Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 05:33:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjp_0235/04_2023/6hjp_0235_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjp_0235/04_2023/6hjp_0235.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/6hjp_0235/04_2023/6hjp_0235.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjp_0235/04_2023/6hjp_0235.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjp_0235/04_2023/6hjp_0235_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjp_0235/04_2023/6hjp_0235_updated.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= 0.002 sd= 0.123 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 90 5.16 5 C 13878 2.51 5 N 3690 2.21 5 O 4476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 106": "NH1" <-> "NH2" Residue "C TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 106": "NH1" <-> "NH2" Residue "E TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 106": "NH1" <-> "NH2" Residue "G PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 22134 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2510 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 17, 'TRANS': 306} Chain: "B" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1403 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain: "C" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2510 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 17, 'TRANS': 306} Chain: "D" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1403 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain: "E" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2510 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 17, 'TRANS': 306} Chain: "F" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1403 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain: "G" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1611 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 204} Chain: "H" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 201} Chain: "I" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1611 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 204} Chain: "K" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1611 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 204} Chain: "J" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 201} Chain: "L" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 201} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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: 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: "R" 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: "S" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "U" 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: "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 chiralities: 3 Chain: "W" 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: "X" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "Z" 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: "a" 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: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'UPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.86, per 1000 atoms: 0.49 Number of scatterers: 22134 At special positions: 0 Unit cell: (178.948, 164.934, 174.636, 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 90 16.00 O 4476 8.00 N 3690 7.00 C 13878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS B 137 " distance=2.04 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.01 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.02 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.04 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS D 137 " distance=2.04 Simple disulfide: pdb=" SG CYS C 47 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.01 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.04 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS F 137 " distance=2.05 Simple disulfide: pdb=" SG CYS E 47 " - pdb=" SG CYS E 278 " distance=2.03 Simple disulfide: pdb=" SG CYS E 59 " - pdb=" SG CYS E 71 " distance=2.01 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 306 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.05 Simple disulfide: pdb=" SG CYS G 143 " - pdb=" SG CYS G 199 " distance=2.05 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.05 Simple disulfide: pdb=" SG CYS H 135 " - pdb=" SG CYS H 195 " distance=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.05 Simple disulfide: pdb=" SG CYS I 143 " - pdb=" SG CYS I 199 " distance=2.05 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.05 Simple disulfide: pdb=" SG CYS K 143 " - pdb=" SG CYS K 199 " distance=2.05 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.05 Simple disulfide: pdb=" SG CYS J 135 " - pdb=" SG CYS J 195 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA T 3 " - " MAN T 4 " " BMA Y 3 " - " MAN Y 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA T 3 " - " MAN T 5 " " BMA Y 3 " - " MAN Y 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG 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 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 V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " 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 a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " BETA1-6 " NAG N 1 " - " FUC N 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 4 " " NAG X 1 " - " FUC X 4 " NAG-ASN " NAG M 1 " - " ASN A 15 " " NAG N 1 " - " ASN A 27 " " NAG O 1 " - " ASN A 91 " " NAG P 1 " - " ASN A 290 " " NAG Q 1 " - " ASN B 154 " " NAG R 1 " - " ASN C 15 " " NAG S 1 " - " ASN C 27 " " NAG T 1 " - " ASN C 91 " " NAG U 1 " - " ASN C 290 " " NAG V 1 " - " ASN D 154 " " NAG W 1 " - " ASN E 15 " " NAG X 1 " - " ASN E 27 " " NAG Y 1 " - " ASN E 91 " " NAG Z 1 " - " ASN E 290 " " NAG a 1 " - " ASN F 154 " Time building additional restraints: 9.41 Conformation dependent library (CDL) restraints added in 3.2 seconds 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 42 sheets defined 15.6% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 49 through 50 No H-bonds generated for 'chain 'A' and resid 49 through 50' Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 102 through 111 removed outlier: 3.599A pdb=" N SER A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N SER A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'B' and resid 38 through 58 removed outlier: 3.737A pdb=" N GLN B 42 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 124 removed outlier: 3.954A pdb=" N GLU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 154 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 163 through 173 removed outlier: 3.708A pdb=" N LYS B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 50 No H-bonds generated for 'chain 'C' and resid 49 through 50' Processing helix chain 'C' and resid 61 through 66 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 102 through 111 removed outlier: 3.598A pdb=" N SER C 110 " --> pdb=" O ARG C 106 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 195 Processing helix chain 'D' and resid 38 through 58 removed outlier: 3.736A pdb=" N GLN D 42 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 124 removed outlier: 3.955A pdb=" N GLU D 105 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 154 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 163 through 173 removed outlier: 3.707A pdb=" N LYS D 167 " --> pdb=" O SER D 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 50 No H-bonds generated for 'chain 'E' and resid 49 through 50' Processing helix chain 'E' and resid 61 through 66 Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 102 through 111 removed outlier: 3.598A pdb=" N SER E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N SER E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 195 Processing helix chain 'F' and resid 38 through 58 removed outlier: 3.736A pdb=" N GLN F 42 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 124 removed outlier: 3.954A pdb=" N GLU F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 154 Processing helix chain 'F' and resid 159 through 161 No H-bonds generated for 'chain 'F' and resid 159 through 161' Processing helix chain 'F' and resid 163 through 173 removed outlier: 3.707A pdb=" N LYS F 167 " --> pdb=" O SER F 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 31 No H-bonds generated for 'chain 'G' and resid 29 through 31' Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'H' and resid 123 through 128 Processing helix chain 'H' and resid 184 through 189 Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 88 through 90 No H-bonds generated for 'chain 'I' and resid 88 through 90' Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'J' and resid 123 through 128 Processing helix chain 'J' and resid 184 through 189 Processing helix chain 'L' and resid 123 through 128 Processing helix chain 'L' and resid 184 through 189 Processing sheet with id= A, first strand: chain 'A' and resid 268 through 270 removed outlier: 6.633A pdb=" N ILE A 83 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU A 54 " --> pdb=" O ILE A 84 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.996A pdb=" N MET A 230 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 115 through 118 Processing sheet with id= D, first strand: chain 'A' and resid 164 through 169 Processing sheet with id= E, first strand: chain 'A' and resid 282 through 284 Processing sheet with id= F, first strand: chain 'C' and resid 268 through 270 removed outlier: 6.632A pdb=" N ILE C 83 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU C 54 " --> pdb=" O ILE C 84 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 97 through 99 removed outlier: 6.994A pdb=" N MET C 230 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 115 through 118 Processing sheet with id= I, first strand: chain 'C' and resid 164 through 169 Processing sheet with id= J, first strand: chain 'C' and resid 282 through 284 Processing sheet with id= K, first strand: chain 'E' and resid 268 through 270 removed outlier: 6.633A pdb=" N ILE E 83 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU E 54 " --> pdb=" O ILE E 84 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 97 through 99 removed outlier: 6.995A pdb=" N MET E 230 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 115 through 118 Processing sheet with id= N, first strand: chain 'E' and resid 164 through 169 Processing sheet with id= O, first strand: chain 'E' and resid 282 through 284 Processing sheet with id= P, first strand: chain 'G' and resid 3 through 7 Processing sheet with id= Q, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.868A pdb=" N THR G 119 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ALA G 40 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU G 45 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 129 through 133 removed outlier: 6.149A pdb=" N TYR G 179 " --> pdb=" O ASP G 147 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU G 178 " --> pdb=" O GLN G 174 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 153 through 157 Processing sheet with id= T, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.634A pdb=" N GLU H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER H 67 " --> pdb=" O GLU H 70 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.588A pdb=" N ARG H 104 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL H 13 " --> pdb=" O ARG H 104 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLU H 106 " --> pdb=" O VAL H 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'H' and resid 85 through 90 removed outlier: 3.895A pdb=" N ILE H 48 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLN H 37 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU H 46 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 115 through 119 removed outlier: 5.697A pdb=" N TYR H 174 " --> pdb=" O ASN H 139 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 145 through 151 Processing sheet with id= Y, first strand: chain 'I' and resid 3 through 7 Processing sheet with id= Z, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.863A pdb=" N THR I 119 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA I 40 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU I 45 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 129 through 133 removed outlier: 6.149A pdb=" N TYR I 179 " --> pdb=" O ASP I 147 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU I 178 " --> pdb=" O GLN I 174 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'I' and resid 153 through 157 Processing sheet with id= AC, first strand: chain 'K' and resid 3 through 7 Processing sheet with id= AD, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.865A pdb=" N THR K 119 " --> pdb=" O GLY K 10 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA K 40 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU K 45 " --> pdb=" O ALA K 40 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'K' and resid 129 through 133 removed outlier: 6.149A pdb=" N TYR K 179 " --> pdb=" O ASP K 147 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU K 178 " --> pdb=" O GLN K 174 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 153 through 157 Processing sheet with id= AG, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.634A pdb=" N GLU J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER J 67 " --> pdb=" O GLU J 70 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.588A pdb=" N ARG J 104 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL J 13 " --> pdb=" O ARG J 104 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLU J 106 " --> pdb=" O VAL J 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'J' and resid 85 through 90 removed outlier: 3.895A pdb=" N ILE J 48 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'J' and resid 115 through 119 removed outlier: 5.698A pdb=" N TYR J 174 " --> pdb=" O ASN J 139 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'J' and resid 145 through 151 Processing sheet with id= AL, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.634A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER L 67 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.588A pdb=" N ARG L 104 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL L 13 " --> pdb=" O ARG L 104 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLU L 106 " --> pdb=" O VAL L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'L' and resid 85 through 90 removed outlier: 3.896A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.698A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'L' and resid 145 through 151 678 hydrogen bonds defined for protein. 1863 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: 6.47 Time building geometry restraints manager: 9.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4368 1.32 - 1.45: 5889 1.45 - 1.57: 12246 1.57 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 22623 Sorted by residual: bond pdb=" N GLU B 139 " pdb=" CA GLU B 139 " ideal model delta sigma weight residual 1.459 1.396 0.063 9.10e-03 1.21e+04 4.76e+01 bond pdb=" N GLU F 139 " pdb=" CA GLU F 139 " ideal model delta sigma weight residual 1.459 1.397 0.063 9.10e-03 1.21e+04 4.75e+01 bond pdb=" N GLU D 139 " pdb=" CA GLU D 139 " ideal model delta sigma weight residual 1.459 1.397 0.062 9.10e-03 1.21e+04 4.65e+01 bond pdb=" N HIS D 142 " pdb=" CA HIS D 142 " ideal model delta sigma weight residual 1.456 1.415 0.042 1.14e-02 7.69e+03 1.33e+01 bond pdb=" N HIS F 142 " pdb=" CA HIS F 142 " ideal model delta sigma weight residual 1.456 1.415 0.042 1.14e-02 7.69e+03 1.33e+01 ... (remaining 22618 not shown) Histogram of bond angle deviations from ideal: 97.83 - 105.22: 522 105.22 - 112.61: 11678 112.61 - 120.00: 8195 120.00 - 127.39: 10040 127.39 - 134.78: 288 Bond angle restraints: 30723 Sorted by residual: angle pdb=" CA PHE F 140 " pdb=" CB PHE F 140 " pdb=" CG PHE F 140 " ideal model delta sigma weight residual 113.80 107.03 6.77 1.00e+00 1.00e+00 4.58e+01 angle pdb=" CA PHE D 140 " pdb=" CB PHE D 140 " pdb=" CG PHE D 140 " ideal model delta sigma weight residual 113.80 107.07 6.73 1.00e+00 1.00e+00 4.53e+01 angle pdb=" CA PHE B 140 " pdb=" CB PHE B 140 " pdb=" CG PHE B 140 " ideal model delta sigma weight residual 113.80 107.12 6.68 1.00e+00 1.00e+00 4.47e+01 angle pdb=" C TYR B 141 " pdb=" CA TYR B 141 " pdb=" CB TYR B 141 " ideal model delta sigma weight residual 110.79 101.02 9.77 1.66e+00 3.63e-01 3.46e+01 angle pdb=" C TYR D 141 " pdb=" CA TYR D 141 " pdb=" CB TYR D 141 " ideal model delta sigma weight residual 110.79 101.18 9.61 1.66e+00 3.63e-01 3.35e+01 ... (remaining 30718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 12083 15.99 - 31.98: 809 31.98 - 47.97: 176 47.97 - 63.96: 27 63.96 - 79.95: 18 Dihedral angle restraints: 13113 sinusoidal: 5103 harmonic: 8010 Sorted by residual: dihedral pdb=" C ASP F 158 " pdb=" N ASP F 158 " pdb=" CA ASP F 158 " pdb=" CB ASP F 158 " ideal model delta harmonic sigma weight residual -122.60 -138.20 15.60 0 2.50e+00 1.60e-01 3.90e+01 dihedral pdb=" C ASP B 158 " pdb=" N ASP B 158 " pdb=" CA ASP B 158 " pdb=" CB ASP B 158 " ideal model delta harmonic sigma weight residual -122.60 -137.92 15.32 0 2.50e+00 1.60e-01 3.76e+01 dihedral pdb=" C ASP D 158 " pdb=" N ASP D 158 " pdb=" CA ASP D 158 " pdb=" CB ASP D 158 " ideal model delta harmonic sigma weight residual -122.60 -137.67 15.07 0 2.50e+00 1.60e-01 3.63e+01 ... (remaining 13110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 3411 0.168 - 0.336: 108 0.336 - 0.504: 13 0.504 - 0.672: 2 0.672 - 0.840: 3 Chirality restraints: 3537 Sorted by residual: chirality pdb=" C1 MAN Y 4 " pdb=" O3 BMA Y 3 " pdb=" C2 MAN Y 4 " pdb=" O5 MAN Y 4 " both_signs ideal model delta sigma weight residual False 2.40 1.56 0.84 2.00e-02 2.50e+03 1.77e+03 chirality pdb=" C1 MAN T 4 " pdb=" O3 BMA T 3 " pdb=" C2 MAN T 4 " pdb=" O5 MAN T 4 " both_signs ideal model delta sigma weight residual False 2.40 1.57 0.83 2.00e-02 2.50e+03 1.73e+03 chirality pdb=" C1 MAN O 4 " pdb=" O3 BMA O 3 " pdb=" C2 MAN O 4 " pdb=" O5 MAN O 4 " both_signs ideal model delta sigma weight residual False 2.40 1.59 0.81 2.00e-02 2.50e+03 1.65e+03 ... (remaining 3534 not shown) Planarity restraints: 3915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.339 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" C7 NAG N 1 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.144 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.518 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 1 " -0.339 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" C7 NAG S 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG S 1 " -0.145 2.00e-02 2.50e+03 pdb=" N2 NAG S 1 " 0.517 2.00e-02 2.50e+03 pdb=" O7 NAG S 1 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG X 1 " -0.338 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG X 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG X 1 " -0.146 2.00e-02 2.50e+03 pdb=" N2 NAG X 1 " 0.516 2.00e-02 2.50e+03 pdb=" O7 NAG X 1 " -0.117 2.00e-02 2.50e+03 ... (remaining 3912 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 981 2.71 - 3.25: 19802 3.25 - 3.80: 33977 3.80 - 4.35: 41605 4.35 - 4.90: 72394 Nonbonded interactions: 168759 Sorted by model distance: nonbonded pdb=" O3 NAG Y 1 " pdb=" O7 NAG Y 1 " model vdw 2.158 2.440 nonbonded pdb=" O3 NAG O 1 " pdb=" O7 NAG O 1 " model vdw 2.159 2.440 nonbonded pdb=" O3 NAG T 1 " pdb=" O7 NAG T 1 " model vdw 2.159 2.440 nonbonded pdb=" OG SER D 151 " pdb=" O THR D 156 " model vdw 2.230 2.440 nonbonded pdb=" OG SER B 151 " pdb=" O THR B 156 " model vdw 2.230 2.440 ... (remaining 168754 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 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'R' selection = chain 'U' selection = chain 'W' selection = chain 'Z' } ncs_group { reference = chain 'N' selection = chain 'S' selection = chain 'X' } ncs_group { reference = chain 'O' selection = chain 'T' selection = chain 'Y' } ncs_group { reference = chain 'Q' selection = chain 'V' selection = chain 'a' } 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: 11.620 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: 0.050 Extract box with map and model: 31.350 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 54.680 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 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 : 0.008 0.063 22623 Z= 0.523 Angle : 1.170 10.130 30723 Z= 0.697 Chirality : 0.088 0.840 3537 Planarity : 0.018 0.292 3900 Dihedral : 11.652 79.953 7905 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.90 % Favored : 91.88 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.14), residues: 2760 helix: -0.78 (0.22), residues: 423 sheet: -0.57 (0.17), residues: 843 loop : -2.46 (0.13), residues: 1494 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 314 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 11 residues processed: 363 average time/residue: 0.4169 time to fit residues: 218.5502 Evaluate side-chains 159 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 148 time to evaluate : 2.408 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1874 time to fit residues: 6.9792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 0.9980 chunk 206 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 0.0670 chunk 213 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 247 optimal weight: 9.9990 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 184 HIS A 196 GLN A 239 GLN A 250 ASN A 299 HIS A 323 ASN B 169 ASN C 184 HIS C 250 ASN C 261 ASN C 299 HIS C 323 ASN D 169 ASN E 55 GLN E 184 HIS E 239 GLN E 250 ASN E 261 ASN E 299 HIS E 323 ASN G 200 ASN H 37 GLN H 156 GLN I 13 GLN I 114 GLN K 114 GLN K 200 ASN J 6 GLN J 37 GLN J 167 GLN L 6 GLN L 37 GLN L 139 ASN L 156 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 22623 Z= 0.263 Angle : 0.698 13.847 30723 Z= 0.345 Chirality : 0.045 0.255 3537 Planarity : 0.004 0.057 3900 Dihedral : 5.859 55.183 3018 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 2.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.15), residues: 2760 helix: 0.79 (0.25), residues: 423 sheet: -0.25 (0.17), residues: 897 loop : -2.05 (0.14), residues: 1440 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 165 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 30 residues processed: 203 average time/residue: 0.4365 time to fit residues: 128.2253 Evaluate side-chains 166 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 2.373 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2179 time to fit residues: 14.6981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 248 optimal weight: 9.9990 chunk 268 optimal weight: 9.9990 chunk 221 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 chunk 84 optimal weight: 0.0770 chunk 199 optimal weight: 0.8980 overall best weight: 1.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS C 184 HIS E 184 HIS E 261 ASN G 114 GLN H 6 GLN I 200 ASN K 200 ASN J 211 ASN L 139 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 22623 Z= 0.302 Angle : 0.658 16.895 30723 Z= 0.325 Chirality : 0.045 0.190 3537 Planarity : 0.004 0.057 3900 Dihedral : 5.305 44.078 3018 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.15), residues: 2760 helix: 1.33 (0.25), residues: 423 sheet: 0.06 (0.17), residues: 885 loop : -1.73 (0.15), residues: 1452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 2.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 14 residues processed: 166 average time/residue: 0.4411 time to fit residues: 109.0965 Evaluate side-chains 138 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 2.705 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2391 time to fit residues: 9.6177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 2.9990 chunk 186 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 chunk 249 optimal weight: 0.6980 chunk 263 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 236 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS C 32 HIS C 196 GLN C 283 GLN E 261 ASN H 6 GLN I 114 GLN J 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 22623 Z= 0.356 Angle : 0.666 18.454 30723 Z= 0.328 Chirality : 0.045 0.178 3537 Planarity : 0.004 0.052 3900 Dihedral : 5.158 33.307 3018 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.16), residues: 2760 helix: 1.46 (0.25), residues: 423 sheet: 0.15 (0.17), residues: 912 loop : -1.47 (0.15), residues: 1425 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 137 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 19 residues processed: 174 average time/residue: 0.4471 time to fit residues: 114.8311 Evaluate side-chains 145 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 2.665 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2081 time to fit residues: 10.9606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 236 optimal weight: 0.0020 chunk 66 optimal weight: 2.9990 overall best weight: 1.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 ASN C 12 HIS C 283 GLN H 6 GLN J 6 GLN L 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 22623 Z= 0.329 Angle : 0.645 20.320 30723 Z= 0.315 Chirality : 0.044 0.177 3537 Planarity : 0.004 0.052 3900 Dihedral : 4.969 27.422 3018 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.16), residues: 2760 helix: 1.60 (0.25), residues: 423 sheet: 0.25 (0.17), residues: 912 loop : -1.36 (0.16), residues: 1425 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 2.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 153 average time/residue: 0.4314 time to fit residues: 96.9431 Evaluate side-chains 138 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 2.790 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2049 time to fit residues: 8.2091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 2.9990 chunk 237 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 264 optimal weight: 5.9990 chunk 219 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 138 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN C 296 GLN D 129 ASN L 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 22623 Z= 0.257 Angle : 0.610 21.357 30723 Z= 0.296 Chirality : 0.043 0.174 3537 Planarity : 0.004 0.051 3900 Dihedral : 4.734 22.924 3018 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.16), residues: 2760 helix: 1.77 (0.25), residues: 423 sheet: 0.28 (0.17), residues: 942 loop : -1.30 (0.16), residues: 1395 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 134 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 13 residues processed: 154 average time/residue: 0.4387 time to fit residues: 99.4640 Evaluate side-chains 139 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 2.641 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2093 time to fit residues: 8.4258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 6.9990 chunk 29 optimal weight: 0.0570 chunk 150 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 222 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 chunk 263 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 GLN E 239 GLN E 296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 22623 Z= 0.188 Angle : 0.583 21.553 30723 Z= 0.281 Chirality : 0.042 0.169 3537 Planarity : 0.004 0.051 3900 Dihedral : 4.500 20.988 3018 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.16), residues: 2760 helix: 1.95 (0.26), residues: 423 sheet: 0.45 (0.17), residues: 927 loop : -1.16 (0.16), residues: 1410 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 2.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 153 average time/residue: 0.4646 time to fit residues: 103.1228 Evaluate side-chains 133 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 2.706 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2019 time to fit residues: 6.4521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 167 optimal weight: 0.4980 chunk 179 optimal weight: 7.9990 chunk 130 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 206 optimal weight: 0.0470 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN C 183 HIS C 296 GLN E 296 GLN H 167 GLN I 158 ASN L 159 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 22623 Z= 0.146 Angle : 0.558 20.604 30723 Z= 0.268 Chirality : 0.041 0.167 3537 Planarity : 0.004 0.051 3900 Dihedral : 4.233 18.665 3018 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.16), residues: 2760 helix: 2.24 (0.26), residues: 420 sheet: 0.61 (0.18), residues: 921 loop : -1.09 (0.16), residues: 1419 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 152 average time/residue: 0.4245 time to fit residues: 96.1099 Evaluate side-chains 129 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 2.632 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1914 time to fit residues: 3.7456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 2.9990 chunk 252 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 chunk 245 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 chunk 221 optimal weight: 6.9990 chunk 231 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS A 196 GLN A 231 ASN A 261 ASN C 239 GLN C 296 GLN D 128 ASN ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 GLN F 128 ASN H 167 GLN I 158 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.049 22623 Z= 0.523 Angle : 0.709 22.414 30723 Z= 0.354 Chirality : 0.046 0.192 3537 Planarity : 0.005 0.054 3900 Dihedral : 4.929 25.583 3018 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2760 helix: 1.69 (0.25), residues: 426 sheet: 0.38 (0.17), residues: 939 loop : -1.27 (0.16), residues: 1395 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 131 average time/residue: 0.4858 time to fit residues: 92.8219 Evaluate side-chains 122 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 2.483 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2749 time to fit residues: 5.8544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 8.9990 chunk 259 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 180 optimal weight: 0.0170 chunk 271 optimal weight: 2.9990 chunk 250 optimal weight: 9.9990 chunk 216 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 167 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN C 239 GLN C 296 GLN E 231 ASN H 167 GLN I 158 ASN L 159 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 22623 Z= 0.198 Angle : 0.593 22.824 30723 Z= 0.288 Chirality : 0.042 0.172 3537 Planarity : 0.004 0.047 3900 Dihedral : 4.522 18.944 3018 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.16), residues: 2760 helix: 2.00 (0.26), residues: 423 sheet: 0.52 (0.17), residues: 936 loop : -1.17 (0.16), residues: 1401 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5520 Ramachandran restraints generated. 2760 Oldfield, 0 Emsley, 2760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 2.617 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 133 average time/residue: 0.4408 time to fit residues: 86.9926 Evaluate side-chains 125 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 2.600 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2028 time to fit residues: 5.3456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 0.8980 chunk 230 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 199 optimal weight: 0.0050 chunk 31 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN C 296 GLN E 231 ASN F 129 ASN ** I 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.076357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.048746 restraints weight = 63065.928| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 3.40 r_work: 0.2536 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 22623 Z= 0.171 Angle : 0.570 21.332 30723 Z= 0.276 Chirality : 0.042 0.168 3537 Planarity : 0.004 0.049 3900 Dihedral : 4.252 17.735 3018 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 2760 helix: 2.16 (0.26), residues: 426 sheet: 0.64 (0.18), residues: 921 loop : -1.01 (0.16), residues: 1413 =============================================================================== Job complete usr+sys time: 4137.95 seconds wall clock time: 77 minutes 31.75 seconds (4651.75 seconds total)