Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 13 00:31:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kex_22842/08_2023/7kex_22842.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kex_22842/08_2023/7kex_22842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kex_22842/08_2023/7kex_22842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kex_22842/08_2023/7kex_22842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kex_22842/08_2023/7kex_22842.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kex_22842/08_2023/7kex_22842.pdb" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.089 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 48 5.16 5 C 8181 2.51 5 N 2163 2.21 5 O 2517 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 12909 Number of models: 1 Model: "" Number of chains: 21 Chain: "J" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "G" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 923 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain breaks: 1 Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 735 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "K" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 923 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "B" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain breaks: 1 Chain: "E" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 735 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "I" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 923 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "C" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 11, 'TRANS': 208} Chain breaks: 1 Chain: "F" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 735 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "A" 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: "B" 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.34, per 1000 atoms: 0.49 Number of scatterers: 12909 At special positions: 0 Unit cell: (136.85, 146.05, 118.45, 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 48 16.00 O 2517 8.00 N 2163 7.00 C 8181 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.02 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.02 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.02 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.02 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A 401 " - " ASN A 228 " " NAG A 402 " - " ASN A 238 " " NAG B 401 " - " ASN B 228 " " NAG B 402 " - " ASN B 238 " " NAG C 401 " - " ASN C 228 " " NAG C 402 " - " ASN C 238 " " NAG M 1 " - " ASN A 257 " " NAG N 1 " - " ASN D 563 " " NAG O 1 " - " ASN B 257 " " NAG P 1 " - " ASN E 563 " " NAG Q 1 " - " ASN C 257 " " NAG R 1 " - " ASN F 563 " Time building additional restraints: 6.04 Conformation dependent library (CDL) restraints added in 1.9 seconds 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2934 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 33 sheets defined 20.0% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'J' and resid 30 through 32 No H-bonds generated for 'chain 'J' and resid 30 through 32' Processing helix chain 'J' and resid 51 through 53 No H-bonds generated for 'chain 'J' and resid 51 through 53' Processing helix chain 'J' and resid 80 through 84 Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 101 through 104 Processing helix chain 'A' and resid 59 through 63 Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 84 Processing helix chain 'A' and resid 249 through 264 Processing helix chain 'D' and resid 527 through 532 removed outlier: 4.305A pdb=" N ALA D 530 " --> pdb=" O ILE D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 541 Processing helix chain 'D' and resid 553 through 575 removed outlier: 4.316A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 598 removed outlier: 4.074A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 32 No H-bonds generated for 'chain 'K' and resid 30 through 32' Processing helix chain 'K' and resid 51 through 53 No H-bonds generated for 'chain 'K' and resid 51 through 53' Processing helix chain 'K' and resid 80 through 84 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 101 through 104 Processing helix chain 'B' and resid 59 through 63 Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 78 through 84 Processing helix chain 'B' and resid 249 through 264 Processing helix chain 'E' and resid 527 through 532 removed outlier: 4.304A pdb=" N ALA E 530 " --> pdb=" O ILE E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 541 Processing helix chain 'E' and resid 553 through 575 removed outlier: 4.315A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 598 removed outlier: 4.073A pdb=" N ARG E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 51 through 53 No H-bonds generated for 'chain 'L' and resid 51 through 53' Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 74 through 76 No H-bonds generated for 'chain 'I' and resid 74 through 76' Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 101 through 104 Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 84 Processing helix chain 'C' and resid 249 through 264 Processing helix chain 'F' and resid 527 through 532 removed outlier: 4.305A pdb=" N ALA F 530 " --> pdb=" O ILE F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 541 Processing helix chain 'F' and resid 553 through 575 removed outlier: 4.316A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 598 removed outlier: 4.074A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N PHE J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TYR J 50 " --> pdb=" O PHE J 34 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AA6, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.658A pdb=" N TYR G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARG G 50 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA G 40 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR G 60 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A 274 " --> pdb=" O TYR G 60 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR A 241 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL A 277 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N GLN A 243 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 35 through 38 removed outlier: 3.927A pdb=" N LEU A 35 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 159 through 161 removed outlier: 5.656A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AB1, first strand: chain 'A' and resid 96 through 97 removed outlier: 6.865A pdb=" N VAL A 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 105 through 109 removed outlier: 6.644A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AB4, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N PHE K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TYR K 50 " --> pdb=" O PHE K 34 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.658A pdb=" N TYR H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG H 50 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR H 60 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE B 274 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TYR B 241 " --> pdb=" O TRP B 275 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL B 277 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLN B 243 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 35 through 38 removed outlier: 3.927A pdb=" N LEU B 35 " --> pdb=" O SER B 46 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 159 through 161 removed outlier: 5.657A pdb=" N ASN B 69 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AC3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.866A pdb=" N VAL B 96 " --> pdb=" O THR E 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 105 through 109 removed outlier: 6.644A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N PHE L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TYR L 50 " --> pdb=" O PHE L 34 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.175A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 12 Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.659A pdb=" N TYR I 34 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ARG I 50 " --> pdb=" O TYR I 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TYR I 60 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE C 274 " --> pdb=" O TYR I 60 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR C 241 " --> pdb=" O TRP C 275 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL C 277 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N GLN C 243 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 35 through 38 removed outlier: 3.926A pdb=" N LEU C 35 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 159 through 161 removed outlier: 5.657A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AD5, first strand: chain 'C' and resid 96 through 97 removed outlier: 6.866A pdb=" N VAL C 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 105 through 109 removed outlier: 6.645A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1179 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: 4.59 Time building geometry restraints manager: 6.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2316 1.31 - 1.45: 4144 1.45 - 1.58: 6590 1.58 - 1.72: 90 1.72 - 1.85: 60 Bond restraints: 13200 Sorted by residual: bond pdb=" CB PHE H 108 " pdb=" CG PHE H 108 " ideal model delta sigma weight residual 1.502 1.356 0.146 2.30e-02 1.89e+03 4.04e+01 bond pdb=" CB ILE B 185 " pdb=" CG1 ILE B 185 " ideal model delta sigma weight residual 1.530 1.657 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" CB PHE G 108 " pdb=" CG PHE G 108 " ideal model delta sigma weight residual 1.502 1.356 0.146 2.30e-02 1.89e+03 4.02e+01 bond pdb=" CB PHE I 108 " pdb=" CG PHE I 108 " ideal model delta sigma weight residual 1.502 1.357 0.145 2.30e-02 1.89e+03 3.99e+01 bond pdb=" CB ILE C 185 " pdb=" CG1 ILE C 185 " ideal model delta sigma weight residual 1.530 1.656 -0.126 2.00e-02 2.50e+03 3.97e+01 ... (remaining 13195 not shown) Histogram of bond angle deviations from ideal: 97.37 - 104.74: 322 104.74 - 112.12: 5851 112.12 - 119.49: 5260 119.49 - 126.86: 6345 126.86 - 134.23: 156 Bond angle restraints: 17934 Sorted by residual: angle pdb=" C PRO B 93 " pdb=" N PRO B 94 " pdb=" CA PRO B 94 " ideal model delta sigma weight residual 120.31 127.77 -7.46 9.80e-01 1.04e+00 5.80e+01 angle pdb=" C PRO A 93 " pdb=" N PRO A 94 " pdb=" CA PRO A 94 " ideal model delta sigma weight residual 120.31 127.74 -7.43 9.80e-01 1.04e+00 5.75e+01 angle pdb=" C PRO C 93 " pdb=" N PRO C 94 " pdb=" CA PRO C 94 " ideal model delta sigma weight residual 120.31 127.70 -7.39 9.80e-01 1.04e+00 5.69e+01 angle pdb=" C GLY D 536 " pdb=" N PRO D 537 " pdb=" CA PRO D 537 " ideal model delta sigma weight residual 120.03 127.28 -7.25 9.90e-01 1.02e+00 5.37e+01 angle pdb=" C GLY E 536 " pdb=" N PRO E 537 " pdb=" CA PRO E 537 " ideal model delta sigma weight residual 120.03 127.28 -7.25 9.90e-01 1.02e+00 5.36e+01 ... (remaining 17929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7276 17.97 - 35.95: 179 35.95 - 53.92: 39 53.92 - 71.89: 33 71.89 - 89.86: 24 Dihedral angle restraints: 7551 sinusoidal: 2940 harmonic: 4611 Sorted by residual: dihedral pdb=" C TYR B 220 " pdb=" N TYR B 220 " pdb=" CA TYR B 220 " pdb=" CB TYR B 220 " ideal model delta harmonic sigma weight residual -122.60 -113.96 -8.64 0 2.50e+00 1.60e-01 1.19e+01 dihedral pdb=" C TYR C 220 " pdb=" N TYR C 220 " pdb=" CA TYR C 220 " pdb=" CB TYR C 220 " ideal model delta harmonic sigma weight residual -122.60 -113.97 -8.63 0 2.50e+00 1.60e-01 1.19e+01 dihedral pdb=" C TYR A 220 " pdb=" N TYR A 220 " pdb=" CA TYR A 220 " pdb=" CB TYR A 220 " ideal model delta harmonic sigma weight residual -122.60 -114.00 -8.60 0 2.50e+00 1.60e-01 1.18e+01 ... (remaining 7548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1347 0.095 - 0.189: 500 0.189 - 0.284: 144 0.284 - 0.379: 43 0.379 - 0.474: 36 Chirality restraints: 2070 Sorted by residual: chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.06e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.06e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.04e+02 ... (remaining 2067 not shown) Planarity restraints: 2274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 228 " 0.055 2.00e-02 2.50e+03 5.68e-02 4.03e+01 pdb=" CG ASN C 228 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN C 228 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN C 228 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG C 401 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 228 " -0.055 2.00e-02 2.50e+03 5.65e-02 4.00e+01 pdb=" CG ASN B 228 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 228 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 228 " 0.087 2.00e-02 2.50e+03 pdb=" C1 NAG B 401 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 228 " 0.054 2.00e-02 2.50e+03 5.64e-02 3.97e+01 pdb=" CG ASN A 228 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN A 228 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 228 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG A 401 " 0.068 2.00e-02 2.50e+03 ... (remaining 2271 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 6622 2.96 - 3.45: 12331 3.45 - 3.93: 22911 3.93 - 4.42: 26180 4.42 - 4.90: 40769 Nonbonded interactions: 108813 Sorted by model distance: nonbonded pdb=" N ASP K 61 " pdb=" OD1 ASP K 61 " model vdw 2.479 2.520 nonbonded pdb=" N ASP L 61 " pdb=" OD1 ASP L 61 " model vdw 2.479 2.520 nonbonded pdb=" N ASP J 61 " pdb=" OD1 ASP J 61 " model vdw 2.480 2.520 nonbonded pdb=" N ASN C 110 " pdb=" O ASN C 110 " model vdw 2.497 2.496 nonbonded pdb=" N ASN B 110 " pdb=" O ASN B 110 " model vdw 2.497 2.496 ... (remaining 108808 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 0.010 Extract box with map and model: 7.920 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 37.410 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 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 : 0.022 0.146 13200 Z= 1.405 Angle : 1.876 10.947 17934 Z= 1.227 Chirality : 0.123 0.474 2070 Planarity : 0.009 0.037 2262 Dihedral : 11.251 89.862 4581 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.57 % Allowed : 3.02 % Favored : 96.42 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.58 (0.20), residues: 1590 helix: 0.25 (0.32), residues: 186 sheet: 0.24 (0.23), residues: 504 loop : 0.68 (0.20), residues: 900 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 336 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 336 average time/residue: 0.2819 time to fit residues: 131.1115 Evaluate side-chains 163 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.596 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.8980 chunk 120 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 GLN ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 13200 Z= 0.347 Angle : 0.814 9.478 17934 Z= 0.429 Chirality : 0.049 0.254 2070 Planarity : 0.005 0.030 2262 Dihedral : 6.131 25.423 1761 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.40 % Favored : 96.48 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.03 (0.22), residues: 1590 helix: -0.31 (0.34), residues: 204 sheet: -0.31 (0.21), residues: 633 loop : 0.59 (0.24), residues: 753 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.2601 time to fit residues: 83.6923 Evaluate side-chains 134 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.617 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 120 optimal weight: 0.0050 chunk 98 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 143 optimal weight: 0.0470 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 40.0000 overall best weight: 1.2096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 1 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 GLN ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 1 GLN K 6 GLN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 508 GLN ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 1 GLN L 6 GLN ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 13200 Z= 0.230 Angle : 0.691 9.254 17934 Z= 0.365 Chirality : 0.046 0.201 2070 Planarity : 0.005 0.049 2262 Dihedral : 5.680 22.110 1761 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.47 % Favored : 95.35 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.29 (0.22), residues: 1590 helix: -0.08 (0.35), residues: 210 sheet: -0.34 (0.21), residues: 618 loop : 0.11 (0.24), residues: 762 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 199 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 201 average time/residue: 0.2311 time to fit residues: 69.1290 Evaluate side-chains 133 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.621 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 0.6980 chunk 108 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 145 optimal weight: 8.9990 chunk 153 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 GLN G 43 GLN ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 13200 Z= 0.295 Angle : 0.675 7.224 17934 Z= 0.354 Chirality : 0.044 0.181 2070 Planarity : 0.005 0.050 2262 Dihedral : 5.679 21.838 1761 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.35 % Favored : 94.47 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.51 (0.22), residues: 1590 helix: -0.06 (0.34), residues: 210 sheet: -0.49 (0.21), residues: 627 loop : -0.08 (0.24), residues: 753 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 173 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 174 average time/residue: 0.2510 time to fit residues: 64.4335 Evaluate side-chains 119 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 1.630 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1619 time to fit residues: 2.3753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 63 optimal weight: 40.0000 chunk 131 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 78 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 GLN ** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 GLN ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN ** C 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.087 13200 Z= 0.509 Angle : 0.875 9.689 17934 Z= 0.457 Chirality : 0.048 0.180 2070 Planarity : 0.006 0.046 2262 Dihedral : 6.482 27.048 1761 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 26.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.17 % Favored : 92.64 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.97 (0.21), residues: 1590 helix: -0.61 (0.33), residues: 210 sheet: -0.66 (0.21), residues: 606 loop : -0.47 (0.23), residues: 774 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 151 average time/residue: 0.2441 time to fit residues: 54.4283 Evaluate side-chains 102 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.425 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1538 time to fit residues: 2.0295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.9990 chunk 30 optimal weight: 0.0770 chunk 90 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 148 optimal weight: 7.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 GLN A 251 GLN ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 570 GLN L 91 GLN I 43 GLN C 251 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.5944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 13200 Z= 0.195 Angle : 0.670 8.292 17934 Z= 0.341 Chirality : 0.046 0.191 2070 Planarity : 0.005 0.038 2262 Dihedral : 5.670 25.756 1761 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.97 % Favored : 94.84 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.72 (0.22), residues: 1590 helix: -0.20 (0.35), residues: 213 sheet: -0.69 (0.22), residues: 585 loop : -0.20 (0.23), residues: 792 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 158 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 161 average time/residue: 0.2491 time to fit residues: 59.7554 Evaluate side-chains 111 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.463 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 112 optimal weight: 20.0000 chunk 129 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 GLN G 43 GLN ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 ASN K 91 GLN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.6424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 13200 Z= 0.331 Angle : 0.696 8.462 17934 Z= 0.358 Chirality : 0.044 0.165 2070 Planarity : 0.005 0.040 2262 Dihedral : 5.797 23.040 1761 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.60 % Favored : 93.33 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.77 (0.22), residues: 1590 helix: -0.14 (0.35), residues: 213 sheet: -0.74 (0.22), residues: 585 loop : -0.26 (0.24), residues: 792 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 140 average time/residue: 0.2344 time to fit residues: 50.4384 Evaluate side-chains 107 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 1.554 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1553 time to fit residues: 2.4821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 5.9990 chunk 46 optimal weight: 0.0030 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 14 optimal weight: 0.0040 chunk 120 optimal weight: 5.9990 chunk 139 optimal weight: 0.5980 chunk 146 optimal weight: 5.9990 overall best weight: 1.9206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 6 GLN ** J 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 GLN G 43 GLN ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 GLN B 251 GLN L 91 GLN I 43 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.6554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 13200 Z= 0.216 Angle : 0.635 7.839 17934 Z= 0.324 Chirality : 0.043 0.173 2070 Planarity : 0.004 0.037 2262 Dihedral : 5.515 22.868 1761 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 (0.22), residues: 1590 helix: 0.06 (0.36), residues: 213 sheet: -0.64 (0.22), residues: 585 loop : -0.27 (0.24), residues: 792 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 146 average time/residue: 0.2266 time to fit residues: 50.6547 Evaluate side-chains 106 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 1.623 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1761 time to fit residues: 2.6544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 7.9990 chunk 142 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 GLN L 91 GLN I 43 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.6979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 13200 Z= 0.331 Angle : 0.703 8.219 17934 Z= 0.361 Chirality : 0.044 0.207 2070 Planarity : 0.005 0.038 2262 Dihedral : 5.741 23.354 1761 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.86 (0.22), residues: 1590 helix: -0.02 (0.35), residues: 210 sheet: -0.70 (0.21), residues: 621 loop : -0.45 (0.24), residues: 759 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 138 average time/residue: 0.2281 time to fit residues: 48.4978 Evaluate side-chains 95 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 94 time to evaluate : 1.560 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1611 time to fit residues: 2.2433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 97 optimal weight: 0.0170 chunk 77 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 43 GLN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 ASN K 91 GLN L 91 GLN I 43 GLN ** F 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.7078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 13200 Z= 0.220 Angle : 0.658 10.384 17934 Z= 0.336 Chirality : 0.044 0.203 2070 Planarity : 0.004 0.042 2262 Dihedral : 5.550 23.338 1761 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -0.68 (0.22), residues: 1590 helix: 0.05 (0.36), residues: 210 sheet: -0.39 (0.23), residues: 546 loop : -0.51 (0.23), residues: 834 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 141 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 143 average time/residue: 0.2124 time to fit residues: 47.6162 Evaluate side-chains 103 residues out of total 1350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 1.583 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1581 time to fit residues: 2.2623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 9.9990 chunk 116 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 91 GLN ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 GLN L 91 GLN I 43 GLN ** F 570 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 = 0.3628 r_free = 0.3628 target = 0.054146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.045074 restraints weight = 130657.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.046423 restraints weight = 81200.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.047364 restraints weight = 57860.610| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.7465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 13200 Z= 0.417 Angle : 0.783 11.982 17934 Z= 0.401 Chirality : 0.045 0.199 2070 Planarity : 0.005 0.045 2262 Dihedral : 5.979 27.515 1761 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 22.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: -1.01 (0.21), residues: 1590 helix: -0.43 (0.34), residues: 210 sheet: -0.51 (0.22), residues: 570 loop : -0.75 (0.22), residues: 810 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2380.54 seconds wall clock time: 44 minutes 57.13 seconds (2697.13 seconds total)