 45 through 46 removed outlier: 3.641A pdb=" N LYS K 46 " --> pdb=" O LYS K 490 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL K 242 " --> pdb=" O LEU K 86 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 75 through 76 Processing sheet with id=AD5, first strand: chain 'K' and resid 91 through 94 removed outlier: 3.834A pdb=" N GLU K 91 " --> pdb=" O CYS K 239 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 169 through 176 removed outlier: 4.562A pdb=" N ASN K 156 " --> pdb=" O SER K 132 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 259 through 260 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 259 through 260 current: chain 'K' and resid 284 through 302 removed outlier: 7.712A pdb=" N GLU K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER K 334 " --> pdb=" O GLU K 293 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL K 295 " --> pdb=" O ASN K 332 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 330 through 334 current: chain 'K' and resid 382 through 385 removed outlier: 4.482A pdb=" N PHE K 382 " --> pdb=" O LYS K 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 413 through 421 current: chain 'K' and resid 467 through 470 Processing sheet with id=AD8, first strand: chain 'K' and resid 304 through 308 Processing sheet with id=AD9, first strand: chain 'K' and resid 423 through 425 Processing sheet with id=AE1, first strand: chain 'M' and resid 18 through 22 removed outlier: 3.946A pdb=" N GLU M 82 " --> pdb=" O THR M 69 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR M 69 " --> pdb=" O GLU M 82 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 32 through 39 removed outlier: 6.661A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 58 through 60 current: chain 'M' and resid 116 through 117 Processing sheet with id=AE3, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.773A pdb=" N GLY N 12 " --> pdb=" O THR N 108 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 19 through 23 Processing sheet with id=AE5, first strand: chain 'N' and resid 48 through 50 removed outlier: 3.633A pdb=" N ILE N 50 " --> pdb=" O TRP N 37 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE N 38 " --> pdb=" O TYR N 89 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR N 89 " --> pdb=" O PHE N 38 " (cutoff:3.500A) 515 hydrogen bonds defined for protein. 1356 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.32 Time building geometry restraints manager: 10.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6339 1.35 - 1.48: 5389 1.48 - 1.61: 8402 1.61 - 1.74: 3 1.74 - 1.86: 183 Bond restraints: 20316 Sorted by residual: bond pdb=" CA GLN I 39 " pdb=" CB GLN I 39 " ideal model delta sigma weight residual 1.526 1.600 -0.074 1.70e-02 3.46e+03 1.91e+01 bond pdb=" CB CYS K 433 " pdb=" SG CYS K 433 " ideal model delta sigma weight residual 1.808 1.706 0.102 3.30e-02 9.18e+02 9.64e+00 bond pdb=" CB CYS F 433 " pdb=" SG CYS F 433 " ideal model delta sigma weight residual 1.808 1.715 0.093 3.30e-02 9.18e+02 7.96e+00 bond pdb=" C5 MAN V 7 " pdb=" O5 MAN V 7 " ideal model delta sigma weight residual 1.418 1.471 -0.053 2.00e-02 2.50e+03 7.02e+00 bond pdb=" C5 MAN R 7 " pdb=" O5 MAN R 7 " ideal model delta sigma weight residual 1.418 1.470 -0.052 2.00e-02 2.50e+03 6.77e+00 ... (remaining 20311 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.76: 412 105.76 - 112.85: 10969 112.85 - 119.93: 6928 119.93 - 127.02: 8996 127.02 - 134.10: 331 Bond angle restraints: 27636 Sorted by residual: angle pdb=" C ASN A 67 " pdb=" N VAL A 68 " pdb=" CA VAL A 68 " ideal model delta sigma weight residual 121.70 133.92 -12.22 1.80e+00 3.09e-01 4.61e+01 angle pdb=" C ASN F 67 " pdb=" N VAL F 68 " pdb=" CA VAL F 68 " ideal model delta sigma weight residual 121.70 133.63 -11.93 1.80e+00 3.09e-01 4.39e+01 angle pdb=" C ASN K 67 " pdb=" N VAL K 68 " pdb=" CA VAL K 68 " ideal model delta sigma weight residual 121.70 133.53 -11.83 1.80e+00 3.09e-01 4.32e+01 angle pdb=" C SER M 25 " pdb=" N GLY M 26 " pdb=" CA GLY M 26 " ideal model delta sigma weight residual 121.70 131.44 -9.74 1.80e+00 3.09e-01 2.93e+01 angle pdb=" C SER C 25 " pdb=" N GLY C 26 " pdb=" CA GLY C 26 " ideal model delta sigma weight residual 121.70 131.35 -9.65 1.80e+00 3.09e-01 2.88e+01 ... (remaining 27631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 10558 18.05 - 36.09: 943 36.09 - 54.14: 182 54.14 - 72.19: 28 72.19 - 90.24: 16 Dihedral angle restraints: 11727 sinusoidal: 4632 harmonic: 7095 Sorted by residual: dihedral pdb=" CA VAL G 570 " pdb=" C VAL G 570 " pdb=" N TRP G 571 " pdb=" CA TRP G 571 " ideal model delta harmonic sigma weight residual 180.00 143.21 36.79 0 5.00e+00 4.00e-02 5.41e+01 dihedral pdb=" CA GLY K 431 " pdb=" C GLY K 431 " pdb=" N ARG K 432 " pdb=" CA ARG K 432 " ideal model delta harmonic sigma weight residual -180.00 -146.01 -33.99 0 5.00e+00 4.00e-02 4.62e+01 dihedral pdb=" CA GLY F 431 " pdb=" C GLY F 431 " pdb=" N ARG F 432 " pdb=" CA ARG F 432 " ideal model delta harmonic sigma weight residual 180.00 -146.65 -33.35 0 5.00e+00 4.00e-02 4.45e+01 ... (remaining 11724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2715 0.067 - 0.133: 474 0.133 - 0.200: 60 0.200 - 0.267: 5 0.267 - 0.333: 7 Chirality restraints: 3261 Sorted by residual: chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 7.04e+00 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.74e+00 ... (remaining 3258 not shown) Planarity restraints: 3465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 252 " -0.073 5.00e-02 4.00e+02 1.11e-01 1.97e+01 pdb=" N PRO A 253 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG K 252 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO K 253 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO K 253 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO K 253 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 112 " -0.022 2.00e-02 2.50e+03 2.15e-02 1.16e+01 pdb=" CG TRP F 112 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP F 112 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP F 112 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP F 112 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP F 112 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP F 112 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 112 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 112 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 112 " 0.000 2.00e-02 2.50e+03 ... (remaining 3462 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 243 2.63 - 3.20: 18003 3.20 - 3.77: 28629 3.77 - 4.33: 41696 4.33 - 4.90: 67547 Nonbonded interactions: 156118 Sorted by model distance: nonbonded pdb=" O LEU K 84 " pdb=" OG SER K 243 " model vdw 2.063 2.440 nonbonded pdb=" OE2 GLU K 83 " pdb=" OG SER K 243 " model vdw 2.065 2.440 nonbonded pdb=" O LYS A 360 " pdb=" OG1 THR A 467 " model vdw 2.068 2.440 nonbonded pdb=" O LYS F 360 " pdb=" OG1 THR F 467 " model vdw 2.070 2.440 nonbonded pdb=" OE2 GLU A 83 " pdb=" OG SER A 243 " model vdw 2.088 2.440 ... (remaining 156113 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'V' } ncs_group { reference = chain 'O' selection = chain 'S' selection = chain 'T' selection = chain 'W' } ncs_group { reference = chain 'P' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.640 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 52.640 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.102 20316 Z= 0.404 Angle : 0.993 12.219 27636 Z= 0.518 Chirality : 0.054 0.333 3261 Planarity : 0.006 0.111 3453 Dihedral : 14.244 90.235 7050 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.17 % Favored : 92.51 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.16), residues: 2442 helix: -1.57 (0.23), residues: 444 sheet: -1.18 (0.19), residues: 642 loop : -1.56 (0.16), residues: 1356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 560 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 561 average time/residue: 0.3153 time to fit residues: 267.3946 Evaluate side-chains 348 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 2.223 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 2.9990 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN A 287 HIS C 52 ASN C 60 ASN ** D 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 HIS F 72 HIS F 241 ASN F 287 HIS G 590 GLN H 113 ASN H 116 HIS K 105 HIS K 241 ASN K 287 HIS L 543 ASN L 577 GLN L 653 GLN M 52 ASN M 119 GLN ** N 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 20316 Z= 0.400 Angle : 0.836 17.295 27636 Z= 0.427 Chirality : 0.053 0.340 3261 Planarity : 0.006 0.076 3453 Dihedral : 6.521 28.132 2646 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.10 % Favored : 93.53 % Rotamer Outliers : 2.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % 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: -2.13 (0.16), residues: 2442 helix: -0.85 (0.25), residues: 429 sheet: -1.24 (0.18), residues: 684 loop : -1.69 (0.16), residues: 1329 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 365 time to evaluate : 2.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 45 residues processed: 398 average time/residue: 0.3611 time to fit residues: 212.3026 Evaluate side-chains 339 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 294 time to evaluate : 2.462 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 45 outliers final: 1 residues processed: 45 average time/residue: 0.1864 time to fit residues: 18.8667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 122 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 238 optimal weight: 7.9990 chunk 196 optimal weight: 0.8980 chunk 219 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 HIS F 72 HIS F 105 HIS F 343 GLN F 389 ASN ** G 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 591 GLN H 116 HIS K 246 GLN ** K 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 362 ASN L 543 ASN L 591 GLN L 625 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 20316 Z= 0.333 Angle : 0.736 19.035 27636 Z= 0.371 Chirality : 0.049 0.209 3261 Planarity : 0.005 0.053 3453 Dihedral : 6.076 28.511 2646 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.43 % Favored : 93.33 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.16), residues: 2442 helix: -0.69 (0.25), residues: 429 sheet: -0.85 (0.19), residues: 648 loop : -1.55 (0.16), residues: 1365 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 307 time to evaluate : 2.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 30 residues processed: 349 average time/residue: 0.3603 time to fit residues: 188.3146 Evaluate side-chains 307 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 277 time to evaluate : 2.308 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 30 outliers final: 1 residues processed: 30 average time/residue: 0.1798 time to fit residues: 13.3264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 218 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 221 optimal weight: 4.9990 chunk 234 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 HIS C 119 GLN F 72 HIS G 543 ASN ** G 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 543 ASN M 119 GLN N 41 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 20316 Z= 0.381 Angle : 0.755 20.988 27636 Z= 0.378 Chirality : 0.049 0.210 3261 Planarity : 0.005 0.049 3453 Dihedral : 6.062 27.909 2646 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.98 % Favored : 93.78 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.16), residues: 2442 helix: -0.43 (0.26), residues: 408 sheet: -1.01 (0.19), residues: 690 loop : -1.60 (0.16), residues: 1344 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 284 time to evaluate : 2.361 Fit side-chains revert: symmetry clash outliers start: 67 outliers final: 42 residues processed: 322 average time/residue: 0.3526 time to fit residues: 169.4134 Evaluate side-chains 310 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 268 time to evaluate : 2.322 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.1793 time to fit residues: 17.3609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 174 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 210 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 HIS G 543 ASN ** G 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 119 GLN L 543 ASN N 54 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 20316 Z= 0.229 Angle : 0.655 19.777 27636 Z= 0.327 Chirality : 0.045 0.185 3261 Planarity : 0.004 0.047 3453 Dihedral : 5.634 27.121 2646 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.86 % Favored : 93.90 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.16), residues: 2442 helix: 0.17 (0.27), residues: 381 sheet: -0.62 (0.20), residues: 633 loop : -1.52 (0.15), residues: 1428 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 280 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 21 residues processed: 302 average time/residue: 0.3623 time to fit residues: 161.6086 Evaluate side-chains 286 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 265 time to evaluate : 2.324 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2102 time to fit residues: 11.1179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 79 optimal weight: 0.9990 chunk 211 optimal weight: 0.2980 chunk 46 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 235 optimal weight: 0.7980 chunk 195 optimal weight: 0.2980 chunk 108 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN D 54 ASN F 66 HIS ** G 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 119 GLN L 625 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 20316 Z= 0.195 Angle : 0.620 18.893 27636 Z= 0.308 Chirality : 0.044 0.189 3261 Planarity : 0.004 0.043 3453 Dihedral : 5.317 26.038 2646 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.69 % Favored : 94.06 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.16), residues: 2442 helix: 0.19 (0.26), residues: 402 sheet: -0.45 (0.20), residues: 630 loop : -1.42 (0.16), residues: 1410 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 284 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 22 residues processed: 308 average time/residue: 0.3584 time to fit residues: 164.6527 Evaluate side-chains 291 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 269 time to evaluate : 2.306 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1860 time to fit residues: 10.9966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 226 optimal weight: 0.2980 chunk 26 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 171 optimal weight: 0.7980 chunk 197 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 234 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 144 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 389 ASN G 543 ASN ** G 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 119 GLN L 543 ASN L 653 GLN M 119 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 20316 Z= 0.188 Angle : 0.616 23.539 27636 Z= 0.302 Chirality : 0.044 0.179 3261 Planarity : 0.004 0.042 3453 Dihedral : 5.162 27.402 2646 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.61 % Favored : 94.14 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.17), residues: 2442 helix: 0.36 (0.26), residues: 402 sheet: -0.52 (0.20), residues: 666 loop : -1.28 (0.16), residues: 1374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 276 time to evaluate : 2.488 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 9 residues processed: 290 average time/residue: 0.3750 time to fit residues: 160.7478 Evaluate side-chains 278 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 269 time to evaluate : 2.316 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1754 time to fit residues: 6.2069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 93 optimal weight: 0.0000 chunk 139 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 213 optimal weight: 0.7980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN H 119 GLN L 543 ASN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 20316 Z= 0.202 Angle : 0.620 22.188 27636 Z= 0.308 Chirality : 0.044 0.179 3261 Planarity : 0.004 0.042 3453 Dihedral : 5.210 27.151 2646 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.32 % Favored : 94.43 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.17), residues: 2442 helix: 0.41 (0.26), residues: 402 sheet: -0.48 (0.20), residues: 666 loop : -1.28 (0.16), residues: 1374 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 275 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 285 average time/residue: 0.3638 time to fit residues: 153.6284 Evaluate side-chains 273 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 259 time to evaluate : 2.459 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1904 time to fit residues: 8.3723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 224 optimal weight: 0.0570 chunk 204 optimal weight: 2.9990 chunk 218 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 95 optimal weight: 0.3980 chunk 171 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 197 optimal weight: 2.9990 chunk 206 optimal weight: 0.9990 chunk 217 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 543 ASN H 119 GLN L 543 ASN M 119 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 20316 Z= 0.171 Angle : 0.604 21.791 27636 Z= 0.299 Chirality : 0.043 0.175 3261 Planarity : 0.004 0.042 3453 Dihedral : 5.023 28.930 2646 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.04 % Favored : 94.72 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.17), residues: 2442 helix: 0.56 (0.26), residues: 402 sheet: -0.42 (0.20), residues: 666 loop : -1.24 (0.16), residues: 1374 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 277 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 283 average time/residue: 0.3712 time to fit residues: 154.7650 Evaluate side-chains 264 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 257 time to evaluate : 2.333 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1774 time to fit residues: 5.7158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 230 optimal weight: 0.4980 chunk 140 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 222 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 153 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 616 ASN H 119 GLN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 20316 Z= 0.222 Angle : 0.626 22.297 27636 Z= 0.311 Chirality : 0.044 0.177 3261 Planarity : 0.004 0.042 3453 Dihedral : 5.092 27.205 2646 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.16 % Favored : 94.59 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.17), residues: 2442 helix: 0.54 (0.26), residues: 402 sheet: -0.43 (0.20), residues: 660 loop : -1.21 (0.16), residues: 1380 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4884 Ramachandran restraints generated. 2442 Oldfield, 0 Emsley, 2442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 258 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 263 average time/residue: 0.3824 time to fit residues: 148.4624 Evaluate side-chains 260 residues out of total 2130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 253 time to evaluate : 2.439 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2022 time to fit residues: 6.0879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 205 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 chunk 28 optimal weight: 0.0870 chunk 53 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 198 optimal weight: 0.0030 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 169 optimal weight: 0.5980 overall best weight: 0.4768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN B 543 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 GLN G 543 ASN H 119 GLN L 543 ASN ** L 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.199209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.163394 restraints weight = 26290.436| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 3.46 r_work: 0.3829 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 20316 Z= 0.171 Angle : 0.602 21.925 27636 Z= 0.298 Chirality : 0.043 0.173 3261 Planarity : 0.004 0.041 3453 Dihedral : 4.954 31.928 2646 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.12 % Favored : 94.64 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.38 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.17), residues: 2442 helix: 0.68 (0.27), residues: 402 sheet: -0.29 (0.20), residues: 636 loop : -1.24 (0.16), residues: 1404 =============================================================================== Job complete usr+sys time: 4404.04 seconds wall clock time: 81 minutes 3.52 seconds (4863.52 seconds total)