Starting phenix.real_space_refine (version: dev) on Sat May 14 23:49:11 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjp_0235/05_2022/6hjp_0235_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjp_0235/05_2022/6hjp_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_0235/05_2022/6hjp_0235.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjp_0235/05_2022/6hjp_0235.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjp_0235/05_2022/6hjp_0235_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hjp_0235/05_2022/6hjp_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 Convert atoms to be neutral 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-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 22134 Number of models: 1 Model: "" Number of chains: 18 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: {'PTRANS': 10, 'TRANS': 204, 'PCIS': 1} Chain: "H" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 8, 'TRANS': 201, 'PCIS': 4} Chain: "I" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1611 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 10, 'TRANS': 204, 'PCIS': 1} Chain: "K" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1611 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 10, 'TRANS': 204, 'PCIS': 1} Chain: "J" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 8, 'TRANS': 201, 'PCIS': 4} Chain: "L" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 8, 'TRANS': 201, 'PCIS': 4} Chain: "A" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 166 Unusual residues: {'MAN': 2, 'BMA': 2, 'NAG': 8, 'FUC': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {'UPL': 1, 'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 166 Unusual residues: {'MAN': 2, 'BMA': 2, 'NAG': 8, 'FUC': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 13 Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {'UPL': 1, 'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 166 Unusual residues: {'MAN': 2, 'BMA': 2, 'NAG': 8, 'FUC': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 13 Chain: "F" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 51 Unusual residues: {'UPL': 1, 'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 13.02, per 1000 atoms: 0.59 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 A 409 " - " MAN A 411 " " BMA C 409 " - " MAN C 411 " " BMA E 409 " - " MAN E 411 " ALPHA1-6 " BMA A 409 " - " MAN A 410 " " BMA C 409 " - " MAN C 410 " " BMA E 409 " - " MAN E 410 " BETA1-4 " NAG A 401 " - " NAG A 402 " " NAG A 403 " - " NAG A 404 " " NAG A 404 " - " BMA A 405 " " NAG A 407 " - " NAG A 408 " " NAG A 408 " - " BMA A 409 " " NAG A 412 " - " NAG A 413 " " NAG B 202 " - " NAG B 203 " " NAG B 203 " - " BMA B 204 " " NAG C 401 " - " NAG C 402 " " NAG C 403 " - " NAG C 404 " " NAG C 404 " - " BMA C 405 " " NAG C 407 " - " NAG C 408 " " NAG C 408 " - " BMA C 409 " " NAG C 412 " - " NAG C 413 " " NAG D 202 " - " NAG D 203 " " NAG D 203 " - " BMA D 204 " " NAG E 401 " - " NAG E 402 " " NAG E 403 " - " NAG E 404 " " NAG E 404 " - " BMA E 405 " " NAG E 407 " - " NAG E 408 " " NAG E 408 " - " BMA E 409 " " NAG E 412 " - " NAG E 413 " " NAG F 202 " - " NAG F 203 " " NAG F 203 " - " BMA F 204 " BETA1-6 " NAG A 403 " - " FUC A 406 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG C 403 " - " FUC C 406 " " NAG E 403 " - " FUC E 406 " NAG-ASN " NAG A 401 " - " ASN A 15 " " NAG A 403 " - " ASN A 27 " " NAG A 407 " - " ASN A 91 " " NAG A 412 " - " ASN A 290 " " NAG B 202 " - " ASN B 154 " " NAG C 401 " - " ASN C 15 " " NAG C 403 " - " ASN C 27 " " NAG C 407 " - " ASN C 91 " " NAG C 412 " - " ASN C 290 " " NAG D 202 " - " ASN D 154 " " NAG E 401 " - " ASN E 15 " " NAG E 403 " - " ASN E 27 " " NAG E 407 " - " ASN E 91 " " NAG E 412 " - " ASN E 290 " " NAG F 202 " - " ASN F 154 " Time building additional restraints: 9.30 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: 2.15 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: 7.30 Time building geometry restraints manager: 9.94 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: 12429 15.99 - 31.98: 820 31.98 - 47.97: 176 47.97 - 63.96: 27 63.96 - 79.95: 18 Dihedral angle restraints: 13470 sinusoidal: 5460 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 13467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 3428 0.168 - 0.336: 91 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 E 411 " pdb=" O3 BMA E 409 " pdb=" C2 MAN E 411 " pdb=" O5 MAN E 411 " 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 C 411 " pdb=" O3 BMA C 409 " pdb=" C2 MAN C 411 " pdb=" O5 MAN C 411 " 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 A 411 " pdb=" O3 BMA A 409 " pdb=" C2 MAN A 411 " pdb=" O5 MAN A 411 " 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 A 403 " 0.339 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" C7 NAG A 403 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG A 403 " 0.144 2.00e-02 2.50e+03 pdb=" N2 NAG A 403 " -0.518 2.00e-02 2.50e+03 pdb=" O7 NAG A 403 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 403 " -0.339 2.00e-02 2.50e+03 2.92e-01 1.06e+03 pdb=" C7 NAG C 403 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG C 403 " -0.145 2.00e-02 2.50e+03 pdb=" N2 NAG C 403 " 0.517 2.00e-02 2.50e+03 pdb=" O7 NAG C 403 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 403 " -0.338 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG E 403 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG E 403 " -0.146 2.00e-02 2.50e+03 pdb=" N2 NAG E 403 " 0.516 2.00e-02 2.50e+03 pdb=" O7 NAG E 403 " -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 E 407 " pdb=" O7 NAG E 407 " model vdw 2.158 2.440 nonbonded pdb=" O3 NAG A 407 " pdb=" O7 NAG A 407 " model vdw 2.159 2.440 nonbonded pdb=" O3 NAG C 407 " pdb=" O7 NAG C 407 " 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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. 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: 7.520 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: 30.990 Check model and map are aligned: 0.340 Convert atoms to be neutral: 0.180 Process input model: 58.670 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 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= 0.507 Angle : 1.154 10.130 30723 Z= 0.713 Chirality : 0.086 0.840 3537 Planarity : 0.018 0.292 3900 Dihedral : 11.499 79.953 8262 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.98 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 : 2.719 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: 0.3959 time to fit residues: 210.0545 Evaluate side-chains 159 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 148 time to evaluate : 2.571 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1886 time to fit residues: 7.1739 ------------------------------------------------------------------------------- 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 C 184 HIS C 250 ASN C 261 ASN C 299 HIS C 323 ASN E 55 GLN E 184 HIS E 239 GLN 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: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 22623 Z= 0.271 Angle : 0.653 13.918 30723 Z= 0.348 Chirality : 0.046 0.264 3537 Planarity : 0.004 0.057 3900 Dihedral : 6.116 56.131 3375 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 2.19 % 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: 0.83 (0.25), residues: 423 sheet: -0.27 (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 217 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 165 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 27 residues processed: 205 average time/residue: 0.4144 time to fit residues: 125.0729 Evaluate side-chains 163 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 136 time to evaluate : 2.678 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2217 time to fit residues: 14.0270 ------------------------------------------------------------------------------- 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: 4.9990 chunk 206 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 268 optimal weight: 9.9990 chunk 221 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 chunk 84 optimal weight: 0.0470 chunk 199 optimal weight: 1.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS C 32 HIS C 184 HIS E 184 HIS ** E 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN H 6 GLN H 156 GLN I 200 ASN K 200 ASN J 167 GLN J 211 ASN L 139 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.079 22623 Z= 0.475 Angle : 0.697 18.889 30723 Z= 0.364 Chirality : 0.048 0.275 3537 Planarity : 0.005 0.057 3900 Dihedral : 5.928 45.838 3375 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.27 % Favored : 93.66 % Rotamer Outliers : 2.02 % 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: -1.09 (0.15), residues: 2760 helix: 1.17 (0.25), residues: 423 sheet: -0.01 (0.17), residues: 900 loop : -1.85 (0.15), residues: 1437 *********************** 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 189 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 141 time to evaluate : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 21 residues processed: 182 average time/residue: 0.4082 time to fit residues: 111.0259 Evaluate side-chains 147 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 2.444 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2181 time to fit residues: 11.3966 ------------------------------------------------------------------------------- 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: 8.9990 chunk 186 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 249 optimal weight: 0.1980 chunk 263 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 236 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS A 231 ASN C 283 GLN E 250 ASN G 114 GLN I 114 GLN J 6 GLN J 167 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 22623 Z= 0.287 Angle : 0.613 19.765 30723 Z= 0.314 Chirality : 0.045 0.287 3537 Planarity : 0.004 0.052 3900 Dihedral : 5.570 36.858 3375 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 1.47 % 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: -0.70 (0.16), residues: 2760 helix: 1.50 (0.25), residues: 423 sheet: 0.12 (0.17), residues: 909 loop : -1.51 (0.15), residues: 1428 *********************** 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 176 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 141 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 15 residues processed: 169 average time/residue: 0.4255 time to fit residues: 104.9849 Evaluate side-chains 145 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 2.549 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1872 time to fit residues: 8.4319 ------------------------------------------------------------------------------- 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: 4.9990 chunk 149 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 196 optimal weight: 0.0570 chunk 108 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 236 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 129 ASN C 283 GLN D 129 ASN J 6 GLN L 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 22623 Z= 0.223 Angle : 0.579 20.828 30723 Z= 0.292 Chirality : 0.044 0.281 3537 Planarity : 0.004 0.054 3900 Dihedral : 5.285 34.191 3375 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 1.05 % 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: -0.46 (0.16), residues: 2760 helix: 1.70 (0.26), residues: 423 sheet: 0.26 (0.17), residues: 912 loop : -1.35 (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 164 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 159 average time/residue: 0.4194 time to fit residues: 98.4508 Evaluate side-chains 143 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 2.578 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2093 time to fit residues: 8.5339 ------------------------------------------------------------------------------- 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: 7.9990 chunk 52 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 264 optimal weight: 9.9990 chunk 219 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 ASN F 129 ASN J 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 22623 Z= 0.271 Angle : 0.583 21.826 30723 Z= 0.294 Chirality : 0.044 0.277 3537 Planarity : 0.004 0.051 3900 Dihedral : 5.198 35.040 3375 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 1.09 % 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: 1.80 (0.25), residues: 423 sheet: 0.27 (0.17), residues: 945 loop : -1.30 (0.16), residues: 1392 *********************** 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 158 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 2.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 11 residues processed: 153 average time/residue: 0.4256 time to fit residues: 95.8818 Evaluate side-chains 138 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 2.536 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1880 time to fit residues: 6.9295 ------------------------------------------------------------------------------- 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: 1.9990 chunk 150 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 222 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 chunk 164 optimal weight: 0.0060 chunk 160 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN J 6 GLN L 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.078 22623 Z= 0.286 Angle : 0.588 22.487 30723 Z= 0.295 Chirality : 0.044 0.277 3537 Planarity : 0.004 0.056 3900 Dihedral : 5.162 35.487 3375 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 0.84 % 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: -0.28 (0.16), residues: 2760 helix: 1.87 (0.25), residues: 423 sheet: 0.34 (0.17), residues: 942 loop : -1.24 (0.16), residues: 1395 *********************** 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 149 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 145 average time/residue: 0.4278 time to fit residues: 92.5488 Evaluate side-chains 132 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 2.788 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1937 time to fit residues: 6.1128 ------------------------------------------------------------------------------- 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: 8.9990 chunk 105 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 51 optimal weight: 0.0370 chunk 50 optimal weight: 0.9980 chunk 167 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 chunk 130 optimal weight: 0.0040 chunk 24 optimal weight: 3.9990 chunk 206 optimal weight: 0.1980 overall best weight: 0.3670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 231 ASN I 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.079 22623 Z= 0.151 Angle : 0.547 21.318 30723 Z= 0.273 Chirality : 0.043 0.274 3537 Planarity : 0.004 0.051 3900 Dihedral : 4.859 35.309 3375 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % 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: -0.01 (0.16), residues: 2760 helix: 2.13 (0.26), residues: 423 sheet: 0.58 (0.18), residues: 921 loop : -1.12 (0.16), residues: 1416 *********************** 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: 12 poor density : 142 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 150 average time/residue: 0.4370 time to fit residues: 96.3754 Evaluate side-chains 131 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 125 time to evaluate : 2.647 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2050 time to fit residues: 5.8271 ------------------------------------------------------------------------------- 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: 4.9990 chunk 252 optimal weight: 0.0000 chunk 229 optimal weight: 7.9990 chunk 245 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 75 optimal weight: 0.0770 chunk 221 optimal weight: 6.9990 chunk 231 optimal weight: 0.8980 chunk 244 optimal weight: 5.9990 overall best weight: 1.9946 ------------------------------------------------------------------------------- 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 C 183 HIS E 231 ASN E 296 GLN I 158 ASN L 159 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 22623 Z= 0.342 Angle : 0.605 21.079 30723 Z= 0.305 Chirality : 0.044 0.263 3537 Planarity : 0.004 0.052 3900 Dihedral : 5.036 35.977 3375 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % 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: -0.09 (0.16), residues: 2760 helix: 2.08 (0.25), residues: 423 sheet: 0.46 (0.17), residues: 942 loop : -1.13 (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 131 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 131 average time/residue: 0.4311 time to fit residues: 84.1171 Evaluate side-chains 123 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 2.635 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1902 time to fit residues: 3.8530 ------------------------------------------------------------------------------- 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: 5.9990 chunk 259 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 180 optimal weight: 0.0980 chunk 271 optimal weight: 5.9990 chunk 250 optimal weight: 8.9990 chunk 216 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 183 HIS E 296 GLN I 158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 22623 Z= 0.256 Angle : 0.578 21.477 30723 Z= 0.292 Chirality : 0.043 0.270 3537 Planarity : 0.004 0.050 3900 Dihedral : 5.016 36.630 3375 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 0.34 % 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: -0.06 (0.16), residues: 2760 helix: 2.10 (0.26), residues: 423 sheet: 0.48 (0.17), residues: 942 loop : -1.11 (0.16), residues: 1395 ********************** 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 135 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 2.594 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 133 average time/residue: 0.4295 time to fit residues: 84.3623 Evaluate side-chains 124 residues out of total 2376 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 2.427 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1834 time to fit residues: 3.5543 ------------------------------------------------------------------------------- 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: 0.9990 chunk 230 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 199 optimal weight: 3.9990 chunk 31 optimal weight: 0.0000 chunk 60 optimal weight: 1.9990 chunk 216 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 222 optimal weight: 0.0370 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.076899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.049418 restraints weight = 63034.376| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.38 r_work: 0.2686 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work: 0.2665 rms_B_bonded: 3.10 restraints_weight: 0.1250 r_work: 0.2655 rms_B_bonded: 3.13 restraints_weight: 0.0625 r_work: 0.2645 rms_B_bonded: 3.17 restraints_weight: 0.0312 r_work: 0.2634 rms_B_bonded: 3.24 restraints_weight: 0.0156 r_work: 0.2623 rms_B_bonded: 3.32 restraints_weight: 0.0078 r_work: 0.2611 rms_B_bonded: 3.42 restraints_weight: 0.0039 r_work: 0.2599 rms_B_bonded: 3.53 restraints_weight: 0.0020 r_work: 0.2587 rms_B_bonded: 3.66 restraints_weight: 0.0010 r_work: 0.2575 rms_B_bonded: 3.81 restraints_weight: 0.0005 r_work: 0.2561 rms_B_bonded: 3.98 restraints_weight: 0.0002 r_work: 0.2548 rms_B_bonded: 4.17 restraints_weight: 0.0001 r_work: 0.2533 rms_B_bonded: 4.38 restraints_weight: 0.0001 r_work: 0.2518 rms_B_bonded: 4.62 restraints_weight: 0.0000 r_work: 0.2503 rms_B_bonded: 4.88 restraints_weight: 0.0000 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 22623 Z= 0.170 Angle : 0.546 20.393 30723 Z= 0.273 Chirality : 0.042 0.265 3537 Planarity : 0.004 0.051 3900 Dihedral : 4.786 36.523 3375 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 0.21 % 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: 0.15 (0.16), residues: 2760 helix: 2.34 (0.26), residues: 420 sheet: 0.69 (0.18), residues: 915 loop : -1.02 (0.16), residues: 1425 =============================================================================== Job complete usr+sys time: 3945.61 seconds wall clock time: 73 minutes 32.84 seconds (4412.84 seconds total)