Starting phenix.real_space_refine on Mon Dec 11 07:47:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uds_26458/12_2023/7uds_26458.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uds_26458/12_2023/7uds_26458.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uds_26458/12_2023/7uds_26458.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uds_26458/12_2023/7uds_26458.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uds_26458/12_2023/7uds_26458.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uds_26458/12_2023/7uds_26458.pdb" } resolution = 3.1 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= 0.001 sd= 0.017 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 105 5.16 5 C 10672 2.51 5 N 2837 2.21 5 O 3418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 54": "OE1" <-> "OE2" Residue "L TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 307": "OE1" <-> "OE2" Residue "b TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 17032 Number of models: 1 Model: "" Number of chains: 32 Chain: "D" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1616 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Chain: "F" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1616 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Chain: "L" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1603 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 198} Chain: "H" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1616 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Chain: "G" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1603 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 198} Chain: "E" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1603 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 198} Chain: "A" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1093 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 3, 'TRANS': 133} Chain breaks: 3 Chain: "C" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1093 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 3, 'TRANS': 133} Chain breaks: 3 Chain: "B" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1093 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 3, 'TRANS': 133} Chain breaks: 3 Chain: "a" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1133 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain: "c" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1133 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain: "b" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1133 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 5 Chain: "J" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.28, per 1000 atoms: 0.54 Number of scatterers: 17032 At special positions: 0 Unit cell: (209.336, 198.376, 89.872, 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 105 16.00 O 3418 8.00 N 2837 7.00 C 10672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 204 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS L 131 " - pdb=" SG CYS L 191 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 87 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 191 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 191 " distance=2.04 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS C 85 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 154 " distance=2.03 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 154 " distance=2.03 Simple disulfide: pdb=" SG CYS a 278 " - pdb=" SG CYS a 291 " distance=2.04 Simple disulfide: pdb=" SG CYS a 300 " - pdb=" SG CYS a 309 " distance=2.03 Simple disulfide: pdb=" SG CYS a 363 " - pdb=" SG CYS a 384 " distance=2.03 Simple disulfide: pdb=" SG CYS c 278 " - pdb=" SG CYS c 291 " distance=2.05 Simple disulfide: pdb=" SG CYS c 300 " - pdb=" SG CYS c 309 " distance=2.03 Simple disulfide: pdb=" SG CYS c 363 " - pdb=" SG CYS c 384 " distance=2.03 Simple disulfide: pdb=" SG CYS b 278 " - pdb=" SG CYS b 291 " distance=2.04 Simple disulfide: pdb=" SG CYS b 300 " - pdb=" SG CYS b 309 " distance=2.03 Simple disulfide: pdb=" SG CYS b 363 " - pdb=" SG CYS b 384 " distance=2.03 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 I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA O 3 " - " MAN O 5 " " BMA T 3 " - " MAN T 5 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A 301 " - " ASN A 166 " " NAG A 302 " - " ASN A 118 " " NAG B 301 " - " ASN B 108 " " NAG B 302 " - " ASN B 166 " " NAG B 303 " - " ASN B 118 " " NAG C 301 " - " ASN C 166 " " NAG C 302 " - " ASN C 118 " " NAG I 1 " - " ASN A 78 " " NAG J 1 " - " ASN A 88 " " NAG K 1 " - " ASN A 98 " " NAG M 1 " - " ASN A 108 " " NAG N 1 " - " ASN A 223 " " NAG O 1 " - " ASN C 78 " " NAG P 1 " - " ASN C 88 " " NAG Q 1 " - " ASN C 98 " " NAG R 1 " - " ASN C 108 " " NAG S 1 " - " ASN C 223 " " NAG T 1 " - " ASN B 78 " " NAG U 1 " - " ASN B 88 " " NAG V 1 " - " ASN B 98 " " NAG W 1 " - " ASN B 223 " " NAG a 501 " - " ASN a 372 " " NAG b 501 " - " ASN b 372 " " NAG c 501 " - " ASN c 372 " Time building additional restraints: 6.82 Conformation dependent library (CDL) restraints added in 2.7 seconds 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3942 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 40 sheets defined 23.2% alpha, 33.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.565A pdb=" N LYS D 31 " --> pdb=" O ASN D 28 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 62 through 65 removed outlier: 4.145A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 194 through 200 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.516A pdb=" N LYS F 31 " --> pdb=" O ASN F 28 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.531A pdb=" N LYS F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 194 through 200 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.997A pdb=" N PHE L 82 " --> pdb=" O PRO L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 125 Processing helix chain 'L' and resid 179 through 185 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.510A pdb=" N LYS H 31 " --> pdb=" O ASN H 28 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 194 through 200 Processing helix chain 'G' and resid 78 through 82 removed outlier: 3.953A pdb=" N PHE G 82 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 125 Processing helix chain 'G' and resid 179 through 185 Processing helix chain 'E' and resid 78 through 82 removed outlier: 3.955A pdb=" N PHE E 82 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 125 Processing helix chain 'E' and resid 179 through 185 Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.766A pdb=" N THR A 76 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 removed outlier: 4.019A pdb=" N ASN A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 142 removed outlier: 3.553A pdb=" N MET A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 4.078A pdb=" N LYS A 160 " --> pdb=" O ASN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 237 through 244 Processing helix chain 'C' and resid 73 through 78 removed outlier: 4.026A pdb=" N THR C 76 " --> pdb=" O ASN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 removed outlier: 4.057A pdb=" N ASN C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 142 removed outlier: 3.559A pdb=" N MET C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 removed outlier: 4.044A pdb=" N LYS C 160 " --> pdb=" O ASN C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 237 through 244 Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.850A pdb=" N THR B 76 " --> pdb=" O ASN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 removed outlier: 4.028A pdb=" N ASN B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 142 removed outlier: 3.683A pdb=" N MET B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 removed outlier: 4.078A pdb=" N LYS B 160 " --> pdb=" O ASN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 194 Processing helix chain 'B' and resid 237 through 244 Processing helix chain 'a' and resid 293 through 298 Processing helix chain 'a' and resid 299 through 302 Processing helix chain 'a' and resid 308 through 324 Processing helix chain 'a' and resid 332 through 344 removed outlier: 3.529A pdb=" N ILE a 336 " --> pdb=" O SER a 332 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN a 341 " --> pdb=" O ASN a 337 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA a 342 " --> pdb=" O LYS a 338 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE a 344 " --> pdb=" O VAL a 340 " (cutoff:3.500A) Processing helix chain 'a' and resid 345 through 358 Processing helix chain 'a' and resid 395 through 397 No H-bonds generated for 'chain 'a' and resid 395 through 397' Processing helix chain 'a' and resid 398 through 414 removed outlier: 3.620A pdb=" N ILE a 402 " --> pdb=" O PHE a 398 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU a 414 " --> pdb=" O ILE a 410 " (cutoff:3.500A) Processing helix chain 'c' and resid 293 through 298 Processing helix chain 'c' and resid 299 through 302 removed outlier: 3.588A pdb=" N GLU c 302 " --> pdb=" O LYS c 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 299 through 302' Processing helix chain 'c' and resid 308 through 325 Processing helix chain 'c' and resid 333 through 344 removed outlier: 4.047A pdb=" N ASN c 341 " --> pdb=" O ASN c 337 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA c 342 " --> pdb=" O LYS c 338 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE c 344 " --> pdb=" O VAL c 340 " (cutoff:3.500A) Processing helix chain 'c' and resid 345 through 357 Processing helix chain 'c' and resid 394 through 397 Processing helix chain 'c' and resid 398 through 414 removed outlier: 3.520A pdb=" N ILE c 402 " --> pdb=" O PHE c 398 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU c 414 " --> pdb=" O ILE c 410 " (cutoff:3.500A) Processing helix chain 'b' and resid 293 through 298 Processing helix chain 'b' and resid 299 through 302 removed outlier: 3.650A pdb=" N GLU b 302 " --> pdb=" O LYS b 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 299 through 302' Processing helix chain 'b' and resid 308 through 324 Processing helix chain 'b' and resid 332 through 344 removed outlier: 3.573A pdb=" N ILE b 336 " --> pdb=" O SER b 332 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN b 341 " --> pdb=" O ASN b 337 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA b 342 " --> pdb=" O LYS b 338 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE b 344 " --> pdb=" O VAL b 340 " (cutoff:3.500A) Processing helix chain 'b' and resid 345 through 358 Processing helix chain 'b' and resid 398 through 414 removed outlier: 3.595A pdb=" N ILE b 402 " --> pdb=" O PHE b 398 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU b 414 " --> pdb=" O ILE b 410 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.786A pdb=" N ASN D 33 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N MET D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SER D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.952A pdb=" N ARG D 98 " --> pdb=" O ASP D 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 128 through 132 Processing sheet with id=AA5, first strand: chain 'D' and resid 128 through 132 Processing sheet with id=AA6, first strand: chain 'D' and resid 159 through 162 Processing sheet with id=AA7, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.871A pdb=" N MET F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AB1, first strand: chain 'F' and resid 128 through 132 removed outlier: 5.878A pdb=" N TYR F 184 " --> pdb=" O ASP F 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 159 through 162 Processing sheet with id=AB3, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AB4, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.644A pdb=" N ASP L 102 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU L 32 " --> pdb=" O TYR L 48 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TYR L 48 " --> pdb=" O LEU L 32 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP L 34 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 111 through 115 Processing sheet with id=AB6, first strand: chain 'L' and resid 141 through 147 Processing sheet with id=AB7, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.896A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.970A pdb=" N LEU H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE H 100 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ALA H 108 " --> pdb=" O ILE H 100 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.846A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.846A pdb=" N TYR H 184 " --> pdb=" O ASP H 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 159 through 162 Processing sheet with id=AC4, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'G' and resid 9 through 11 removed outlier: 3.753A pdb=" N ASP G 102 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU G 32 " --> pdb=" O TYR G 48 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TYR G 48 " --> pdb=" O LEU G 32 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TRP G 34 " --> pdb=" O LEU G 46 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 111 through 115 Processing sheet with id=AC7, first strand: chain 'G' and resid 141 through 147 Processing sheet with id=AC8, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC9, first strand: chain 'E' and resid 9 through 11 removed outlier: 3.548A pdb=" N ASP E 102 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TRP E 34 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 111 through 115 Processing sheet with id=AD2, first strand: chain 'E' and resid 141 through 147 Processing sheet with id=AD3, first strand: chain 'A' and resid 67 through 71 Processing sheet with id=AD4, first strand: chain 'A' and resid 83 through 88 removed outlier: 3.548A pdb=" N LYS A 87 " --> pdb=" O HIS A 91 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N HIS A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 67 through 71 Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 88 removed outlier: 3.686A pdb=" N LYS C 87 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N HIS C 91 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 100 " --> pdb=" O VAL C 96 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 67 through 71 Processing sheet with id=AD8, first strand: chain 'B' and resid 83 through 88 removed outlier: 3.613A pdb=" N TYR B 93 " --> pdb=" O CYS B 85 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 87 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 100 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'a' and resid 387 through 388 Processing sheet with id=AE1, first strand: chain 'c' and resid 278 through 279 removed outlier: 3.704A pdb=" N LEU c 279 " --> pdb=" O LYS c 290 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS c 290 " --> pdb=" O LEU c 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'c' and resid 387 through 388 Processing sheet with id=AE3, first strand: chain 'b' and resid 278 through 279 removed outlier: 3.748A pdb=" N LEU b 279 " --> pdb=" O LYS b 290 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS b 290 " --> pdb=" O LEU b 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'b' and resid 387 through 388 741 hydrogen bonds defined for protein. 1941 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.15 Time building geometry restraints manager: 7.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5361 1.35 - 1.47: 4536 1.47 - 1.60: 7317 1.60 - 1.73: 1 1.73 - 1.85: 153 Bond restraints: 17368 Sorted by residual: bond pdb=" C1 MAN V 4 " pdb=" C2 MAN V 4 " ideal model delta sigma weight residual 1.526 1.620 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C1 NAG A 301 " pdb=" O5 NAG A 301 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C1 NAG B 302 " pdb=" O5 NAG B 302 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1 NAG C 301 " pdb=" O5 NAG C 301 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1 MAN V 4 " pdb=" O5 MAN V 4 " ideal model delta sigma weight residual 1.399 1.474 -0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 17363 not shown) Histogram of bond angle deviations from ideal: 98.54 - 105.64: 326 105.64 - 112.75: 9681 112.75 - 119.85: 5299 119.85 - 126.95: 8026 126.95 - 134.05: 202 Bond angle restraints: 23534 Sorted by residual: angle pdb=" C SER G 29 " pdb=" CA SER G 29 " pdb=" CB SER G 29 " ideal model delta sigma weight residual 117.23 110.83 6.40 1.36e+00 5.41e-01 2.21e+01 angle pdb=" CA CYS c 291 " pdb=" CB CYS c 291 " pdb=" SG CYS c 291 " ideal model delta sigma weight residual 114.40 122.17 -7.77 2.30e+00 1.89e-01 1.14e+01 angle pdb=" CA SER G 29 " pdb=" C SER G 29 " pdb=" N SER G 30 " ideal model delta sigma weight residual 119.98 117.11 2.87 8.50e-01 1.38e+00 1.14e+01 angle pdb=" N TRP a 385 " pdb=" CA TRP a 385 " pdb=" C TRP a 385 " ideal model delta sigma weight residual 110.55 106.31 4.24 1.35e+00 5.49e-01 9.85e+00 angle pdb=" CA CYS a 291 " pdb=" CB CYS a 291 " pdb=" SG CYS a 291 " ideal model delta sigma weight residual 114.40 121.28 -6.88 2.30e+00 1.89e-01 8.94e+00 ... (remaining 23529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.15: 10135 23.15 - 46.30: 639 46.30 - 69.45: 74 69.45 - 92.61: 9 92.61 - 115.76: 9 Dihedral angle restraints: 10866 sinusoidal: 4767 harmonic: 6099 Sorted by residual: dihedral pdb=" CB CYS c 363 " pdb=" SG CYS c 363 " pdb=" SG CYS c 384 " pdb=" CB CYS c 384 " ideal model delta sinusoidal sigma weight residual -86.00 -170.32 84.32 1 1.00e+01 1.00e-02 8.65e+01 dihedral pdb=" CB CYS b 363 " pdb=" SG CYS b 363 " pdb=" SG CYS b 384 " pdb=" CB CYS b 384 " ideal model delta sinusoidal sigma weight residual -86.00 -168.32 82.32 1 1.00e+01 1.00e-02 8.32e+01 dihedral pdb=" CB CYS a 363 " pdb=" SG CYS a 363 " pdb=" SG CYS a 384 " pdb=" CB CYS a 384 " ideal model delta sinusoidal sigma weight residual -86.00 -168.12 82.12 1 1.00e+01 1.00e-02 8.28e+01 ... (remaining 10863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2273 0.057 - 0.113: 453 0.113 - 0.170: 66 0.170 - 0.227: 10 0.227 - 0.283: 10 Chirality restraints: 2812 Sorted by residual: chirality pdb=" C5 BMA T 3 " pdb=" C4 BMA T 3 " pdb=" C6 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A 78 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN B 78 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 2809 not shown) Planarity restraints: 2936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 385 " -0.030 2.00e-02 2.50e+03 2.74e-02 1.88e+01 pdb=" CG TRP a 385 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP a 385 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP a 385 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP a 385 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP a 385 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP a 385 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 385 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 385 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP a 385 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL H 192 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO H 193 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO H 193 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 193 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 192 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO D 193 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 193 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 193 " -0.027 5.00e-02 4.00e+02 ... (remaining 2933 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 172 2.59 - 3.17: 13658 3.17 - 3.75: 24480 3.75 - 4.32: 34315 4.32 - 4.90: 56703 Nonbonded interactions: 129328 Sorted by model distance: nonbonded pdb=" OE1 GLU L 192 " pdb=" OG1 THR L 203 " model vdw 2.015 2.440 nonbonded pdb=" OE1 GLU G 192 " pdb=" OG1 THR G 203 " model vdw 2.097 2.440 nonbonded pdb=" O TRP F 106 " pdb=" OG SER G 90 " model vdw 2.127 2.440 nonbonded pdb=" OE1 GLU E 192 " pdb=" OG1 THR E 203 " model vdw 2.164 2.440 nonbonded pdb=" OG SER B 90 " pdb=" O7 NAG U 1 " model vdw 2.213 2.440 ... (remaining 129323 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' and (resid 66 through 244 or resid 301 through 302)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'O' selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'K' selection = chain 'Q' selection = chain 'V' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 11.180 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 46.870 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 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 : 0.005 0.094 17368 Z= 0.317 Angle : 0.743 11.743 23534 Z= 0.355 Chirality : 0.049 0.283 2812 Planarity : 0.004 0.050 2912 Dihedral : 14.301 115.758 6843 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.23 (0.19), residues: 2046 helix: 0.69 (0.29), residues: 345 sheet: 0.67 (0.19), residues: 783 loop : -1.22 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP a 385 HIS 0.006 0.001 HIS a 353 PHE 0.017 0.002 PHE G 70 TYR 0.019 0.002 TYR E 48 ARG 0.009 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.920 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: 0 outliers final: 0 residues processed: 269 average time/residue: 0.2674 time to fit residues: 111.7608 Evaluate side-chains 254 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 1.771 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 182 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 352 ASN ** a 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 405 GLN b 353 HIS b 364 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 17368 Z= 0.353 Angle : 0.728 12.139 23534 Z= 0.357 Chirality : 0.047 0.284 2812 Planarity : 0.005 0.052 2912 Dihedral : 9.047 87.061 3036 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.08 % Allowed : 9.32 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.36 (0.19), residues: 2046 helix: 0.50 (0.28), residues: 357 sheet: 0.66 (0.19), residues: 774 loop : -1.34 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP a 385 HIS 0.004 0.001 HIS c 353 PHE 0.019 0.002 PHE D 80 TYR 0.028 0.002 TYR F 94 ARG 0.006 0.001 ARG G 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 261 time to evaluate : 1.887 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: 20 outliers final: 18 residues processed: 267 average time/residue: 0.2781 time to fit residues: 114.6160 Evaluate side-chains 270 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 252 time to evaluate : 1.730 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1692 time to fit residues: 8.1128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 151 optimal weight: 0.3980 chunk 124 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 182 optimal weight: 0.5980 chunk 197 optimal weight: 0.0970 chunk 162 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 353 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17368 Z= 0.242 Angle : 0.643 11.774 23534 Z= 0.317 Chirality : 0.044 0.259 2812 Planarity : 0.005 0.052 2912 Dihedral : 7.361 58.753 3036 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.98 % Allowed : 13.33 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.33 (0.19), residues: 2046 helix: 0.59 (0.28), residues: 357 sheet: 0.61 (0.19), residues: 783 loop : -1.30 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP a 385 HIS 0.005 0.001 HIS A 92 PHE 0.023 0.002 PHE G 70 TYR 0.018 0.002 TYR G 48 ARG 0.004 0.000 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 262 time to evaluate : 2.058 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: 18 outliers final: 11 residues processed: 268 average time/residue: 0.2749 time to fit residues: 113.4983 Evaluate side-chains 269 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 258 time to evaluate : 1.893 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.1570 time to fit residues: 5.8926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 180 optimal weight: 3.9990 chunk 137 optimal weight: 0.2980 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 122 optimal weight: 0.0670 chunk 183 optimal weight: 0.0060 chunk 194 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 173 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.2934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 318 ASN a 405 GLN b 353 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17368 Z= 0.168 Angle : 0.579 11.245 23534 Z= 0.288 Chirality : 0.042 0.256 2812 Planarity : 0.004 0.052 2912 Dihedral : 6.705 57.316 3036 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.30 % Allowed : 15.61 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.23 (0.19), residues: 2046 helix: 0.77 (0.28), residues: 357 sheet: 0.55 (0.19), residues: 807 loop : -1.20 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 385 HIS 0.008 0.001 HIS A 92 PHE 0.019 0.001 PHE G 70 TYR 0.013 0.001 TYR G 48 ARG 0.003 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 259 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 271 average time/residue: 0.2906 time to fit residues: 120.1100 Evaluate side-chains 256 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 246 time to evaluate : 1.792 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1656 time to fit residues: 5.7441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 161 optimal weight: 0.2980 chunk 110 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 144 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 165 optimal weight: 0.4980 chunk 134 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 174 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 HIS ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 353 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17368 Z= 0.206 Angle : 0.606 10.849 23534 Z= 0.298 Chirality : 0.043 0.251 2812 Planarity : 0.004 0.052 2912 Dihedral : 6.595 56.849 3036 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.92 % Allowed : 18.27 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.18 (0.19), residues: 2046 helix: 0.78 (0.28), residues: 357 sheet: 0.69 (0.19), residues: 783 loop : -1.23 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 385 HIS 0.011 0.001 HIS b 353 PHE 0.021 0.001 PHE G 70 TYR 0.017 0.001 TYR G 48 ARG 0.003 0.000 ARG G 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 252 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 outliers start: 17 outliers final: 9 residues processed: 260 average time/residue: 0.2735 time to fit residues: 109.1943 Evaluate side-chains 258 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 249 time to evaluate : 1.760 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1552 time to fit residues: 5.0651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 65 optimal weight: 0.6980 chunk 174 optimal weight: 0.1980 chunk 38 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 194 optimal weight: 0.5980 chunk 161 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 353 HIS b 353 HIS b 364 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17368 Z= 0.231 Angle : 0.624 10.874 23534 Z= 0.307 Chirality : 0.043 0.251 2812 Planarity : 0.004 0.052 2912 Dihedral : 6.582 57.103 3036 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.30 % Allowed : 18.86 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.19 (0.19), residues: 2046 helix: 0.79 (0.28), residues: 357 sheet: 0.68 (0.19), residues: 780 loop : -1.23 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 111 HIS 0.005 0.001 HIS a 353 PHE 0.022 0.001 PHE G 70 TYR 0.018 0.001 TYR G 48 ARG 0.009 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 260 time to evaluate : 1.736 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: 24 outliers final: 17 residues processed: 273 average time/residue: 0.2883 time to fit residues: 121.2493 Evaluate side-chains 270 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 253 time to evaluate : 1.707 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1631 time to fit residues: 7.5513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 187 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 163 optimal weight: 0.0870 chunk 108 optimal weight: 0.7980 chunk 193 optimal weight: 0.0170 chunk 121 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 353 HIS b 364 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17368 Z= 0.230 Angle : 0.637 10.931 23534 Z= 0.313 Chirality : 0.043 0.251 2812 Planarity : 0.004 0.052 2912 Dihedral : 6.607 57.277 3036 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.25 % Allowed : 19.19 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.18 (0.19), residues: 2046 helix: 0.81 (0.28), residues: 354 sheet: 0.66 (0.19), residues: 780 loop : -1.20 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 111 HIS 0.004 0.001 HIS A 92 PHE 0.022 0.002 PHE G 70 TYR 0.018 0.002 TYR G 48 ARG 0.008 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 256 time to evaluate : 1.825 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: 23 outliers final: 16 residues processed: 266 average time/residue: 0.2777 time to fit residues: 114.4143 Evaluate side-chains 269 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 253 time to evaluate : 1.714 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1494 time to fit residues: 7.1011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 77 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 131 optimal weight: 0.0470 chunk 95 optimal weight: 1.9990 chunk 18 optimal weight: 0.0070 chunk 152 optimal weight: 0.6980 chunk 176 optimal weight: 0.8980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17368 Z= 0.221 Angle : 0.636 10.870 23534 Z= 0.314 Chirality : 0.043 0.249 2812 Planarity : 0.005 0.052 2912 Dihedral : 6.527 57.253 3036 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.60 % Allowed : 20.11 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.19 (0.19), residues: 2046 helix: 0.80 (0.28), residues: 354 sheet: 0.66 (0.19), residues: 780 loop : -1.20 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 111 HIS 0.004 0.001 HIS A 92 PHE 0.023 0.002 PHE G 70 TYR 0.017 0.001 TYR G 48 ARG 0.007 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 254 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 258 average time/residue: 0.2852 time to fit residues: 111.9178 Evaluate side-chains 257 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 252 time to evaluate : 1.784 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1627 time to fit residues: 3.9235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 185 optimal weight: 0.4980 chunk 169 optimal weight: 1.9990 chunk 180 optimal weight: 0.0670 chunk 108 optimal weight: 0.6980 chunk 78 optimal weight: 0.0060 chunk 141 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 163 optimal weight: 0.4980 chunk 170 optimal weight: 0.1980 chunk 179 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 overall best weight: 0.2534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 364 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17368 Z= 0.161 Angle : 0.594 10.554 23534 Z= 0.294 Chirality : 0.042 0.233 2812 Planarity : 0.004 0.052 2912 Dihedral : 6.272 56.296 3036 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.22 % Allowed : 21.03 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.19), residues: 2046 helix: 0.88 (0.28), residues: 354 sheet: 0.67 (0.19), residues: 786 loop : -1.12 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 226 HIS 0.007 0.001 HIS b 353 PHE 0.022 0.001 PHE G 70 TYR 0.012 0.001 TYR b 365 ARG 0.008 0.000 ARG C 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 254 time to evaluate : 1.823 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: 4 outliers final: 3 residues processed: 255 average time/residue: 0.2802 time to fit residues: 108.8456 Evaluate side-chains 251 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 248 time to evaluate : 2.221 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1754 time to fit residues: 3.4987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 190 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 200 optimal weight: 0.3980 chunk 184 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17368 Z= 0.301 Angle : 0.679 11.599 23534 Z= 0.334 Chirality : 0.045 0.250 2812 Planarity : 0.005 0.053 2912 Dihedral : 6.586 57.578 3036 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.33 % Allowed : 21.25 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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: -0.21 (0.19), residues: 2046 helix: 0.74 (0.28), residues: 354 sheet: 0.78 (0.19), residues: 759 loop : -1.29 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 111 HIS 0.006 0.001 HIS b 353 PHE 0.023 0.002 PHE G 70 TYR 0.021 0.002 TYR L 48 ARG 0.006 0.001 ARG B 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 259 time to evaluate : 1.823 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: 6 outliers final: 4 residues processed: 259 average time/residue: 0.2845 time to fit residues: 112.5470 Evaluate side-chains 261 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 257 time to evaluate : 1.646 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1699 time to fit residues: 3.8617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 169 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 GLN ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 352 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.172147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.147297 restraints weight = 27515.728| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.33 r_work: 0.3790 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17368 Z= 0.352 Angle : 0.728 12.741 23534 Z= 0.360 Chirality : 0.048 0.280 2812 Planarity : 0.005 0.055 2912 Dihedral : 6.923 59.805 3036 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.38 % Allowed : 21.19 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 (0.19), residues: 2046 helix: 0.52 (0.28), residues: 354 sheet: 0.51 (0.19), residues: 774 loop : -1.36 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 111 HIS 0.005 0.001 HIS A 92 PHE 0.026 0.002 PHE G 70 TYR 0.025 0.002 TYR G 48 ARG 0.006 0.001 ARG B 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4052.17 seconds wall clock time: 74 minutes 36.97 seconds (4476.97 seconds total)