Starting phenix.real_space_refine on Sat Feb 17 13:41:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m8l_23719/02_2024/7m8l_23719.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m8l_23719/02_2024/7m8l_23719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m8l_23719/02_2024/7m8l_23719.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m8l_23719/02_2024/7m8l_23719.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m8l_23719/02_2024/7m8l_23719.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m8l_23719/02_2024/7m8l_23719.pdb" } resolution = 3.9 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= 0.000 sd= 0.003 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 57 5.16 5 C 11838 2.51 5 N 3147 2.21 5 O 3711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 178": "OE1" <-> "OE2" Residue "G TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "H TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "I TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18753 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1730 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "G" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1028 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain: "J" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "D" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 722 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "M" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 951 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "P" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "B" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1730 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1028 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain: "K" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "E" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 722 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "N" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 951 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "Q" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "C" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1730 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1028 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "F" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 722 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain breaks: 1 Chain: "O" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 951 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "R" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "S" 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: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" 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: "U" 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: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" 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: 15 Unresolved non-hydrogen chiralities: 5 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: "X" 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: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" 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: 15 Unresolved non-hydrogen chiralities: 5 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: "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 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 Time building chain proxies: 10.06, per 1000 atoms: 0.54 Number of scatterers: 18753 At special positions: 0 Unit cell: (141.11, 152.44, 119.48, 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 57 16.00 O 3711 8.00 N 3147 7.00 C 11838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 101 " distance=2.02 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.02 Simple disulfide: pdb=" SG CYS D 511 " - pdb=" SG CYS D 556 " distance=2.05 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 97 " distance=2.02 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 147 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 101 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.02 Simple disulfide: pdb=" SG CYS E 511 " - pdb=" SG CYS E 556 " distance=2.05 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 97 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 135 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 147 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 101 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.02 Simple disulfide: pdb=" SG CYS F 511 " - pdb=" SG CYS F 556 " distance=2.05 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 97 " distance=2.02 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " 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 S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA U 3 " - " MAN U 5 " " BMA V 3 " - " MAN V 5 " " BMA X 3 " - " MAN X 5 " " BMA Y 3 " - " MAN Y 5 " " BMA a 3 " - " MAN a 5 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " NAG-ASN " NAG A 401 " - " ASN A 268 " " NAG A 402 " - " ASN A 238 " " NAG B 401 " - " ASN B 268 " " NAG B 402 " - " ASN B 238 " " NAG C 401 " - " ASN C 268 " " NAG C 402 " - " ASN C 238 " " NAG S 1 " - " ASN A 257 " " NAG T 1 " - " ASN A 228 " " NAG U 1 " - " ASN D 563 " " NAG V 1 " - " ASN B 257 " " NAG W 1 " - " ASN B 228 " " NAG X 1 " - " ASN E 563 " " NAG Y 1 " - " ASN C 257 " " NAG Z 1 " - " ASN C 228 " " NAG a 1 " - " ASN F 563 " Time building additional restraints: 7.22 Conformation dependent library (CDL) restraints added in 3.3 seconds 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4224 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 45 sheets defined 12.9% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 59 through 61 No H-bonds generated for 'chain 'A' and resid 59 through 61' Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 249 through 263 Processing helix chain 'G' and resid 67 through 70 Processing helix chain 'G' and resid 92 through 96 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 80 through 84 Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 550 through 552 No H-bonds generated for 'chain 'D' and resid 550 through 552' Processing helix chain 'D' and resid 553 through 576 removed outlier: 4.809A pdb=" N GLN D 567 " --> pdb=" O ASN D 563 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA D 568 " --> pdb=" O GLU D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 597 removed outlier: 3.590A pdb=" N ARG D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 66 Processing helix chain 'M' and resid 88 through 92 Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 249 through 263 Processing helix chain 'H' and resid 67 through 70 Processing helix chain 'H' and resid 92 through 96 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 80 through 84 Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 550 through 552 No H-bonds generated for 'chain 'E' and resid 550 through 552' Processing helix chain 'E' and resid 553 through 576 removed outlier: 4.809A pdb=" N GLN E 567 " --> pdb=" O ASN E 563 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA E 568 " --> pdb=" O GLU E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 597 removed outlier: 3.590A pdb=" N ARG E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 66 Processing helix chain 'N' and resid 88 through 92 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 249 through 263 Processing helix chain 'I' and resid 67 through 70 Processing helix chain 'I' and resid 92 through 96 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 80 through 84 Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 550 through 552 No H-bonds generated for 'chain 'F' and resid 550 through 552' Processing helix chain 'F' and resid 553 through 576 removed outlier: 4.809A pdb=" N GLN F 567 " --> pdb=" O ASN F 563 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA F 568 " --> pdb=" O GLU F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 597 removed outlier: 3.590A pdb=" N ARG F 596 " --> pdb=" O PHE F 592 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 66 Processing helix chain 'O' and resid 88 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 45 removed outlier: 6.713A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 114 through 119 removed outlier: 6.901A pdb=" N TYR A 241 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL A 277 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLN A 243 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ARG A 219 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE A 218 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU A 106 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N HIS A 139 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 12.023A pdb=" N ALA A 105 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 13.774A pdb=" N VAL A 180 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N ASN A 107 " --> pdb=" O GLU A 178 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLU A 178 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A 96 " --> pdb=" O THR D 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AA4, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.707A pdb=" N THR G 83 " --> pdb=" O ASP G 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.005A pdb=" N MET G 37 " --> pdb=" O ARG G 53 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG G 53 " --> pdb=" O MET G 37 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TRP G 39 " --> pdb=" O ILE G 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AA8, first strand: chain 'J' and resid 10 through 12 removed outlier: 5.910A pdb=" N LEU J 11 " --> pdb=" O GLU J 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 10 through 12 removed outlier: 5.910A pdb=" N LEU J 11 " --> pdb=" O GLU J 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 49 through 50 Processing sheet with id=AB2, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'M' and resid 11 through 12 removed outlier: 7.495A pdb=" N TYR M 34 " --> pdb=" O ASP M 54 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ASP M 54 " --> pdb=" O TYR M 34 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP M 36 " --> pdb=" O TYR M 52 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR M 52 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP M 38 " --> pdb=" O ILE M 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AB5, first strand: chain 'P' and resid 5 through 7 removed outlier: 5.744A pdb=" N THR P 69 " --> pdb=" O ALA P 25 " (cutoff:3.500A) removed outlier: 9.720A pdb=" N GLN P 27 " --> pdb=" O SER P 67 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N SER P 67 " --> pdb=" O GLN P 27 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N VAL P 29 " --> pdb=" O SER P 65 " (cutoff:3.500A) removed outlier: 11.461A pdb=" N SER P 65 " --> pdb=" O VAL P 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.634A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 43 through 45 removed outlier: 6.712A pdb=" N GLY B 36 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASN B 69 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 114 through 119 removed outlier: 6.900A pdb=" N TYR B 241 " --> pdb=" O TRP B 275 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL B 277 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N GLN B 243 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ARG B 219 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ILE B 218 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL B 138 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR B 220 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LYS B 140 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ALA B 222 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER B 142 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU B 106 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N HIS B 139 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N CYS B 108 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL B 141 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASN B 110 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLY B 143 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLU B 112 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 12.024A pdb=" N ALA B 105 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 13.774A pdb=" N VAL B 180 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ASN B 107 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLU B 178 " --> pdb=" O ASN B 107 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B 96 " --> pdb=" O THR E 581 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 86 through 89 Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.707A pdb=" N THR H 83 " --> pdb=" O ASP H 78 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.005A pdb=" N MET H 37 " --> pdb=" O ARG H 53 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG H 53 " --> pdb=" O MET H 37 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TRP H 39 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AC4, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.911A pdb=" N LEU K 11 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.911A pdb=" N LEU K 11 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 49 through 50 Processing sheet with id=AC8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.495A pdb=" N TYR N 34 " --> pdb=" O ASP N 54 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ASP N 54 " --> pdb=" O TYR N 34 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP N 36 " --> pdb=" O TYR N 52 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR N 52 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP N 38 " --> pdb=" O ILE N 50 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AD2, first strand: chain 'Q' and resid 5 through 7 removed outlier: 5.744A pdb=" N THR Q 69 " --> pdb=" O ALA Q 25 " (cutoff:3.500A) removed outlier: 9.720A pdb=" N GLN Q 27 " --> pdb=" O SER Q 67 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N SER Q 67 " --> pdb=" O GLN Q 27 " (cutoff:3.500A) removed outlier: 11.408A pdb=" N VAL Q 29 " --> pdb=" O SER Q 65 " (cutoff:3.500A) removed outlier: 11.461A pdb=" N SER Q 65 " --> pdb=" O VAL Q 29 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.634A pdb=" N LEU Q 33 " --> pdb=" O TYR Q 49 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TYR Q 49 " --> pdb=" O LEU Q 33 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 43 through 45 removed outlier: 6.712A pdb=" N GLY C 36 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASN C 69 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 114 through 119 removed outlier: 6.901A pdb=" N TYR C 241 " --> pdb=" O TRP C 275 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N VAL C 277 " --> pdb=" O TYR C 241 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLN C 243 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ARG C 219 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE C 218 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL C 138 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR C 220 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS C 140 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ALA C 222 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER C 142 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU C 106 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N HIS C 139 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N CYS C 108 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL C 141 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASN C 110 " --> pdb=" O VAL C 141 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLY C 143 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU C 112 " --> pdb=" O GLY C 143 " (cutoff:3.500A) removed outlier: 12.024A pdb=" N ALA C 105 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 13.773A pdb=" N VAL C 180 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N ASN C 107 " --> pdb=" O GLU C 178 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLU C 178 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL C 96 " --> pdb=" O THR F 581 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 86 through 89 Processing sheet with id=AD7, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.707A pdb=" N THR I 83 " --> pdb=" O ASP I 78 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.005A pdb=" N MET I 37 " --> pdb=" O ARG I 53 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG I 53 " --> pdb=" O MET I 37 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TRP I 39 " --> pdb=" O ILE I 51 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 10 through 12 Processing sheet with id=AE1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.910A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.910A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 49 through 50 Processing sheet with id=AE5, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'O' and resid 11 through 12 removed outlier: 7.495A pdb=" N TYR O 34 " --> pdb=" O ASP O 54 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ASP O 54 " --> pdb=" O TYR O 34 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP O 36 " --> pdb=" O TYR O 52 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR O 52 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP O 38 " --> pdb=" O ILE O 50 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 11 through 12 Processing sheet with id=AE8, first strand: chain 'R' and resid 5 through 7 removed outlier: 5.744A pdb=" N THR R 69 " --> pdb=" O ALA R 25 " (cutoff:3.500A) removed outlier: 9.719A pdb=" N GLN R 27 " --> pdb=" O SER R 67 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N SER R 67 " --> pdb=" O GLN R 27 " (cutoff:3.500A) removed outlier: 11.409A pdb=" N VAL R 29 " --> pdb=" O SER R 65 " (cutoff:3.500A) removed outlier: 11.461A pdb=" N SER R 65 " --> pdb=" O VAL R 29 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 10 through 12 removed outlier: 6.634A pdb=" N LEU R 33 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TYR R 49 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) 726 hydrogen bonds defined for protein. 1719 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: 6.80 Time building geometry restraints manager: 7.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3581 1.32 - 1.46: 6795 1.46 - 1.60: 8701 1.60 - 1.73: 60 1.73 - 1.87: 57 Bond restraints: 19194 Sorted by residual: bond pdb=" CB TYR A 99 " pdb=" CG TYR A 99 " ideal model delta sigma weight residual 1.512 1.331 0.181 2.20e-02 2.07e+03 6.77e+01 bond pdb=" CB TYR B 99 " pdb=" CG TYR B 99 " ideal model delta sigma weight residual 1.512 1.331 0.181 2.20e-02 2.07e+03 6.77e+01 bond pdb=" CB TYR C 99 " pdb=" CG TYR C 99 " ideal model delta sigma weight residual 1.512 1.331 0.181 2.20e-02 2.07e+03 6.76e+01 bond pdb=" CB ILE J 107 " pdb=" CG1 ILE J 107 " ideal model delta sigma weight residual 1.530 1.652 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" CB ILE L 107 " pdb=" CG1 ILE L 107 " ideal model delta sigma weight residual 1.530 1.652 -0.122 2.00e-02 2.50e+03 3.72e+01 ... (remaining 19189 not shown) Histogram of bond angle deviations from ideal: 90.94 - 99.57: 9 99.57 - 108.21: 1861 108.21 - 116.84: 11599 116.84 - 125.47: 12135 125.47 - 134.10: 484 Bond angle restraints: 26088 Sorted by residual: angle pdb=" N GLN N 41 " pdb=" CA GLN N 41 " pdb=" C GLN N 41 " ideal model delta sigma weight residual 111.36 120.62 -9.26 1.09e+00 8.42e-01 7.21e+01 angle pdb=" N GLN M 41 " pdb=" CA GLN M 41 " pdb=" C GLN M 41 " ideal model delta sigma weight residual 111.36 120.61 -9.25 1.09e+00 8.42e-01 7.21e+01 angle pdb=" N GLN O 41 " pdb=" CA GLN O 41 " pdb=" C GLN O 41 " ideal model delta sigma weight residual 111.36 120.61 -9.25 1.09e+00 8.42e-01 7.20e+01 angle pdb=" CA ASP H 78 " pdb=" CB ASP H 78 " pdb=" CG ASP H 78 " ideal model delta sigma weight residual 112.60 120.72 -8.12 1.00e+00 1.00e+00 6.60e+01 angle pdb=" CA ASP I 78 " pdb=" CB ASP I 78 " pdb=" CG ASP I 78 " ideal model delta sigma weight residual 112.60 120.71 -8.11 1.00e+00 1.00e+00 6.58e+01 ... (remaining 26083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.39: 11396 21.39 - 42.77: 238 42.77 - 64.16: 84 64.16 - 85.55: 48 85.55 - 106.93: 27 Dihedral angle restraints: 11793 sinusoidal: 5121 harmonic: 6672 Sorted by residual: dihedral pdb=" CB CYS I 22 " pdb=" SG CYS I 22 " pdb=" SG CYS I 101 " pdb=" CB CYS I 101 " ideal model delta sinusoidal sigma weight residual 93.00 32.57 60.43 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 101 " pdb=" CB CYS H 101 " ideal model delta sinusoidal sigma weight residual 93.00 32.58 60.42 1 1.00e+01 1.00e-02 4.86e+01 dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 101 " pdb=" CB CYS G 101 " ideal model delta sinusoidal sigma weight residual 93.00 32.60 60.40 1 1.00e+01 1.00e-02 4.86e+01 ... (remaining 11790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2104 0.105 - 0.211: 656 0.211 - 0.316: 149 0.316 - 0.421: 54 0.421 - 0.527: 19 Chirality restraints: 2982 Sorted by residual: chirality pdb=" C1 NAG Z 2 " pdb=" O4 NAG Z 1 " pdb=" C2 NAG Z 2 " pdb=" O5 NAG Z 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.67e+01 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.61e+01 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.55e+01 ... (remaining 2979 not shown) Planarity restraints: 3297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 99 " 0.104 2.00e-02 2.50e+03 5.63e-02 6.33e+01 pdb=" CG TYR B 99 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 99 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR B 99 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR B 99 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR B 99 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR B 99 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 99 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 99 " -0.105 2.00e-02 2.50e+03 5.63e-02 6.33e+01 pdb=" CG TYR C 99 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR C 99 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR C 99 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR C 99 " 0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR C 99 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR C 99 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 99 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 99 " -0.104 2.00e-02 2.50e+03 5.62e-02 6.31e+01 pdb=" CG TYR A 99 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 99 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR A 99 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR A 99 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR A 99 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR A 99 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 99 " -0.083 2.00e-02 2.50e+03 ... (remaining 3294 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 6995 2.88 - 3.39: 16279 3.39 - 3.89: 32370 3.89 - 4.40: 37598 4.40 - 4.90: 61464 Nonbonded interactions: 154706 Sorted by model distance: nonbonded pdb=" N THR Q 31 " pdb=" N ASN Q 32 " model vdw 2.378 2.560 nonbonded pdb=" N THR P 31 " pdb=" N ASN P 32 " model vdw 2.379 2.560 nonbonded pdb=" N THR R 31 " pdb=" N ASN R 32 " model vdw 2.380 2.560 nonbonded pdb=" OD2 ASP O 74 " pdb=" NZ LYS O 77 " model vdw 2.405 2.520 nonbonded pdb=" OD2 ASP M 74 " pdb=" NZ LYS M 77 " model vdw 2.406 2.520 ... (remaining 154701 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 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'a' } ncs_group { reference = chain 'T' selection = chain 'W' selection = chain 'Z' } 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: 1.580 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: 7.530 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 50.380 Find NCS groups from input model: 1.200 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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 : 0.021 0.181 19194 Z= 1.393 Angle : 1.844 11.278 26088 Z= 1.214 Chirality : 0.117 0.527 2982 Planarity : 0.009 0.060 3282 Dihedral : 12.535 106.932 7506 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.65 % Allowed : 1.69 % Favored : 97.65 % Rotamer: Outliers : 0.15 % Allowed : 1.68 % Favored : 98.17 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 5.13 % 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: 0.75 (0.17), residues: 2301 helix: 1.11 (0.34), residues: 150 sheet: 0.34 (0.17), residues: 903 loop : 0.74 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.008 TRP L 36 HIS 0.007 0.003 HIS E 516 PHE 0.027 0.006 PHE N 80 TYR 0.105 0.011 TYR C 99 ARG 0.012 0.001 ARG G 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 623 time to evaluate : 2.194 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: A 44 GLN cc_start: 0.8107 (mm-40) cc_final: 0.7799 (mt0) REVERT: A 99 TYR cc_start: 0.7365 (m-10) cc_final: 0.6853 (m-10) REVERT: A 106 GLU cc_start: 0.8431 (tt0) cc_final: 0.8230 (tt0) REVERT: G 39 TRP cc_start: 0.6916 (m100) cc_final: 0.6030 (m100) REVERT: G 87 GLN cc_start: 0.5925 (tp40) cc_final: 0.5601 (mp10) REVERT: J 32 LYS cc_start: 0.8084 (pttt) cc_final: 0.7837 (ptmm) REVERT: J 61 ASP cc_start: 0.6822 (p0) cc_final: 0.6362 (t0) REVERT: J 97 TRP cc_start: 0.6069 (m-10) cc_final: 0.5718 (m-10) REVERT: D 565 THR cc_start: 0.9022 (p) cc_final: 0.8673 (t) REVERT: D 596 ARG cc_start: 0.6937 (mtp85) cc_final: 0.6627 (mtt-85) REVERT: D 597 TRP cc_start: 0.5878 (m-90) cc_final: 0.5415 (m100) REVERT: M 6 GLU cc_start: 0.8301 (mp0) cc_final: 0.7971 (mp0) REVERT: M 17 THR cc_start: 0.8712 (m) cc_final: 0.8392 (p) REVERT: M 54 ASP cc_start: 0.8273 (t0) cc_final: 0.7829 (t0) REVERT: M 74 ASP cc_start: 0.7031 (t0) cc_final: 0.6065 (p0) REVERT: M 116 THR cc_start: 0.8140 (t) cc_final: 0.7940 (t) REVERT: P 37 GLN cc_start: 0.8729 (tt0) cc_final: 0.8270 (tt0) REVERT: P 85 VAL cc_start: 0.8704 (t) cc_final: 0.8329 (m) REVERT: H 39 TRP cc_start: 0.6885 (m100) cc_final: 0.6172 (m100) REVERT: H 87 GLN cc_start: 0.6064 (tp40) cc_final: 0.5558 (mp10) REVERT: K 59 ILE cc_start: 0.1979 (mm) cc_final: 0.1566 (mm) REVERT: K 61 ASP cc_start: 0.6732 (p0) cc_final: 0.6294 (t70) REVERT: K 73 THR cc_start: 0.7988 (m) cc_final: 0.7785 (t) REVERT: E 565 THR cc_start: 0.8976 (p) cc_final: 0.8607 (t) REVERT: E 597 TRP cc_start: 0.6089 (m-90) cc_final: 0.5536 (m100) REVERT: N 6 GLU cc_start: 0.8245 (mp0) cc_final: 0.7849 (mp0) REVERT: N 17 THR cc_start: 0.8885 (m) cc_final: 0.8579 (p) REVERT: N 54 ASP cc_start: 0.8336 (t0) cc_final: 0.7817 (t0) REVERT: N 74 ASP cc_start: 0.7170 (t0) cc_final: 0.6277 (p0) REVERT: Q 39 LYS cc_start: 0.8411 (mttt) cc_final: 0.8051 (mttt) REVERT: Q 85 VAL cc_start: 0.8614 (t) cc_final: 0.8322 (m) REVERT: Q 105 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6777 (mm-30) REVERT: C 44 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7647 (mt0) REVERT: C 99 TYR cc_start: 0.7404 (m-10) cc_final: 0.6529 (m-10) REVERT: C 103 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8336 (mt-10) REVERT: I 39 TRP cc_start: 0.7032 (m100) cc_final: 0.5913 (m100) REVERT: I 87 GLN cc_start: 0.5948 (tp40) cc_final: 0.5480 (mp10) REVERT: I 88 MET cc_start: 0.7390 (mtm) cc_final: 0.7094 (ptp) REVERT: L 61 ASP cc_start: 0.7097 (p0) cc_final: 0.6625 (t70) REVERT: L 97 TRP cc_start: 0.6347 (m-10) cc_final: 0.5410 (m-10) REVERT: F 565 THR cc_start: 0.8893 (p) cc_final: 0.8605 (t) REVERT: F 597 TRP cc_start: 0.6067 (m-90) cc_final: 0.5642 (m100) REVERT: O 6 GLU cc_start: 0.8430 (mp0) cc_final: 0.8117 (mp0) REVERT: O 17 THR cc_start: 0.8954 (m) cc_final: 0.8627 (p) REVERT: O 34 TYR cc_start: 0.8830 (m-80) cc_final: 0.8611 (m-80) REVERT: O 54 ASP cc_start: 0.8298 (t0) cc_final: 0.7809 (t0) REVERT: O 74 ASP cc_start: 0.6916 (t0) cc_final: 0.6095 (p0) REVERT: R 4 MET cc_start: 0.7684 (mmm) cc_final: 0.7216 (mmm) REVERT: R 11 LEU cc_start: 0.8752 (tp) cc_final: 0.8529 (tt) REVERT: R 37 GLN cc_start: 0.8602 (tt0) cc_final: 0.8148 (tt0) REVERT: R 85 VAL cc_start: 0.8713 (t) cc_final: 0.8399 (m) outliers start: 3 outliers final: 0 residues processed: 623 average time/residue: 0.3679 time to fit residues: 323.7624 Evaluate side-chains 390 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 178 optimal weight: 0.0270 chunk 69 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 133 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 GLN M 41 GLN M 78 ASN M 79 HIS P 92 ASN B 62 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 41 GLN N 78 ASN N 79 HIS Q 37 GLN Q 79 GLN Q 89 GLN C 39 HIS ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 41 GLN O 78 ASN O 79 HIS O 114 GLN R 79 GLN R 92 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19194 Z= 0.240 Angle : 0.728 8.293 26088 Z= 0.377 Chirality : 0.049 0.262 2982 Planarity : 0.005 0.043 3282 Dihedral : 11.302 88.939 3423 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.48 % Favored : 97.31 % Rotamer: Outliers : 1.93 % Allowed : 10.89 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.30 (0.17), residues: 2301 helix: 2.20 (0.37), residues: 156 sheet: 0.07 (0.16), residues: 1017 loop : 0.19 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP R 94 HIS 0.008 0.001 HIS O 79 PHE 0.036 0.002 PHE K 72 TYR 0.023 0.002 TYR G 100 ARG 0.010 0.001 ARG J 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 431 time to evaluate : 2.101 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: A 100 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7193 (mp0) REVERT: A 227 THR cc_start: 0.8380 (t) cc_final: 0.8173 (p) REVERT: G 39 TRP cc_start: 0.6752 (m100) cc_final: 0.6060 (m100) REVERT: G 87 GLN cc_start: 0.5775 (tp40) cc_final: 0.5350 (mp10) REVERT: J 61 ASP cc_start: 0.7311 (p0) cc_final: 0.6837 (t0) REVERT: J 90 HIS cc_start: 0.6601 (t-90) cc_final: 0.5938 (t-170) REVERT: D 565 THR cc_start: 0.8807 (p) cc_final: 0.8507 (t) REVERT: D 578 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7775 (tt0) REVERT: D 596 ARG cc_start: 0.7060 (mtp85) cc_final: 0.6843 (mtt-85) REVERT: D 597 TRP cc_start: 0.6126 (m-90) cc_final: 0.5657 (m100) REVERT: M 3 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8441 (mp10) REVERT: M 6 GLU cc_start: 0.8305 (mp0) cc_final: 0.7953 (mp0) REVERT: M 17 THR cc_start: 0.8733 (m) cc_final: 0.8482 (p) REVERT: M 74 ASP cc_start: 0.6787 (t0) cc_final: 0.5478 (p0) REVERT: P 105 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6870 (mm-30) REVERT: B 100 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7342 (mp0) REVERT: H 39 TRP cc_start: 0.6957 (m100) cc_final: 0.6428 (m100) REVERT: H 87 GLN cc_start: 0.5745 (tp40) cc_final: 0.5211 (mp10) REVERT: K 36 TRP cc_start: 0.6070 (m100) cc_final: 0.5706 (m-10) REVERT: K 61 ASP cc_start: 0.6924 (p0) cc_final: 0.6548 (t0) REVERT: K 79 LEU cc_start: 0.6371 (tp) cc_final: 0.5756 (tt) REVERT: K 80 GLU cc_start: 0.5293 (mm-30) cc_final: 0.4977 (tp30) REVERT: K 90 HIS cc_start: 0.6777 (t-90) cc_final: 0.6207 (t70) REVERT: E 565 THR cc_start: 0.8557 (p) cc_final: 0.8285 (t) REVERT: E 578 GLU cc_start: 0.8048 (tt0) cc_final: 0.7815 (tt0) REVERT: E 597 TRP cc_start: 0.6216 (m-90) cc_final: 0.5673 (m100) REVERT: N 3 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8357 (mp10) REVERT: N 6 GLU cc_start: 0.8161 (mp0) cc_final: 0.7841 (mp0) REVERT: N 17 THR cc_start: 0.8690 (m) cc_final: 0.8466 (p) REVERT: N 74 ASP cc_start: 0.6643 (t0) cc_final: 0.5637 (p0) REVERT: N 83 ARG cc_start: 0.7852 (ttm-80) cc_final: 0.7641 (ttm-80) REVERT: Q 39 LYS cc_start: 0.8171 (mttt) cc_final: 0.7925 (mttt) REVERT: I 39 TRP cc_start: 0.6810 (m100) cc_final: 0.5906 (m100) REVERT: I 87 GLN cc_start: 0.5868 (tp40) cc_final: 0.5396 (mp10) REVERT: L 61 ASP cc_start: 0.7312 (p0) cc_final: 0.6956 (t70) REVERT: L 80 GLU cc_start: 0.5359 (mm-30) cc_final: 0.5112 (tp30) REVERT: L 90 HIS cc_start: 0.6483 (t-90) cc_final: 0.5925 (t70) REVERT: F 565 THR cc_start: 0.8767 (p) cc_final: 0.8552 (t) REVERT: F 578 GLU cc_start: 0.8049 (tt0) cc_final: 0.7701 (tt0) REVERT: F 597 TRP cc_start: 0.6246 (m-90) cc_final: 0.5728 (m100) REVERT: O 3 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8414 (mp10) REVERT: O 6 GLU cc_start: 0.8448 (mp0) cc_final: 0.8112 (mp0) REVERT: O 74 ASP cc_start: 0.6625 (t0) cc_final: 0.5481 (p0) REVERT: R 98 TYR cc_start: 0.8607 (m-80) cc_final: 0.8345 (m-80) REVERT: R 105 GLU cc_start: 0.6459 (mm-30) cc_final: 0.5719 (mm-30) outliers start: 38 outliers final: 24 residues processed: 449 average time/residue: 0.3680 time to fit residues: 236.5584 Evaluate side-chains 398 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 374 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain D residue 552 ASP Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 78 ASN Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain R residue 106 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 207 optimal weight: 0.3980 chunk 224 optimal weight: 0.5980 chunk 184 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 514 ASN D 595 GLN M 41 GLN M 79 HIS P 79 GLN ** P 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 514 ASN N 79 HIS Q 79 GLN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN ** F 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 595 GLN O 79 HIS O 114 GLN R 79 GLN R 92 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 19194 Z= 0.393 Angle : 0.736 9.877 26088 Z= 0.372 Chirality : 0.049 0.296 2982 Planarity : 0.005 0.049 3282 Dihedral : 10.430 84.332 3423 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.91 % Favored : 96.87 % Rotamer: Outliers : 3.61 % Allowed : 12.72 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.12 (0.17), residues: 2301 helix: 1.32 (0.39), residues: 174 sheet: -0.22 (0.16), residues: 1035 loop : -0.00 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP Q 94 HIS 0.008 0.002 HIS N 79 PHE 0.017 0.002 PHE L 72 TYR 0.023 0.002 TYR M 35 ARG 0.010 0.001 ARG F 587 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 391 time to evaluate : 2.121 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: A 100 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7409 (mp0) REVERT: A 184 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8982 (pp) REVERT: A 261 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.7743 (m-80) REVERT: G 39 TRP cc_start: 0.6785 (m100) cc_final: 0.6348 (m100) REVERT: J 59 ILE cc_start: 0.1999 (OUTLIER) cc_final: 0.1721 (pt) REVERT: J 61 ASP cc_start: 0.7227 (p0) cc_final: 0.6769 (t0) REVERT: J 90 HIS cc_start: 0.6479 (t-90) cc_final: 0.5669 (t70) REVERT: D 565 THR cc_start: 0.8977 (p) cc_final: 0.8576 (t) REVERT: D 597 TRP cc_start: 0.6234 (m-90) cc_final: 0.5701 (m100) REVERT: M 3 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8544 (mp10) REVERT: M 6 GLU cc_start: 0.8315 (mp0) cc_final: 0.7911 (mp0) REVERT: M 17 THR cc_start: 0.8776 (m) cc_final: 0.8428 (p) REVERT: M 74 ASP cc_start: 0.6635 (t0) cc_final: 0.5716 (p0) REVERT: B 100 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7616 (mp0) REVERT: B 130 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8118 (ttm-80) REVERT: B 229 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8114 (pp20) REVERT: B 231 GLU cc_start: 0.8601 (mp0) cc_final: 0.8156 (mp0) REVERT: H 87 GLN cc_start: 0.5318 (tp40) cc_final: 0.4664 (pm20) REVERT: K 61 ASP cc_start: 0.6933 (p0) cc_final: 0.6536 (t0) REVERT: K 79 LEU cc_start: 0.6433 (tp) cc_final: 0.5754 (tt) REVERT: K 80 GLU cc_start: 0.5359 (mm-30) cc_final: 0.5013 (tp30) REVERT: K 90 HIS cc_start: 0.7024 (t-90) cc_final: 0.6341 (t70) REVERT: E 565 THR cc_start: 0.8691 (p) cc_final: 0.8366 (t) REVERT: E 597 TRP cc_start: 0.6336 (m-90) cc_final: 0.5863 (m100) REVERT: N 3 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8468 (mp10) REVERT: N 6 GLU cc_start: 0.8303 (mp0) cc_final: 0.7658 (mp0) REVERT: N 17 THR cc_start: 0.8825 (m) cc_final: 0.8556 (p) REVERT: N 74 ASP cc_start: 0.6761 (t0) cc_final: 0.5751 (p0) REVERT: N 83 ARG cc_start: 0.7939 (ttm-80) cc_final: 0.7711 (ttm-80) REVERT: N 100 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7923 (mm-30) REVERT: C 130 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7927 (mtm-85) REVERT: I 39 TRP cc_start: 0.6849 (m100) cc_final: 0.5815 (m100) REVERT: I 41 ARG cc_start: 0.5374 (ptp90) cc_final: 0.5096 (ptm160) REVERT: L 32 LYS cc_start: 0.7883 (ptmm) cc_final: 0.7489 (mmtt) REVERT: L 59 ILE cc_start: 0.2158 (OUTLIER) cc_final: 0.1944 (pt) REVERT: L 61 ASP cc_start: 0.7285 (p0) cc_final: 0.6959 (t0) REVERT: L 80 GLU cc_start: 0.5444 (mm-30) cc_final: 0.5061 (tp30) REVERT: L 90 HIS cc_start: 0.6444 (t-90) cc_final: 0.5698 (t70) REVERT: F 565 THR cc_start: 0.8799 (p) cc_final: 0.8554 (t) REVERT: F 578 GLU cc_start: 0.7977 (tt0) cc_final: 0.7740 (tt0) REVERT: F 597 TRP cc_start: 0.6351 (m-90) cc_final: 0.5852 (m100) REVERT: O 3 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8502 (mp10) REVERT: O 6 GLU cc_start: 0.8417 (mp0) cc_final: 0.7998 (mp0) REVERT: O 74 ASP cc_start: 0.6886 (t0) cc_final: 0.5886 (p0) REVERT: R 98 TYR cc_start: 0.8596 (m-80) cc_final: 0.8326 (m-80) outliers start: 71 outliers final: 50 residues processed: 431 average time/residue: 0.3543 time to fit residues: 221.7390 Evaluate side-chains 422 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 366 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 40 LYS Chi-restraints excluded: chain J residue 59 ILE Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 552 ASP Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 106 GLU Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 101 SER Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 59 ILE Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 552 ASP Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 114 GLN Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 106 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 0.6980 chunk 155 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 220 optimal weight: 0.7980 chunk 108 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 43 GLN M 79 HIS P 79 GLN P 92 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN N 78 ASN N 79 HIS Q 32 ASN Q 37 GLN Q 79 GLN Q 92 ASN ** L 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 514 ASN O 79 HIS R 79 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19194 Z= 0.240 Angle : 0.652 10.822 26088 Z= 0.327 Chirality : 0.046 0.266 2982 Planarity : 0.005 0.057 3282 Dihedral : 9.720 78.686 3423 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.00 % Favored : 96.78 % Rotamer: Outliers : 3.66 % Allowed : 13.33 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.12 (0.18), residues: 2301 helix: 1.54 (0.39), residues: 174 sheet: -0.15 (0.16), residues: 1032 loop : -0.13 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 39 HIS 0.008 0.001 HIS O 79 PHE 0.014 0.001 PHE K 72 TYR 0.028 0.002 TYR I 85 ARG 0.011 0.001 ARG F 596 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 386 time to evaluate : 2.085 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: A 99 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.5813 (m-10) REVERT: A 231 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: A 261 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.7881 (m-80) REVERT: G 39 TRP cc_start: 0.6595 (m100) cc_final: 0.6099 (m100) REVERT: J 32 LYS cc_start: 0.7851 (pttp) cc_final: 0.7620 (mmtt) REVERT: J 61 ASP cc_start: 0.7294 (p0) cc_final: 0.6871 (t0) REVERT: J 90 HIS cc_start: 0.6480 (t-90) cc_final: 0.5590 (t70) REVERT: D 551 GLN cc_start: 0.8414 (tp40) cc_final: 0.8190 (tp40) REVERT: D 565 THR cc_start: 0.8856 (p) cc_final: 0.8516 (t) REVERT: D 597 TRP cc_start: 0.6228 (m-90) cc_final: 0.5667 (m100) REVERT: M 3 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8518 (mp10) REVERT: M 6 GLU cc_start: 0.8312 (mp0) cc_final: 0.7893 (mp0) REVERT: M 17 THR cc_start: 0.8731 (m) cc_final: 0.8255 (p) REVERT: M 74 ASP cc_start: 0.6646 (t0) cc_final: 0.5773 (p0) REVERT: P 24 ARG cc_start: 0.8349 (ttp-110) cc_final: 0.8075 (ttm110) REVERT: B 99 TYR cc_start: 0.7074 (OUTLIER) cc_final: 0.6134 (m-10) REVERT: B 100 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7402 (mp0) REVERT: B 130 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7869 (mtm-85) REVERT: B 229 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8035 (pp20) REVERT: B 231 GLU cc_start: 0.8603 (mp0) cc_final: 0.8071 (mp0) REVERT: H 41 ARG cc_start: 0.6017 (ptp90) cc_final: 0.5675 (ptm160) REVERT: H 87 GLN cc_start: 0.5485 (tp40) cc_final: 0.4692 (pm20) REVERT: K 61 ASP cc_start: 0.6933 (p0) cc_final: 0.6562 (t0) REVERT: K 79 LEU cc_start: 0.6545 (tp) cc_final: 0.5854 (tt) REVERT: K 80 GLU cc_start: 0.5410 (mm-30) cc_final: 0.5034 (tp30) REVERT: E 551 GLN cc_start: 0.8162 (tp40) cc_final: 0.7873 (tp40) REVERT: E 565 THR cc_start: 0.8724 (p) cc_final: 0.8377 (t) REVERT: E 597 TRP cc_start: 0.6323 (m-90) cc_final: 0.5883 (m100) REVERT: N 3 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8487 (mp10) REVERT: N 6 GLU cc_start: 0.8237 (mp0) cc_final: 0.7617 (mp0) REVERT: N 17 THR cc_start: 0.8842 (m) cc_final: 0.8584 (p) REVERT: N 74 ASP cc_start: 0.6806 (t0) cc_final: 0.5886 (p0) REVERT: C 130 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7836 (mtm-85) REVERT: C 261 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.8032 (m-80) REVERT: I 33 LYS cc_start: 0.5218 (OUTLIER) cc_final: 0.4320 (mttm) REVERT: I 39 TRP cc_start: 0.6567 (m100) cc_final: 0.5842 (m100) REVERT: I 87 GLN cc_start: 0.6112 (tp40) cc_final: 0.5103 (pm20) REVERT: L 61 ASP cc_start: 0.7275 (p0) cc_final: 0.6973 (t0) REVERT: L 80 GLU cc_start: 0.5542 (mm-30) cc_final: 0.5173 (tp30) REVERT: L 90 HIS cc_start: 0.6517 (t-90) cc_final: 0.5490 (t70) REVERT: L 91 GLN cc_start: 0.6338 (pp30) cc_final: 0.6015 (pp30) REVERT: L 92 TYR cc_start: 0.4663 (OUTLIER) cc_final: 0.4449 (m-80) REVERT: F 597 TRP cc_start: 0.6311 (m-90) cc_final: 0.5826 (m100) REVERT: O 74 ASP cc_start: 0.6839 (t0) cc_final: 0.5942 (p0) REVERT: O 83 ARG cc_start: 0.7625 (ttm-80) cc_final: 0.7379 (ttm-80) REVERT: O 109 ARG cc_start: 0.7696 (ttm-80) cc_final: 0.7469 (ttm-80) REVERT: R 98 TYR cc_start: 0.8548 (m-80) cc_final: 0.8239 (m-80) outliers start: 72 outliers final: 46 residues processed: 428 average time/residue: 0.3512 time to fit residues: 220.1928 Evaluate side-chains 420 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 365 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 40 LYS Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 552 ASP Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 106 GLU Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 545 GLU Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 552 ASP Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 106 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 112 optimal weight: 0.4980 chunk 197 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN M 79 HIS P 79 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 79 HIS ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 43 GLN F 514 ASN F 516 HIS O 79 HIS R 79 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19194 Z= 0.275 Angle : 0.655 9.063 26088 Z= 0.325 Chirality : 0.047 0.276 2982 Planarity : 0.005 0.061 3282 Dihedral : 9.277 73.607 3423 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.35 % Favored : 96.48 % Rotamer: Outliers : 4.58 % Allowed : 13.33 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.18), residues: 2301 helix: 1.32 (0.39), residues: 180 sheet: -0.26 (0.17), residues: 1023 loop : -0.21 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP J 36 HIS 0.008 0.001 HIS O 79 PHE 0.015 0.001 PHE K 72 TYR 0.022 0.002 TYR G 100 ARG 0.012 0.001 ARG F 596 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 377 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.7167 (OUTLIER) cc_final: 0.5851 (m-10) REVERT: A 184 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8867 (pp) REVERT: A 231 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8113 (mp0) REVERT: A 261 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.8143 (m-80) REVERT: G 39 TRP cc_start: 0.6637 (m100) cc_final: 0.6055 (m100) REVERT: G 87 GLN cc_start: 0.5865 (tp40) cc_final: 0.5005 (pm20) REVERT: G 88 MET cc_start: 0.7410 (mtm) cc_final: 0.7145 (pmm) REVERT: J 32 LYS cc_start: 0.7864 (pttp) cc_final: 0.7662 (mmtt) REVERT: J 61 ASP cc_start: 0.7442 (p0) cc_final: 0.7008 (t0) REVERT: J 90 HIS cc_start: 0.6352 (t-90) cc_final: 0.5319 (t70) REVERT: D 551 GLN cc_start: 0.8454 (tp40) cc_final: 0.8212 (tp40) REVERT: D 565 THR cc_start: 0.8975 (p) cc_final: 0.8575 (t) REVERT: D 597 TRP cc_start: 0.6314 (m-90) cc_final: 0.5739 (m100) REVERT: M 6 GLU cc_start: 0.8352 (mp0) cc_final: 0.7946 (mp0) REVERT: M 17 THR cc_start: 0.8745 (m) cc_final: 0.8467 (t) REVERT: M 74 ASP cc_start: 0.6742 (t0) cc_final: 0.5887 (p0) REVERT: P 10 THR cc_start: 0.8896 (m) cc_final: 0.8626 (p) REVERT: B 99 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6249 (m-10) REVERT: B 100 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7478 (mp0) REVERT: B 130 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7925 (mtm-85) REVERT: B 231 GLU cc_start: 0.8646 (mp0) cc_final: 0.8121 (mp0) REVERT: H 33 LYS cc_start: 0.5194 (OUTLIER) cc_final: 0.4430 (mttm) REVERT: H 41 ARG cc_start: 0.5786 (ptp90) cc_final: 0.5525 (ptm160) REVERT: H 87 GLN cc_start: 0.5366 (tp40) cc_final: 0.4609 (pm20) REVERT: K 61 ASP cc_start: 0.7073 (p0) cc_final: 0.6767 (t0) REVERT: K 79 LEU cc_start: 0.6532 (tp) cc_final: 0.5811 (tt) REVERT: K 80 GLU cc_start: 0.5580 (mm-30) cc_final: 0.5208 (tp30) REVERT: K 90 HIS cc_start: 0.6739 (t-90) cc_final: 0.5901 (t70) REVERT: E 551 GLN cc_start: 0.8183 (tp40) cc_final: 0.7854 (tp40) REVERT: E 565 THR cc_start: 0.8688 (p) cc_final: 0.8395 (t) REVERT: E 597 TRP cc_start: 0.6400 (m-90) cc_final: 0.5935 (m100) REVERT: N 3 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8173 (mp10) REVERT: N 6 GLU cc_start: 0.8257 (mp0) cc_final: 0.7583 (mp0) REVERT: N 17 THR cc_start: 0.8856 (m) cc_final: 0.8540 (p) REVERT: C 130 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7861 (mtm-85) REVERT: C 261 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.8201 (m-80) REVERT: I 33 LYS cc_start: 0.5275 (OUTLIER) cc_final: 0.4427 (mttm) REVERT: I 39 TRP cc_start: 0.6455 (m100) cc_final: 0.6045 (m100) REVERT: I 87 GLN cc_start: 0.5888 (tp40) cc_final: 0.4864 (pm20) REVERT: L 61 ASP cc_start: 0.7251 (p0) cc_final: 0.6942 (t0) REVERT: L 80 GLU cc_start: 0.5599 (mm-30) cc_final: 0.5227 (tp30) REVERT: L 91 GLN cc_start: 0.6368 (pp30) cc_final: 0.6026 (pp30) REVERT: L 92 TYR cc_start: 0.4576 (OUTLIER) cc_final: 0.4279 (m-80) REVERT: F 587 ARG cc_start: 0.8280 (ttm110) cc_final: 0.7939 (mtp-110) REVERT: F 597 TRP cc_start: 0.6297 (m-90) cc_final: 0.5850 (m100) REVERT: O 6 GLU cc_start: 0.8440 (mp0) cc_final: 0.7958 (mp0) REVERT: O 74 ASP cc_start: 0.6962 (t0) cc_final: 0.5968 (p0) REVERT: O 75 THR cc_start: 0.8203 (p) cc_final: 0.7958 (t) REVERT: R 98 TYR cc_start: 0.8513 (m-80) cc_final: 0.8217 (m-80) outliers start: 90 outliers final: 63 residues processed: 427 average time/residue: 0.3321 time to fit residues: 207.1232 Evaluate side-chains 431 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 357 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 63 PHE Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 552 ASP Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain M residue 11 LEU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 106 GLU Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 63 PHE Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 545 GLU Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain F residue 510 LYS Chi-restraints excluded: chain F residue 514 ASN Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 552 ASP Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 81 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 0.7980 chunk 198 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN J 43 GLN M 78 ASN M 79 HIS ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 516 HIS N 79 HIS Q 27 GLN C 62 GLN L 43 GLN F 514 ASN O 79 HIS R 79 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 19194 Z= 0.503 Angle : 0.769 14.134 26088 Z= 0.384 Chirality : 0.051 0.299 2982 Planarity : 0.006 0.058 3282 Dihedral : 9.537 71.719 3423 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.78 % Favored : 96.05 % Rotamer: Outliers : 5.29 % Allowed : 13.08 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.69 (0.18), residues: 2301 helix: 1.01 (0.39), residues: 180 sheet: -0.56 (0.16), residues: 1029 loop : -0.44 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP J 36 HIS 0.005 0.002 HIS N 79 PHE 0.017 0.002 PHE J 72 TYR 0.025 0.002 TYR M 35 ARG 0.011 0.001 ARG F 596 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 366 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.6169 (m-10) REVERT: A 184 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.9000 (pp) REVERT: A 231 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: A 261 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8183 (m-80) REVERT: G 39 TRP cc_start: 0.6547 (m100) cc_final: 0.5807 (m100) REVERT: G 87 GLN cc_start: 0.5679 (tp40) cc_final: 0.4796 (pm20) REVERT: J 61 ASP cc_start: 0.7252 (p0) cc_final: 0.6796 (t0) REVERT: J 90 HIS cc_start: 0.6167 (t-90) cc_final: 0.5598 (t70) REVERT: D 551 GLN cc_start: 0.8565 (tp40) cc_final: 0.8228 (tp40) REVERT: D 565 THR cc_start: 0.8994 (p) cc_final: 0.8549 (t) REVERT: D 597 TRP cc_start: 0.6318 (m-90) cc_final: 0.5802 (m100) REVERT: M 6 GLU cc_start: 0.8407 (mp0) cc_final: 0.8080 (mp0) REVERT: M 17 THR cc_start: 0.8750 (m) cc_final: 0.8481 (t) REVERT: M 74 ASP cc_start: 0.6866 (t0) cc_final: 0.5999 (p0) REVERT: M 75 THR cc_start: 0.8402 (p) cc_final: 0.7999 (t) REVERT: P 10 THR cc_start: 0.8985 (m) cc_final: 0.8757 (p) REVERT: B 99 TYR cc_start: 0.7586 (OUTLIER) cc_final: 0.6708 (m-80) REVERT: B 100 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: B 130 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7884 (mtm-85) REVERT: B 184 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8979 (pt) REVERT: B 231 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8161 (mp0) REVERT: H 33 LYS cc_start: 0.4958 (OUTLIER) cc_final: 0.4048 (mttm) REVERT: K 61 ASP cc_start: 0.6928 (p0) cc_final: 0.6617 (t0) REVERT: K 79 LEU cc_start: 0.6451 (tp) cc_final: 0.5585 (tt) REVERT: K 80 GLU cc_start: 0.5592 (mm-30) cc_final: 0.5194 (tp30) REVERT: E 565 THR cc_start: 0.8605 (p) cc_final: 0.8259 (t) REVERT: E 597 TRP cc_start: 0.6522 (m-90) cc_final: 0.6083 (m100) REVERT: N 3 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8252 (mp10) REVERT: N 6 GLU cc_start: 0.8260 (mp0) cc_final: 0.7541 (mp0) REVERT: N 74 ASP cc_start: 0.6859 (t0) cc_final: 0.5909 (p0) REVERT: Q 70 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8149 (mm-30) REVERT: C 130 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7897 (mtm-85) REVERT: C 261 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.8202 (m-80) REVERT: I 33 LYS cc_start: 0.5353 (OUTLIER) cc_final: 0.4421 (mttm) REVERT: I 87 GLN cc_start: 0.5983 (tp40) cc_final: 0.4804 (pm20) REVERT: L 17 GLU cc_start: 0.7268 (mt-10) cc_final: 0.7020 (mm-30) REVERT: L 61 ASP cc_start: 0.7074 (p0) cc_final: 0.6789 (t0) REVERT: L 80 GLU cc_start: 0.5646 (mm-30) cc_final: 0.5237 (tp30) REVERT: L 91 GLN cc_start: 0.6267 (pp30) cc_final: 0.5934 (pp30) REVERT: L 92 TYR cc_start: 0.4506 (OUTLIER) cc_final: 0.4203 (m-80) REVERT: F 551 GLN cc_start: 0.8600 (tp40) cc_final: 0.8354 (tp40) REVERT: F 587 ARG cc_start: 0.8287 (ttm110) cc_final: 0.7939 (mtp-110) REVERT: F 597 TRP cc_start: 0.6421 (m-90) cc_final: 0.6021 (m100) REVERT: O 6 GLU cc_start: 0.8479 (mp0) cc_final: 0.7956 (mp0) REVERT: R 70 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7882 (mm-30) REVERT: R 98 TYR cc_start: 0.8586 (m-80) cc_final: 0.8308 (m-80) outliers start: 104 outliers final: 72 residues processed: 424 average time/residue: 0.3565 time to fit residues: 220.3461 Evaluate side-chains 440 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 354 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 63 PHE Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 92 TYR Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 552 ASP Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 78 ASN Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 106 GLU Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 106 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 33 LYS Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 113 PHE Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain F residue 510 LYS Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 552 ASP Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 106 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 185 optimal weight: 0.9980 chunk 123 optimal weight: 0.3980 chunk 219 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN M 78 ASN M 79 HIS N 79 HIS Q 27 GLN R 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19194 Z= 0.221 Angle : 0.654 12.988 26088 Z= 0.325 Chirality : 0.047 0.263 2982 Planarity : 0.005 0.057 3282 Dihedral : 8.970 66.904 3423 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.35 % Favored : 96.44 % Rotamer: Outliers : 3.87 % Allowed : 14.96 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.55 (0.18), residues: 2301 helix: 1.40 (0.39), residues: 180 sheet: -0.52 (0.16), residues: 1020 loop : -0.36 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP K 36 HIS 0.007 0.001 HIS N 79 PHE 0.017 0.001 PHE M 80 TYR 0.019 0.002 TYR L 50 ARG 0.010 0.001 ARG F 596 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 386 time to evaluate : 1.876 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: A 99 TYR cc_start: 0.7230 (OUTLIER) cc_final: 0.6018 (m-10) REVERT: A 184 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8875 (pp) REVERT: A 231 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8162 (mp0) REVERT: A 261 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: G 39 TRP cc_start: 0.6547 (m100) cc_final: 0.6129 (m100) REVERT: J 40 LYS cc_start: 0.5788 (mmmt) cc_final: 0.5359 (mmmt) REVERT: J 61 ASP cc_start: 0.7370 (p0) cc_final: 0.6958 (t0) REVERT: J 90 HIS cc_start: 0.6298 (t-90) cc_final: 0.5090 (t70) REVERT: D 551 GLN cc_start: 0.8537 (tp40) cc_final: 0.8176 (tp40) REVERT: D 565 THR cc_start: 0.8946 (p) cc_final: 0.8552 (t) REVERT: D 597 TRP cc_start: 0.6353 (m-90) cc_final: 0.5793 (m100) REVERT: M 6 GLU cc_start: 0.8393 (mp0) cc_final: 0.7927 (mp0) REVERT: M 17 THR cc_start: 0.8742 (m) cc_final: 0.8454 (t) REVERT: M 83 ARG cc_start: 0.7898 (ttm-80) cc_final: 0.7585 (ttm-80) REVERT: P 10 THR cc_start: 0.8947 (m) cc_final: 0.8715 (p) REVERT: B 99 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.6288 (m-10) REVERT: B 100 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: B 130 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7832 (mtm-85) REVERT: B 184 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8842 (pt) REVERT: B 231 GLU cc_start: 0.8682 (mp0) cc_final: 0.8143 (mp0) REVERT: H 33 LYS cc_start: 0.5114 (OUTLIER) cc_final: 0.4146 (mttm) REVERT: K 61 ASP cc_start: 0.6988 (p0) cc_final: 0.6665 (t0) REVERT: K 79 LEU cc_start: 0.6486 (tp) cc_final: 0.5716 (tt) REVERT: K 80 GLU cc_start: 0.5647 (mm-30) cc_final: 0.5275 (tp30) REVERT: K 90 HIS cc_start: 0.6521 (t-90) cc_final: 0.5493 (t70) REVERT: E 565 THR cc_start: 0.8665 (p) cc_final: 0.8383 (t) REVERT: E 597 TRP cc_start: 0.6471 (m-90) cc_final: 0.6012 (m100) REVERT: N 3 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8218 (mp10) REVERT: N 6 GLU cc_start: 0.8283 (mp0) cc_final: 0.7648 (mp0) REVERT: N 74 ASP cc_start: 0.6685 (t0) cc_final: 0.5816 (p0) REVERT: Q 70 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8050 (mm-30) REVERT: Q 103 ARG cc_start: 0.8750 (mmm-85) cc_final: 0.8411 (ttp80) REVERT: C 99 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.6864 (m-80) REVERT: C 231 GLU cc_start: 0.8020 (mp0) cc_final: 0.7770 (mp0) REVERT: C 261 TYR cc_start: 0.8714 (OUTLIER) cc_final: 0.8203 (m-80) REVERT: I 39 TRP cc_start: 0.6394 (m100) cc_final: 0.5861 (m100) REVERT: I 87 GLN cc_start: 0.5931 (tp40) cc_final: 0.4831 (pm20) REVERT: L 17 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6926 (mm-30) REVERT: L 61 ASP cc_start: 0.7162 (p0) cc_final: 0.6849 (t0) REVERT: L 80 GLU cc_start: 0.5717 (mm-30) cc_final: 0.5325 (tp30) REVERT: L 91 GLN cc_start: 0.6343 (pp30) cc_final: 0.5980 (pp30) REVERT: L 92 TYR cc_start: 0.4418 (OUTLIER) cc_final: 0.4151 (m-80) REVERT: F 587 ARG cc_start: 0.8218 (ttm110) cc_final: 0.7881 (mtp-110) REVERT: F 597 TRP cc_start: 0.6261 (m-90) cc_final: 0.5871 (m100) REVERT: O 6 GLU cc_start: 0.8501 (mp0) cc_final: 0.7970 (mp0) REVERT: R 98 TYR cc_start: 0.8526 (m-80) cc_final: 0.8212 (m-80) outliers start: 76 outliers final: 52 residues processed: 431 average time/residue: 0.3345 time to fit residues: 210.3916 Evaluate side-chains 435 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 371 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 48 LEU Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 552 ASP Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain D residue 577 THR Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 106 GLU Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 33 LYS Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 48 LEU Chi-restraints excluded: chain K residue 63 PHE Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 552 ASP Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 81 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 0.0000 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN M 79 HIS N 79 HIS L 43 GLN ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 19194 Z= 0.440 Angle : 0.745 11.276 26088 Z= 0.368 Chirality : 0.050 0.306 2982 Planarity : 0.005 0.055 3282 Dihedral : 9.106 63.388 3423 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.39 % Favored : 95.39 % Rotamer: Outliers : 4.78 % Allowed : 14.61 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.85 (0.18), residues: 2301 helix: 1.11 (0.39), residues: 180 sheet: -0.70 (0.16), residues: 1023 loop : -0.56 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP J 36 HIS 0.005 0.002 HIS N 79 PHE 0.016 0.002 PHE K 72 TYR 0.022 0.002 TYR O 35 ARG 0.009 0.001 ARG F 596 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 364 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.7598 (OUTLIER) cc_final: 0.6287 (m-10) REVERT: A 184 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8982 (pp) REVERT: A 231 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8193 (mp0) REVERT: A 261 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.8301 (m-80) REVERT: G 39 TRP cc_start: 0.6618 (m100) cc_final: 0.5781 (m100) REVERT: G 54 ILE cc_start: 0.4940 (OUTLIER) cc_final: 0.4667 (tt) REVERT: J 61 ASP cc_start: 0.7255 (p0) cc_final: 0.6815 (t0) REVERT: J 90 HIS cc_start: 0.6198 (t-90) cc_final: 0.5677 (t70) REVERT: D 551 GLN cc_start: 0.8543 (tp40) cc_final: 0.8161 (tp40) REVERT: D 565 THR cc_start: 0.9002 (p) cc_final: 0.8569 (t) REVERT: D 597 TRP cc_start: 0.6311 (m-90) cc_final: 0.5801 (m100) REVERT: M 6 GLU cc_start: 0.8413 (mp0) cc_final: 0.7903 (mp0) REVERT: M 74 ASP cc_start: 0.7170 (t0) cc_final: 0.5729 (p0) REVERT: M 83 ARG cc_start: 0.7926 (ttm-80) cc_final: 0.7658 (ttm-80) REVERT: P 4 MET cc_start: 0.7879 (mmm) cc_final: 0.7547 (mmm) REVERT: P 10 THR cc_start: 0.8951 (m) cc_final: 0.8745 (p) REVERT: B 99 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.6718 (m-10) REVERT: B 130 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7846 (mtm-85) REVERT: B 184 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8932 (pt) REVERT: B 231 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8159 (mp0) REVERT: K 61 ASP cc_start: 0.6964 (p0) cc_final: 0.6643 (t0) REVERT: K 79 LEU cc_start: 0.6513 (tp) cc_final: 0.5703 (tt) REVERT: K 80 GLU cc_start: 0.5595 (mm-30) cc_final: 0.5220 (tp30) REVERT: K 90 HIS cc_start: 0.6229 (t-90) cc_final: 0.5259 (t70) REVERT: E 565 THR cc_start: 0.8640 (p) cc_final: 0.8309 (t) REVERT: E 597 TRP cc_start: 0.6512 (m-90) cc_final: 0.6127 (m100) REVERT: N 3 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8268 (mp10) REVERT: N 6 GLU cc_start: 0.8285 (mp0) cc_final: 0.7604 (mp0) REVERT: N 74 ASP cc_start: 0.6776 (t0) cc_final: 0.5886 (p0) REVERT: Q 70 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8074 (mm-30) REVERT: C 130 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7882 (mtm-85) REVERT: C 231 GLU cc_start: 0.8150 (mp0) cc_final: 0.7903 (mp0) REVERT: C 261 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.8335 (m-80) REVERT: I 87 GLN cc_start: 0.5965 (tp40) cc_final: 0.4796 (pm20) REVERT: L 32 LYS cc_start: 0.8049 (ptmm) cc_final: 0.7762 (mmtt) REVERT: L 61 ASP cc_start: 0.7077 (p0) cc_final: 0.6754 (t0) REVERT: L 80 GLU cc_start: 0.5482 (mm-30) cc_final: 0.4990 (tp30) REVERT: L 91 GLN cc_start: 0.6367 (pp30) cc_final: 0.5973 (pp30) REVERT: L 92 TYR cc_start: 0.4442 (OUTLIER) cc_final: 0.4179 (m-80) REVERT: F 587 ARG cc_start: 0.8222 (ttm110) cc_final: 0.7910 (mtp-110) REVERT: F 597 TRP cc_start: 0.6408 (m-90) cc_final: 0.6009 (m100) REVERT: O 6 GLU cc_start: 0.8488 (mp0) cc_final: 0.7939 (mp0) REVERT: R 70 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8084 (mm-30) REVERT: R 98 TYR cc_start: 0.8580 (m-80) cc_final: 0.8251 (m-80) outliers start: 94 outliers final: 65 residues processed: 421 average time/residue: 0.3449 time to fit residues: 211.1006 Evaluate side-chains 428 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 351 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 63 PHE Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 552 ASP Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 106 GLU Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 63 PHE Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 113 PHE Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain F residue 510 LYS Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 552 ASP Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 81 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 1.9990 chunk 210 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 204 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN D 516 HIS M 79 HIS E 514 ASN N 79 HIS ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 19194 Z= 0.320 Angle : 0.706 9.799 26088 Z= 0.347 Chirality : 0.050 0.756 2982 Planarity : 0.005 0.054 3282 Dihedral : 8.794 59.704 3423 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.04 % Favored : 95.74 % Rotamer: Outliers : 4.43 % Allowed : 15.27 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.80 (0.18), residues: 2301 helix: 1.29 (0.39), residues: 180 sheet: -0.66 (0.16), residues: 1020 loop : -0.57 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP J 36 HIS 0.006 0.001 HIS N 79 PHE 0.023 0.002 PHE G 30 TYR 0.031 0.002 TYR G 85 ARG 0.010 0.001 ARG N 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 364 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.7654 (OUTLIER) cc_final: 0.6326 (m-10) REVERT: A 184 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8925 (pp) REVERT: A 231 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: A 261 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.8299 (m-80) REVERT: G 33 LYS cc_start: 0.4973 (OUTLIER) cc_final: 0.3891 (mmtp) REVERT: G 39 TRP cc_start: 0.6396 (m100) cc_final: 0.5310 (m100) REVERT: G 54 ILE cc_start: 0.5110 (OUTLIER) cc_final: 0.4825 (tt) REVERT: G 121 ASP cc_start: 0.6858 (t70) cc_final: 0.6199 (t70) REVERT: J 61 ASP cc_start: 0.7205 (p0) cc_final: 0.6757 (t0) REVERT: J 90 HIS cc_start: 0.6149 (t-90) cc_final: 0.5006 (t70) REVERT: D 551 GLN cc_start: 0.8549 (tp40) cc_final: 0.8154 (tp40) REVERT: D 565 THR cc_start: 0.8962 (p) cc_final: 0.8543 (t) REVERT: D 597 TRP cc_start: 0.6196 (m-90) cc_final: 0.5665 (m100) REVERT: M 6 GLU cc_start: 0.8407 (mp0) cc_final: 0.7951 (mp0) REVERT: M 74 ASP cc_start: 0.7068 (t0) cc_final: 0.5623 (p0) REVERT: M 83 ARG cc_start: 0.7906 (ttm-80) cc_final: 0.7625 (ttm-80) REVERT: P 10 THR cc_start: 0.8926 (m) cc_final: 0.8709 (p) REVERT: B 99 TYR cc_start: 0.7300 (OUTLIER) cc_final: 0.6446 (m-10) REVERT: B 130 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7837 (mtm-85) REVERT: B 184 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8863 (pt) REVERT: B 231 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: H 84 LEU cc_start: 0.7960 (pp) cc_final: 0.7714 (pp) REVERT: K 61 ASP cc_start: 0.6999 (p0) cc_final: 0.6647 (t0) REVERT: K 79 LEU cc_start: 0.6528 (tp) cc_final: 0.5717 (tt) REVERT: K 80 GLU cc_start: 0.5572 (mm-30) cc_final: 0.5218 (tp30) REVERT: K 90 HIS cc_start: 0.6209 (t-90) cc_final: 0.5232 (t70) REVERT: E 565 THR cc_start: 0.8713 (p) cc_final: 0.8406 (t) REVERT: E 597 TRP cc_start: 0.6499 (m-90) cc_final: 0.6084 (m100) REVERT: N 3 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8216 (mp10) REVERT: N 6 GLU cc_start: 0.8283 (mp0) cc_final: 0.7669 (mp0) REVERT: N 74 ASP cc_start: 0.6656 (t0) cc_final: 0.5789 (p0) REVERT: Q 70 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8101 (mm-30) REVERT: Q 103 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8278 (tmm-80) REVERT: C 99 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.6868 (m-80) REVERT: C 217 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8657 (t) REVERT: C 231 GLU cc_start: 0.8097 (mp0) cc_final: 0.7810 (mp0) REVERT: C 261 TYR cc_start: 0.8787 (OUTLIER) cc_final: 0.8262 (m-80) REVERT: I 87 GLN cc_start: 0.5939 (tp40) cc_final: 0.4807 (pm20) REVERT: L 32 LYS cc_start: 0.8054 (ptmm) cc_final: 0.7779 (mmtt) REVERT: L 61 ASP cc_start: 0.7124 (p0) cc_final: 0.6807 (t0) REVERT: L 80 GLU cc_start: 0.5605 (mm-30) cc_final: 0.5158 (tp30) REVERT: L 92 TYR cc_start: 0.4530 (OUTLIER) cc_final: 0.4206 (m-80) REVERT: F 587 ARG cc_start: 0.8211 (ttm110) cc_final: 0.7896 (mtp-110) REVERT: F 596 ARG cc_start: 0.7800 (mtt90) cc_final: 0.7379 (mtt90) REVERT: F 597 TRP cc_start: 0.6356 (m-90) cc_final: 0.5987 (m100) REVERT: O 6 GLU cc_start: 0.8503 (mp0) cc_final: 0.7920 (mp0) REVERT: R 70 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8045 (mm-30) outliers start: 87 outliers final: 65 residues processed: 417 average time/residue: 0.3432 time to fit residues: 208.9529 Evaluate side-chains 439 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 359 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 63 PHE Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 552 ASP Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 106 GLU Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 115 GLU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain E residue 514 ASN Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 103 ARG Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain F residue 510 LYS Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 552 ASP Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 77 LYS Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 143 optimal weight: 0.0370 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN M 79 HIS E 514 ASN N 79 HIS ** O 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19194 Z= 0.240 Angle : 0.679 9.844 26088 Z= 0.335 Chirality : 0.048 0.510 2982 Planarity : 0.005 0.056 3282 Dihedral : 8.303 59.802 3423 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.65 % Favored : 96.09 % Rotamer: Outliers : 3.92 % Allowed : 15.78 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 (0.18), residues: 2301 helix: 1.49 (0.39), residues: 180 sheet: -0.61 (0.16), residues: 1023 loop : -0.47 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP J 36 HIS 0.005 0.001 HIS M 79 PHE 0.019 0.001 PHE G 30 TYR 0.037 0.002 TYR G 85 ARG 0.012 0.001 ARG N 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4602 Ramachandran restraints generated. 2301 Oldfield, 0 Emsley, 2301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 376 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.6153 (m-10) REVERT: A 184 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8889 (pp) REVERT: A 231 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8082 (mp0) REVERT: A 261 TYR cc_start: 0.8757 (OUTLIER) cc_final: 0.8398 (m-80) REVERT: G 33 LYS cc_start: 0.5009 (OUTLIER) cc_final: 0.3932 (mmtp) REVERT: G 39 TRP cc_start: 0.6291 (m100) cc_final: 0.5292 (m100) REVERT: G 54 ILE cc_start: 0.5158 (OUTLIER) cc_final: 0.4857 (tt) REVERT: G 121 ASP cc_start: 0.6960 (t70) cc_final: 0.6349 (t70) REVERT: J 61 ASP cc_start: 0.7278 (p0) cc_final: 0.6865 (t0) REVERT: J 90 HIS cc_start: 0.6183 (t-90) cc_final: 0.5348 (t70) REVERT: D 551 GLN cc_start: 0.8435 (tp40) cc_final: 0.8059 (tp40) REVERT: D 565 THR cc_start: 0.8962 (p) cc_final: 0.8569 (t) REVERT: D 597 TRP cc_start: 0.6152 (m-90) cc_final: 0.5644 (m100) REVERT: M 6 GLU cc_start: 0.8414 (mp0) cc_final: 0.7965 (mp0) REVERT: M 74 ASP cc_start: 0.7020 (t0) cc_final: 0.5535 (p0) REVERT: M 83 ARG cc_start: 0.7881 (ttm-80) cc_final: 0.7614 (ttm-80) REVERT: P 70 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8173 (mm-30) REVERT: B 99 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.6393 (m-10) REVERT: B 130 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7866 (mtm-85) REVERT: B 231 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8124 (mp0) REVERT: H 84 LEU cc_start: 0.7948 (pp) cc_final: 0.7713 (pp) REVERT: K 61 ASP cc_start: 0.7071 (p0) cc_final: 0.6670 (t0) REVERT: K 79 LEU cc_start: 0.6699 (tp) cc_final: 0.5934 (tt) REVERT: K 80 GLU cc_start: 0.5908 (mm-30) cc_final: 0.5470 (tp30) REVERT: K 90 HIS cc_start: 0.6374 (t-90) cc_final: 0.5444 (t70) REVERT: E 565 THR cc_start: 0.8721 (p) cc_final: 0.8416 (t) REVERT: E 597 TRP cc_start: 0.6437 (m-90) cc_final: 0.6037 (m100) REVERT: N 3 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8218 (mp10) REVERT: N 6 GLU cc_start: 0.8285 (mp0) cc_final: 0.7724 (mp0) REVERT: N 74 ASP cc_start: 0.6696 (t0) cc_final: 0.5761 (p0) REVERT: Q 70 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8103 (mm-30) REVERT: Q 103 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8291 (tmm-80) REVERT: C 99 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.6858 (m-80) REVERT: C 130 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7819 (mtm-85) REVERT: C 217 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8594 (t) REVERT: C 231 GLU cc_start: 0.8037 (mp0) cc_final: 0.7787 (mp0) REVERT: C 261 TYR cc_start: 0.8742 (OUTLIER) cc_final: 0.8356 (m-80) REVERT: I 39 TRP cc_start: 0.6192 (m100) cc_final: 0.5382 (m100) REVERT: I 87 GLN cc_start: 0.5928 (tp40) cc_final: 0.4803 (pm20) REVERT: L 32 LYS cc_start: 0.8082 (ptmm) cc_final: 0.7791 (mmtt) REVERT: L 61 ASP cc_start: 0.7236 (p0) cc_final: 0.6917 (t0) REVERT: L 80 GLU cc_start: 0.5675 (mm-30) cc_final: 0.5250 (tp30) REVERT: L 92 TYR cc_start: 0.4483 (OUTLIER) cc_final: 0.4222 (m-80) REVERT: F 587 ARG cc_start: 0.8199 (ttm110) cc_final: 0.7894 (mtp-110) REVERT: F 597 TRP cc_start: 0.6284 (m-90) cc_final: 0.5935 (m100) REVERT: O 6 GLU cc_start: 0.8505 (mp0) cc_final: 0.7949 (mp0) REVERT: O 74 ASP cc_start: 0.7195 (t0) cc_final: 0.6599 (t0) REVERT: O 77 LYS cc_start: 0.7494 (mtmt) cc_final: 0.7266 (ptmt) REVERT: R 70 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8044 (mm-30) outliers start: 77 outliers final: 56 residues processed: 425 average time/residue: 0.3420 time to fit residues: 211.5974 Evaluate side-chains 434 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 363 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 89 CYS Chi-restraints excluded: chain D residue 544 THR Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 552 ASP Chi-restraints excluded: chain D residue 564 GLU Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 106 GLU Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain P residue 78 LEU Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 261 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain E residue 514 ASN Chi-restraints excluded: chain E residue 544 THR Chi-restraints excluded: chain E residue 552 ASP Chi-restraints excluded: chain E residue 577 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 119 THR Chi-restraints excluded: chain Q residue 78 LEU Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 103 ARG Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 261 TYR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain F residue 510 LYS Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 552 ASP Chi-restraints excluded: chain F residue 577 THR Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 81 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 26 optimal weight: 0.0970 chunk 50 optimal weight: 0.8980 chunk 181 optimal weight: 0.4980 chunk 75 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 22 optimal weight: 0.0170 chunk 33 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN M 79 HIS H 42 GLN K 39 GLN N 79 HIS O 78 ASN R 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.128354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.101508 restraints weight = 31435.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.100889 restraints weight = 75534.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.101514 restraints weight = 62831.985| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19194 Z= 0.184 Angle : 0.657 10.112 26088 Z= 0.322 Chirality : 0.046 0.372 2982 Planarity : 0.005 0.056 3282 Dihedral : 7.455 59.944 3423 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.00 % Favored : 96.74 % Rotamer: Outliers : 3.00 % Allowed : 16.49 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.53 (0.18), residues: 2301 helix: 1.76 (0.39), residues: 180 sheet: -0.51 (0.17), residues: 990 loop : -0.42 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP K 36 HIS 0.009 0.001 HIS O 79 PHE 0.025 0.001 PHE K 72 TYR 0.028 0.001 TYR G 85 ARG 0.012 0.001 ARG N 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4470.64 seconds wall clock time: 82 minutes 6.13 seconds (4926.13 seconds total)