Starting phenix.real_space_refine on Sat Aug 10 10:21:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v61_31732/08_2024/7v61_31732.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v61_31732/08_2024/7v61_31732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v61_31732/08_2024/7v61_31732.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v61_31732/08_2024/7v61_31732.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v61_31732/08_2024/7v61_31732.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v61_31732/08_2024/7v61_31732.cif" } resolution = 3.2 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= 0.004 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 152 5.16 5 C 18710 2.51 5 N 4696 2.21 5 O 5516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 57": "NH1" <-> "NH2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A GLU 568": "OE1" <-> "OE2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B GLU 37": "OE1" <-> "OE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B ARG 192": "NH1" <-> "NH2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B ARG 245": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B GLU 430": "OE1" <-> "OE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B ARG 518": "NH1" <-> "NH2" Residue "B ARG 671": "NH1" <-> "NH2" Residue "B ARG 678": "NH1" <-> "NH2" Residue "B ARG 716": "NH1" <-> "NH2" Residue "B ARG 768": "NH1" <-> "NH2" Residue "H ARG 104": "NH1" <-> "NH2" Residue "H TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 165": "OE1" <-> "OE2" Residue "K PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C GLU 157": "OE1" <-> "OE2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C GLU 405": "OE1" <-> "OE2" Residue "C GLU 568": "OE1" <-> "OE2" Residue "C ARG 607": "NH1" <-> "NH2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D GLU 231": "OE1" <-> "OE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D GLU 430": "OE1" <-> "OE2" Residue "D GLU 457": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D ARG 671": "NH1" <-> "NH2" Residue "D ARG 678": "NH1" <-> "NH2" Residue "D ARG 716": "NH1" <-> "NH2" Residue "D ARG 768": "NH1" <-> "NH2" Residue "I ARG 104": "NH1" <-> "NH2" Residue "I TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 165": "OE1" <-> "OE2" Residue "M PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 29076 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 4794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4794 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 31, 'TRANS': 573} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 6111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 6111 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 35, 'TRANS': 715} Chain: "H" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1712 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "K" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1652 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "C" Number of atoms: 4794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4794 Classifications: {'peptide': 605} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 31, 'TRANS': 573} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 6 Chain: "D" Number of atoms: 6111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 6111 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 35, 'TRANS': 715} Chain: "I" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1712 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 12, 'TRANS': 210} Chain: "M" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1652 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "E" 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: "F" 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: "G" 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 15.56, per 1000 atoms: 0.54 Number of scatterers: 29076 At special positions: 0 Unit cell: (194.937, 214.323, 200.322, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 152 16.00 O 5516 8.00 N 4696 7.00 C 18710 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 383 " distance=2.05 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 383 " distance=2.05 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 148 " - pdb=" SG CYS I 204 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 194 " 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG J 1 " - " NAG J 2 " " NAG L 1 " - " NAG L 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A 701 " - " ASN A 158 " " NAG A 702 " - " ASN A 182 " " NAG A 703 " - " ASN A 354 " " NAG A 704 " - " ASN A 368 " " NAG B 901 " - " ASN B 322 " " NAG C 701 " - " ASN C 158 " " NAG C 702 " - " ASN C 182 " " NAG C 703 " - " ASN C 354 " " NAG C 704 " - " ASN C 368 " " NAG D 901 " - " ASN D 322 " " NAG E 1 " - " ASN A 258 " " NAG F 1 " - " ASN B 53 " " NAG G 1 " - " ASN B 90 " " NAG J 1 " - " ASN B 103 " " NAG L 1 " - " ASN B 432 " " NAG N 1 " - " ASN B 546 " " NAG O 1 " - " ASN B 690 " " NAG P 1 " - " ASN C 258 " " NAG Q 1 " - " ASN D 53 " " NAG R 1 " - " ASN D 90 " " NAG S 1 " - " ASN D 103 " " NAG T 1 " - " ASN D 432 " " NAG U 1 " - " ASN D 546 " " NAG V 1 " - " ASN D 690 " Time building additional restraints: 12.09 Conformation dependent library (CDL) restraints added in 5.6 seconds 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6716 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 34 sheets defined 50.6% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 4.160A pdb=" N GLU A 25 " --> pdb=" O LEU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 50 removed outlier: 3.683A pdb=" N THR A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.561A pdb=" N GLN A 63 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 79 Processing helix chain 'A' and resid 81 through 97 removed outlier: 3.548A pdb=" N ILE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 removed outlier: 3.682A pdb=" N TRP A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 142 removed outlier: 3.667A pdb=" N LEU A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR A 128 " --> pdb=" O MET A 124 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 169 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.515A pdb=" N TRP A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.767A pdb=" N CYS A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 242 Proline residue: A 230 - end of helix removed outlier: 3.621A pdb=" N ILE A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.536A pdb=" N LEU A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 266 through 279 removed outlier: 3.698A pdb=" N ASP A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 299 through 349 removed outlier: 3.601A pdb=" N SER A 303 " --> pdb=" O CYS A 299 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR A 339 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 349 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 371 removed outlier: 3.775A pdb=" N CYS A 367 " --> pdb=" O MET A 363 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.553A pdb=" N ALA A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 441 removed outlier: 4.224A pdb=" N VAL A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 454 through 470 removed outlier: 3.741A pdb=" N LEU A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A 459 " --> pdb=" O LYS A 455 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 467 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 475 Processing helix chain 'A' and resid 477 through 507 removed outlier: 3.539A pdb=" N TRP A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 485 " --> pdb=" O TRP A 481 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER A 487 " --> pdb=" O SER A 483 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Proline residue: A 493 - end of helix removed outlier: 3.642A pdb=" N CYS A 500 " --> pdb=" O ILE A 496 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 523 removed outlier: 3.520A pdb=" N LYS A 516 " --> pdb=" O ASP A 512 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 536 Processing helix chain 'A' and resid 536 through 553 removed outlier: 3.564A pdb=" N LEU A 543 " --> pdb=" O PRO A 539 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE A 550 " --> pdb=" O PHE A 546 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 551 " --> pdb=" O LEU A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 608 removed outlier: 4.117A pdb=" N VAL A 585 " --> pdb=" O TRP A 581 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Proline residue: A 593 - end of helix removed outlier: 4.670A pdb=" N ILE A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) Proline residue: A 598 - end of helix removed outlier: 3.952A pdb=" N ALA A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN A 608 " --> pdb=" O LYS A 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 53 removed outlier: 3.512A pdb=" N GLU B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 79 removed outlier: 3.688A pdb=" N MET B 62 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 83 removed outlier: 3.589A pdb=" N TYR B 83 " --> pdb=" O ALA B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 83' Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.505A pdb=" N GLN B 96 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN B 102 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.551A pdb=" N SER B 106 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL B 107 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 108 " --> pdb=" O SER B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'B' and resid 109 through 130 removed outlier: 3.533A pdb=" N ASN B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 155 removed outlier: 3.631A pdb=" N MET B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 193 Proline residue: B 178 - end of helix removed outlier: 3.884A pdb=" N GLU B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 204 Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 220 through 231 removed outlier: 3.704A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 249 removed outlier: 3.556A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 278 through 283 Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 305 through 317 removed outlier: 3.519A pdb=" N PHE B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 317 " --> pdb=" O LYS B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 383 removed outlier: 3.533A pdb=" N HIS B 373 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS B 378 " --> pdb=" O HIS B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.551A pdb=" N ALA B 387 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'B' and resid 400 through 413 removed outlier: 3.632A pdb=" N GLY B 405 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 411 " --> pdb=" O ILE B 407 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 413 " --> pdb=" O SER B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 433 through 444 removed outlier: 3.655A pdb=" N LYS B 441 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 449 through 465 Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.744A pdb=" N TRP B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 502 removed outlier: 3.512A pdb=" N SER B 502 " --> pdb=" O ASP B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 513 through 533 removed outlier: 3.647A pdb=" N THR B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 removed outlier: 3.662A pdb=" N LYS B 541 " --> pdb=" O PRO B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.854A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 572 removed outlier: 3.628A pdb=" N GLU B 571 " --> pdb=" O THR B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 588 through 599 removed outlier: 3.643A pdb=" N TRP B 594 " --> pdb=" O PRO B 590 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 597 " --> pdb=" O THR B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 628 removed outlier: 3.824A pdb=" N ALA B 627 " --> pdb=" O SER B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 658 removed outlier: 3.510A pdb=" N MET B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 696 through 707 removed outlier: 3.506A pdb=" N LYS B 702 " --> pdb=" O THR B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 715 removed outlier: 3.678A pdb=" N ASP B 713 " --> pdb=" O SER B 709 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 714 " --> pdb=" O ARG B 710 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE B 715 " --> pdb=" O ILE B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 768 removed outlier: 3.553A pdb=" N VAL B 745 " --> pdb=" O ILE B 741 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL B 752 " --> pdb=" O VAL B 748 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 754 " --> pdb=" O MET B 750 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE B 759 " --> pdb=" O VAL B 755 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 760 " --> pdb=" O GLY B 756 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 56 removed outlier: 3.749A pdb=" N ASP H 56 " --> pdb=" O PRO H 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 53 through 56' Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'K' and resid 121 through 128 Processing helix chain 'K' and resid 183 through 187 Processing helix chain 'C' and resid 20 through 25 removed outlier: 4.160A pdb=" N GLU C 25 " --> pdb=" O LEU C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.683A pdb=" N THR C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 removed outlier: 3.561A pdb=" N GLN C 63 " --> pdb=" O PRO C 59 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 79 Processing helix chain 'C' and resid 81 through 97 removed outlier: 3.548A pdb=" N ILE C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY C 93 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN C 94 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 105 removed outlier: 3.682A pdb=" N TRP C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 142 removed outlier: 3.667A pdb=" N LEU C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR C 128 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN C 130 " --> pdb=" O GLY C 126 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 133 " --> pdb=" O TYR C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 169 Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.515A pdb=" N TRP C 176 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 212 removed outlier: 3.767A pdb=" N CYS C 211 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 242 Proline residue: C 230 - end of helix removed outlier: 3.621A pdb=" N ILE C 239 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 255 removed outlier: 3.536A pdb=" N LEU C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 266 through 279 removed outlier: 3.698A pdb=" N ASP C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL C 275 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 291 Processing helix chain 'C' and resid 299 through 349 removed outlier: 3.601A pdb=" N SER C 303 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 314 " --> pdb=" O ASN C 310 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL C 315 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 318 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR C 339 " --> pdb=" O ASP C 335 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU C 344 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP C 349 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 371 removed outlier: 3.775A pdb=" N CYS C 367 " --> pdb=" O MET C 363 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN C 368 " --> pdb=" O GLN C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.553A pdb=" N ALA C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 441 removed outlier: 4.224A pdb=" N VAL C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET C 423 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL C 441 " --> pdb=" O GLU C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 Processing helix chain 'C' and resid 454 through 470 removed outlier: 3.741A pdb=" N LEU C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR C 459 " --> pdb=" O LYS C 455 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE C 467 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 468 " --> pdb=" O LEU C 464 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 475 Processing helix chain 'C' and resid 477 through 507 removed outlier: 3.539A pdb=" N TRP C 481 " --> pdb=" O SER C 477 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 485 " --> pdb=" O TRP C 481 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N SER C 487 " --> pdb=" O SER C 483 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR C 488 " --> pdb=" O LEU C 484 " (cutoff:3.500A) Proline residue: C 493 - end of helix removed outlier: 3.642A pdb=" N CYS C 500 " --> pdb=" O ILE C 496 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 506 " --> pdb=" O MET C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 523 removed outlier: 3.520A pdb=" N LYS C 516 " --> pdb=" O ASP C 512 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET C 521 " --> pdb=" O ASP C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 536 Processing helix chain 'C' and resid 536 through 553 removed outlier: 3.564A pdb=" N LEU C 543 " --> pdb=" O PRO C 539 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 545 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE C 546 " --> pdb=" O MET C 542 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE C 550 " --> pdb=" O PHE C 546 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 608 removed outlier: 4.117A pdb=" N VAL C 585 " --> pdb=" O TRP C 581 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) Proline residue: C 593 - end of helix removed outlier: 4.670A pdb=" N ILE C 597 " --> pdb=" O PRO C 593 " (cutoff:3.500A) Proline residue: C 598 - end of helix removed outlier: 3.952A pdb=" N ALA C 601 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 605 " --> pdb=" O ALA C 601 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN C 608 " --> pdb=" O LYS C 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 53 removed outlier: 3.512A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 79 removed outlier: 3.688A pdb=" N MET D 62 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 83 removed outlier: 3.589A pdb=" N TYR D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 80 through 83' Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.505A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.551A pdb=" N SER D 106 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'D' and resid 109 through 130 removed outlier: 3.533A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER D 128 " --> pdb=" O SER D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 155 removed outlier: 3.631A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 193 Proline residue: D 178 - end of helix removed outlier: 3.884A pdb=" N GLU D 189 " --> pdb=" O VAL D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 220 through 231 removed outlier: 3.704A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 removed outlier: 3.556A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 295 through 300 Processing helix chain 'D' and resid 305 through 317 removed outlier: 3.519A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER D 317 " --> pdb=" O LYS D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.533A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 removed outlier: 4.551A pdb=" N ALA D 387 " --> pdb=" O ALA D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 400 through 413 removed outlier: 3.632A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D 413 " --> pdb=" O SER D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 419 Processing helix chain 'D' and resid 433 through 444 removed outlier: 3.655A pdb=" N LYS D 441 " --> pdb=" O ASN D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 448 No H-bonds generated for 'chain 'D' and resid 446 through 448' Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.744A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 removed outlier: 3.512A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.647A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.662A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.854A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.628A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.643A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 628 removed outlier: 3.824A pdb=" N ALA D 627 " --> pdb=" O SER D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 658 removed outlier: 3.510A pdb=" N MET D 640 " --> pdb=" O ASN D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 668 No H-bonds generated for 'chain 'D' and resid 666 through 668' Processing helix chain 'D' and resid 696 through 707 removed outlier: 3.506A pdb=" N LYS D 702 " --> pdb=" O THR D 698 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 715 removed outlier: 3.678A pdb=" N ASP D 713 " --> pdb=" O SER D 709 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D 714 " --> pdb=" O ARG D 710 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE D 715 " --> pdb=" O ILE D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 768 removed outlier: 3.553A pdb=" N VAL D 745 " --> pdb=" O ILE D 741 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL D 752 " --> pdb=" O VAL D 748 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL D 754 " --> pdb=" O MET D 750 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE D 759 " --> pdb=" O VAL D 755 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU D 760 " --> pdb=" O GLY D 756 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 56 removed outlier: 3.749A pdb=" N ASP I 56 " --> pdb=" O PRO I 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 53 through 56' Processing helix chain 'I' and resid 195 through 197 No H-bonds generated for 'chain 'I' and resid 195 through 197' Processing helix chain 'M' and resid 121 through 128 Processing helix chain 'M' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'B' and resid 262 through 263 removed outlier: 6.048A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 670 through 676 removed outlier: 3.944A pdb=" N LEU B 675 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER B 680 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP B 693 " --> pdb=" O ALA B 687 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 670 through 676 removed outlier: 3.944A pdb=" N LEU B 675 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER B 680 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA8, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.933A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N CYS H 96 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TRP H 111 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG H 98 " --> pdb=" O ASP H 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.933A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.008A pdb=" N ALA H 145 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL H 192 " --> pdb=" O ALA H 145 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY H 147 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL H 190 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 149 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 188 " --> pdb=" O LEU H 149 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS H 151 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 186 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 128 through 132 removed outlier: 5.008A pdb=" N ALA H 145 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL H 192 " --> pdb=" O ALA H 145 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY H 147 " --> pdb=" O VAL H 190 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL H 190 " --> pdb=" O GLY H 147 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU H 149 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 188 " --> pdb=" O LEU H 149 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS H 151 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 186 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 158 through 162 Processing sheet with id=AB4, first strand: chain 'K' and resid 5 through 6 removed outlier: 3.545A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 10 through 11 Processing sheet with id=AB6, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.367A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 114 through 118 Processing sheet with id=AB8, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AB9, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AC1, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.048A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AC3, first strand: chain 'D' and resid 670 through 676 removed outlier: 3.944A pdb=" N LEU D 675 " --> pdb=" O SER D 680 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER D 680 " --> pdb=" O LEU D 675 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASP D 693 " --> pdb=" O ALA D 687 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 670 through 676 removed outlier: 3.944A pdb=" N LEU D 675 " --> pdb=" O SER D 680 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER D 680 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AC6, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AC7, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.933A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N CYS I 96 " --> pdb=" O TRP I 111 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TRP I 111 " --> pdb=" O CYS I 96 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARG I 98 " --> pdb=" O ASP I 109 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.933A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 128 through 132 removed outlier: 5.008A pdb=" N ALA I 145 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL I 192 " --> pdb=" O ALA I 145 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY I 147 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL I 190 " --> pdb=" O GLY I 147 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 149 " --> pdb=" O SER I 188 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 188 " --> pdb=" O LEU I 149 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS I 151 " --> pdb=" O LEU I 186 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU I 186 " --> pdb=" O LYS I 151 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 128 through 132 removed outlier: 5.008A pdb=" N ALA I 145 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL I 192 " --> pdb=" O ALA I 145 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY I 147 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL I 190 " --> pdb=" O GLY I 147 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 149 " --> pdb=" O SER I 188 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 188 " --> pdb=" O LEU I 149 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS I 151 " --> pdb=" O LEU I 186 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU I 186 " --> pdb=" O LYS I 151 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 158 through 162 Processing sheet with id=AD3, first strand: chain 'M' and resid 5 through 6 removed outlier: 3.545A pdb=" N PHE M 71 " --> pdb=" O CYS M 23 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 10 through 11 Processing sheet with id=AD5, first strand: chain 'M' and resid 45 through 48 removed outlier: 6.367A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 114 through 118 Processing sheet with id=AD7, first strand: chain 'M' and resid 153 through 154 1274 hydrogen bonds defined for protein. 3618 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: 10.22 Time building geometry restraints manager: 13.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8406 1.33 - 1.46: 8202 1.46 - 1.59: 12996 1.59 - 1.72: 0 1.72 - 1.85: 240 Bond restraints: 29844 Sorted by residual: bond pdb=" C ILE A 492 " pdb=" N PRO A 493 " ideal model delta sigma weight residual 1.335 1.401 -0.066 1.38e-02 5.25e+03 2.29e+01 bond pdb=" C ILE C 492 " pdb=" N PRO C 493 " ideal model delta sigma weight residual 1.335 1.401 -0.066 1.38e-02 5.25e+03 2.29e+01 bond pdb=" N PRO C 493 " pdb=" CD PRO C 493 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.19e+01 bond pdb=" N PRO A 493 " pdb=" CD PRO A 493 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.19e+01 bond pdb=" C SER A 170 " pdb=" N PRO A 171 " ideal model delta sigma weight residual 1.336 1.392 -0.056 1.23e-02 6.61e+03 2.10e+01 ... (remaining 29839 not shown) Histogram of bond angle deviations from ideal: 98.78 - 106.69: 1004 106.69 - 114.61: 17350 114.61 - 122.53: 18440 122.53 - 130.45: 3628 130.45 - 138.37: 194 Bond angle restraints: 40616 Sorted by residual: angle pdb=" N LEU A 485 " pdb=" CA LEU A 485 " pdb=" C LEU A 485 " ideal model delta sigma weight residual 111.28 121.07 -9.79 1.09e+00 8.42e-01 8.07e+01 angle pdb=" N LEU C 485 " pdb=" CA LEU C 485 " pdb=" C LEU C 485 " ideal model delta sigma weight residual 111.28 121.07 -9.79 1.09e+00 8.42e-01 8.07e+01 angle pdb=" C ILE A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.24 112.45 6.79 1.04e+00 9.25e-01 4.26e+01 angle pdb=" C ILE C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.24 112.45 6.79 1.04e+00 9.25e-01 4.26e+01 angle pdb=" N MET C 71 " pdb=" CA MET C 71 " pdb=" C MET C 71 " ideal model delta sigma weight residual 111.07 104.39 6.68 1.07e+00 8.73e-01 3.90e+01 ... (remaining 40611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 16062 17.97 - 35.95: 1466 35.95 - 53.92: 404 53.92 - 71.89: 92 71.89 - 89.87: 36 Dihedral angle restraints: 18060 sinusoidal: 7600 harmonic: 10460 Sorted by residual: dihedral pdb=" CB CYS B 344 " pdb=" SG CYS B 344 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 135.97 -42.97 1 1.00e+01 1.00e-02 2.58e+01 dihedral pdb=" CB CYS D 344 " pdb=" SG CYS D 344 " pdb=" SG CYS D 361 " pdb=" CB CYS D 361 " ideal model delta sinusoidal sigma weight residual 93.00 135.97 -42.97 1 1.00e+01 1.00e-02 2.58e+01 dihedral pdb=" CA ILE C 576 " pdb=" C ILE C 576 " pdb=" N SER C 577 " pdb=" CA SER C 577 " ideal model delta harmonic sigma weight residual 180.00 154.71 25.29 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 18057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 4518 0.197 - 0.394: 34 0.394 - 0.591: 8 0.591 - 0.788: 0 0.788 - 0.986: 4 Chirality restraints: 4564 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-02 2.50e+03 2.24e+03 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-02 2.50e+03 2.24e+03 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 6.91e+01 ... (remaining 4561 not shown) Planarity restraints: 5138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 103 " -0.041 2.00e-02 2.50e+03 4.79e-02 2.87e+01 pdb=" CG ASN B 103 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN B 103 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 103 " 0.078 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 103 " -0.041 2.00e-02 2.50e+03 4.79e-02 2.87e+01 pdb=" CG ASN D 103 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN D 103 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN D 103 " 0.078 2.00e-02 2.50e+03 pdb=" C1 NAG S 1 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 492 " -0.068 5.00e-02 4.00e+02 9.96e-02 1.59e+01 pdb=" N PRO A 493 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO A 493 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 493 " -0.059 5.00e-02 4.00e+02 ... (remaining 5135 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 294 2.57 - 3.15: 22710 3.15 - 3.73: 44541 3.73 - 4.32: 63463 4.32 - 4.90: 104591 Nonbonded interactions: 235599 Sorted by model distance: nonbonded pdb=" O ASN H 31 " pdb=" ND1 HIS H 32 " model vdw 1.986 3.120 nonbonded pdb=" O ASN I 31 " pdb=" ND1 HIS I 32 " model vdw 1.986 3.120 nonbonded pdb=" O ASN K 137 " pdb=" O ASN K 138 " model vdw 2.038 3.040 nonbonded pdb=" O ASN M 137 " pdb=" O ASN M 138 " model vdw 2.038 3.040 nonbonded pdb=" O GLN D 18 " pdb=" OG SER D 19 " model vdw 2.117 3.040 ... (remaining 235594 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'K' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 0.030 Extract box with map and model: 1.240 Check model and map are aligned: 0.210 Set scattering table: 0.280 Process input model: 77.500 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 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 : 0.007 0.073 29844 Z= 0.430 Angle : 0.972 13.369 40616 Z= 0.572 Chirality : 0.068 0.986 4564 Planarity : 0.007 0.100 5114 Dihedral : 15.530 89.865 11290 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 1.90 % Allowed : 9.30 % Favored : 88.80 % Rotamer: Outliers : 5.08 % Allowed : 8.89 % Favored : 86.02 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.19 (0.11), residues: 3570 helix: -4.31 (0.06), residues: 1606 sheet: -1.35 (0.22), residues: 454 loop : -2.92 (0.14), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP H 99 HIS 0.006 0.001 HIS H 208 PHE 0.015 0.002 PHE B 683 TYR 0.022 0.002 TYR C 560 ARG 0.005 0.000 ARG C 366 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 539 time to evaluate : 3.037 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: A 352 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6053 (tp30) REVERT: A 386 ASN cc_start: 0.6477 (m110) cc_final: 0.6133 (t0) REVERT: A 430 SER cc_start: 0.6194 (OUTLIER) cc_final: 0.5958 (m) REVERT: B 171 GLU cc_start: 0.5068 (OUTLIER) cc_final: 0.4532 (mt-10) REVERT: B 175 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7419 (mm-40) REVERT: B 678 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.5412 (tpt170) REVERT: H 31 ASN cc_start: 0.8328 (t0) cc_final: 0.7884 (t0) REVERT: H 64 PHE cc_start: 0.6345 (m-80) cc_final: 0.5783 (m-10) REVERT: H 152 ASP cc_start: 0.7694 (m-30) cc_final: 0.7445 (p0) REVERT: H 163 ASN cc_start: 0.5792 (m-40) cc_final: 0.5391 (t0) REVERT: H 164 SER cc_start: 0.6974 (OUTLIER) cc_final: 0.6408 (p) REVERT: H 174 PHE cc_start: -0.0343 (m-80) cc_final: -0.0756 (m-80) REVERT: H 222 LYS cc_start: -0.1379 (OUTLIER) cc_final: -0.2080 (mtmm) REVERT: K 70 ASP cc_start: 0.6493 (m-30) cc_final: 0.6232 (p0) REVERT: K 98 PHE cc_start: 0.6008 (m-80) cc_final: 0.5685 (m-10) REVERT: C 352 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6052 (tp30) REVERT: C 386 ASN cc_start: 0.6479 (m110) cc_final: 0.6136 (t0) REVERT: C 430 SER cc_start: 0.6198 (OUTLIER) cc_final: 0.5961 (m) REVERT: D 171 GLU cc_start: 0.5070 (OUTLIER) cc_final: 0.4535 (mt-10) REVERT: D 175 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7418 (mm-40) REVERT: D 678 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.5410 (tpt170) REVERT: I 31 ASN cc_start: 0.8329 (t0) cc_final: 0.7885 (t0) REVERT: I 64 PHE cc_start: 0.6339 (m-80) cc_final: 0.5774 (m-10) REVERT: I 152 ASP cc_start: 0.7690 (m-30) cc_final: 0.7439 (p0) REVERT: I 163 ASN cc_start: 0.5795 (m-40) cc_final: 0.5395 (t0) REVERT: I 164 SER cc_start: 0.6976 (OUTLIER) cc_final: 0.6413 (p) REVERT: I 174 PHE cc_start: -0.0348 (m-80) cc_final: -0.0758 (m-80) REVERT: I 222 LYS cc_start: -0.1384 (OUTLIER) cc_final: -0.2083 (mtmm) REVERT: M 70 ASP cc_start: 0.6499 (m-30) cc_final: 0.6237 (p0) REVERT: M 98 PHE cc_start: 0.6008 (m-80) cc_final: 0.5688 (m-10) outliers start: 160 outliers final: 26 residues processed: 667 average time/residue: 0.4223 time to fit residues: 443.0446 Evaluate side-chains 319 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 279 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 678 ARG Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 211 SER Chi-restraints excluded: chain H residue 222 LYS Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain K residue 142 ARG Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 763 THR Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 211 SER Chi-restraints excluded: chain I residue 222 LYS Chi-restraints excluded: chain I residue 223 SER Chi-restraints excluded: chain M residue 142 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 chunk 149 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 182 optimal weight: 8.9990 chunk 144 optimal weight: 8.9990 chunk 279 optimal weight: 0.0370 chunk 107 optimal weight: 4.9990 chunk 169 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 323 optimal weight: 3.9990 overall best weight: 2.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 94 GLN A 293 ASN A 297 ASN ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN A 574 GLN B 24 GLN B 33 ASN B 61 ASN B 101 GLN B 117 ASN B 139 GLN B 175 GLN B 194 ASN B 239 HIS B 250 ASN B 277 ASN B 373 HIS B 505 HIS B 586 ASN B 599 ASN ** H 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN C 94 GLN C 293 ASN C 297 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 GLN C 574 GLN D 24 GLN D 33 ASN D 61 ASN D 101 GLN D 117 ASN D 139 GLN D 175 GLN D 194 ASN D 239 HIS D 250 ASN D 277 ASN D 373 HIS D 505 HIS D 586 ASN D 599 ASN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 ASN ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 29844 Z= 0.295 Angle : 0.770 11.406 40616 Z= 0.394 Chirality : 0.049 0.474 4564 Planarity : 0.006 0.051 5114 Dihedral : 8.197 71.209 4744 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.39 % Favored : 92.21 % Rotamer: Outliers : 3.49 % Allowed : 13.34 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.12), residues: 3570 helix: -2.00 (0.11), residues: 1674 sheet: -0.58 (0.22), residues: 480 loop : -2.69 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP I 99 HIS 0.007 0.001 HIS I 33 PHE 0.020 0.002 PHE I 29 TYR 0.018 0.002 TYR D 158 ARG 0.004 0.001 ARG B 559 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 307 time to evaluate : 3.383 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: A 403 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7731 (m-80) REVERT: A 608 ASN cc_start: 0.5022 (p0) cc_final: 0.3519 (m110) REVERT: B 171 GLU cc_start: 0.5618 (OUTLIER) cc_final: 0.5148 (mm-30) REVERT: B 325 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7689 (tm-30) REVERT: H 31 ASN cc_start: 0.8106 (t0) cc_final: 0.7822 (t0) REVERT: H 37 MET cc_start: 0.7463 (mpp) cc_final: 0.6857 (mpp) REVERT: H 74 ARG cc_start: 0.6385 (ttm110) cc_final: 0.6068 (mtm180) REVERT: H 90 ASP cc_start: 0.6738 (m-30) cc_final: 0.6500 (m-30) REVERT: H 163 ASN cc_start: 0.6362 (m-40) cc_final: 0.5716 (t0) REVERT: K 70 ASP cc_start: 0.6461 (m-30) cc_final: 0.6225 (p0) REVERT: K 79 GLU cc_start: 0.2903 (mt-10) cc_final: 0.2427 (mt-10) REVERT: K 98 PHE cc_start: 0.5942 (m-80) cc_final: 0.5581 (m-80) REVERT: C 403 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7733 (m-80) REVERT: C 608 ASN cc_start: 0.5024 (p0) cc_final: 0.3521 (m110) REVERT: D 171 GLU cc_start: 0.5615 (OUTLIER) cc_final: 0.5144 (mm-30) REVERT: D 325 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7689 (tm-30) REVERT: I 31 ASN cc_start: 0.8104 (t0) cc_final: 0.7821 (t0) REVERT: I 37 MET cc_start: 0.7469 (mpp) cc_final: 0.6854 (mpp) REVERT: I 74 ARG cc_start: 0.6381 (ttm110) cc_final: 0.6064 (mtm180) REVERT: I 90 ASP cc_start: 0.6738 (m-30) cc_final: 0.6507 (m-30) REVERT: I 163 ASN cc_start: 0.6360 (m-40) cc_final: 0.5718 (t0) REVERT: M 70 ASP cc_start: 0.6468 (m-30) cc_final: 0.6230 (p0) REVERT: M 79 GLU cc_start: 0.2907 (mt-10) cc_final: 0.2433 (mt-10) REVERT: M 98 PHE cc_start: 0.5941 (m-80) cc_final: 0.5575 (m-80) outliers start: 110 outliers final: 54 residues processed: 399 average time/residue: 0.3977 time to fit residues: 254.6301 Evaluate side-chains 302 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 244 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 143 THR Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 142 ARG Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 403 PHE Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 175 GLN Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain I residue 100 ARG Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 223 SER Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 142 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 179 optimal weight: 1.9990 chunk 100 optimal weight: 0.0970 chunk 269 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 323 optimal weight: 5.9990 chunk 349 optimal weight: 30.0000 chunk 288 optimal weight: 0.7980 chunk 321 optimal weight: 20.0000 chunk 110 optimal weight: 0.6980 chunk 259 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 ASN ** H 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29844 Z= 0.206 Angle : 0.675 11.835 40616 Z= 0.341 Chirality : 0.045 0.398 4564 Planarity : 0.004 0.053 5114 Dihedral : 7.045 69.313 4708 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.89 % Favored : 92.77 % Rotamer: Outliers : 2.86 % Allowed : 14.99 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.13), residues: 3570 helix: -0.74 (0.12), residues: 1666 sheet: -0.46 (0.22), residues: 510 loop : -2.44 (0.15), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 99 HIS 0.015 0.001 HIS K 198 PHE 0.021 0.001 PHE H 154 TYR 0.032 0.001 TYR C 578 ARG 0.008 0.001 ARG C 513 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 258 time to evaluate : 2.999 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: A 403 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7897 (m-80) REVERT: H 31 ASN cc_start: 0.8126 (t0) cc_final: 0.7854 (t0) REVERT: H 154 PHE cc_start: 0.6193 (t80) cc_final: 0.5524 (t80) REVERT: H 163 ASN cc_start: 0.6466 (m-40) cc_final: 0.5955 (t0) REVERT: K 79 GLU cc_start: 0.2898 (mt-10) cc_final: 0.2562 (mt-10) REVERT: K 98 PHE cc_start: 0.6105 (m-80) cc_final: 0.5619 (m-80) REVERT: C 403 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: I 31 ASN cc_start: 0.8121 (t0) cc_final: 0.7852 (t0) REVERT: I 154 PHE cc_start: 0.6197 (t80) cc_final: 0.5530 (t80) REVERT: I 163 ASN cc_start: 0.6469 (m-40) cc_final: 0.5959 (t0) REVERT: M 79 GLU cc_start: 0.2904 (mt-10) cc_final: 0.2564 (mt-10) REVERT: M 98 PHE cc_start: 0.6101 (m-80) cc_final: 0.5617 (m-80) outliers start: 90 outliers final: 54 residues processed: 334 average time/residue: 0.4086 time to fit residues: 219.6586 Evaluate side-chains 290 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 234 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 99 TRP Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 142 ARG Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 403 PHE Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 762 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 99 TRP Chi-restraints excluded: chain I residue 100 ARG Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 106 ILE Chi-restraints excluded: chain M residue 142 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 7.9990 chunk 243 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 154 optimal weight: 0.3980 chunk 217 optimal weight: 0.3980 chunk 325 optimal weight: 40.0000 chunk 344 optimal weight: 7.9990 chunk 169 optimal weight: 0.7980 chunk 308 optimal weight: 4.9990 chunk 92 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 175 GLN ** H 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN D 175 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 179 GLN ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29844 Z= 0.164 Angle : 0.628 9.617 40616 Z= 0.315 Chirality : 0.043 0.382 4564 Planarity : 0.004 0.051 5114 Dihedral : 6.390 66.806 4690 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.17 % Favored : 92.55 % Rotamer: Outliers : 2.80 % Allowed : 15.37 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.14), residues: 3570 helix: -0.09 (0.13), residues: 1660 sheet: -0.21 (0.22), residues: 512 loop : -2.18 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 99 HIS 0.013 0.001 HIS K 198 PHE 0.013 0.001 PHE I 29 TYR 0.014 0.001 TYR A 578 ARG 0.006 0.000 ARG C 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 255 time to evaluate : 3.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 PHE cc_start: 0.6791 (OUTLIER) cc_final: 0.5924 (t80) REVERT: B 297 MET cc_start: 0.7573 (mtm) cc_final: 0.7303 (mtm) REVERT: B 343 VAL cc_start: 0.7651 (OUTLIER) cc_final: 0.7342 (m) REVERT: H 31 ASN cc_start: 0.8204 (t0) cc_final: 0.7890 (t0) REVERT: H 154 PHE cc_start: 0.6170 (t80) cc_final: 0.5914 (t80) REVERT: H 163 ASN cc_start: 0.6496 (m-40) cc_final: 0.5941 (t0) REVERT: C 237 PHE cc_start: 0.6791 (OUTLIER) cc_final: 0.5924 (t80) REVERT: D 297 MET cc_start: 0.7573 (mtm) cc_final: 0.7304 (mtm) REVERT: D 343 VAL cc_start: 0.7651 (OUTLIER) cc_final: 0.7340 (m) REVERT: I 31 ASN cc_start: 0.8203 (t0) cc_final: 0.7889 (t0) REVERT: I 154 PHE cc_start: 0.6166 (t80) cc_final: 0.5911 (t80) REVERT: I 163 ASN cc_start: 0.6490 (m-40) cc_final: 0.5934 (t0) outliers start: 88 outliers final: 46 residues processed: 330 average time/residue: 0.3927 time to fit residues: 210.6672 Evaluate side-chains 274 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 224 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain H residue 99 TRP Chi-restraints excluded: chain H residue 100 ARG Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 762 PHE Chi-restraints excluded: chain I residue 99 TRP Chi-restraints excluded: chain I residue 100 ARG Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 286 optimal weight: 4.9990 chunk 195 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 256 optimal weight: 0.3980 chunk 141 optimal weight: 4.9990 chunk 293 optimal weight: 5.9990 chunk 237 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 175 optimal weight: 20.0000 chunk 308 optimal weight: 4.9990 chunk 86 optimal weight: 0.0770 overall best weight: 2.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** H 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29844 Z= 0.252 Angle : 0.658 10.177 40616 Z= 0.331 Chirality : 0.044 0.375 4564 Planarity : 0.004 0.055 5114 Dihedral : 5.985 58.785 4682 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.28 % Favored : 92.55 % Rotamer: Outliers : 2.67 % Allowed : 16.07 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.14), residues: 3570 helix: 0.17 (0.13), residues: 1650 sheet: 0.10 (0.23), residues: 492 loop : -2.03 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 99 HIS 0.013 0.002 HIS K 198 PHE 0.018 0.001 PHE C 499 TYR 0.024 0.001 TYR C 578 ARG 0.008 0.001 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 230 time to evaluate : 3.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.5942 (t80) REVERT: A 487 SER cc_start: 0.2177 (OUTLIER) cc_final: 0.1575 (p) REVERT: A 543 LEU cc_start: 0.7457 (mt) cc_final: 0.7057 (pp) REVERT: B 37 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7847 (tp30) REVERT: B 61 ASN cc_start: 0.8634 (t0) cc_final: 0.8411 (t0) REVERT: H 31 ASN cc_start: 0.8444 (t0) cc_final: 0.8138 (t0) REVERT: H 163 ASN cc_start: 0.6545 (m-40) cc_final: 0.6052 (t0) REVERT: C 237 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.5938 (t80) REVERT: C 487 SER cc_start: 0.2177 (OUTLIER) cc_final: 0.1575 (p) REVERT: C 543 LEU cc_start: 0.7459 (mt) cc_final: 0.7057 (pp) REVERT: D 37 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7847 (tp30) REVERT: D 61 ASN cc_start: 0.8636 (t0) cc_final: 0.8411 (t0) REVERT: I 31 ASN cc_start: 0.8445 (t0) cc_final: 0.8140 (t0) REVERT: I 163 ASN cc_start: 0.6547 (m-40) cc_final: 0.6053 (t0) outliers start: 84 outliers final: 60 residues processed: 306 average time/residue: 0.3747 time to fit residues: 192.3364 Evaluate side-chains 278 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 212 time to evaluate : 3.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 99 TRP Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 762 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 99 TRP Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 115 optimal weight: 2.9990 chunk 309 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 344 optimal weight: 2.9990 chunk 285 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 113 optimal weight: 0.9980 chunk 180 optimal weight: 0.4980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS B 175 GLN ** H 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS D 175 GLN I 32 HIS ** I 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29844 Z= 0.184 Angle : 0.614 9.628 40616 Z= 0.307 Chirality : 0.043 0.355 4564 Planarity : 0.004 0.058 5114 Dihedral : 5.608 58.041 4682 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.00 % Favored : 92.89 % Rotamer: Outliers : 2.60 % Allowed : 16.26 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3570 helix: 0.42 (0.13), residues: 1652 sheet: 0.43 (0.23), residues: 468 loop : -1.98 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 99 HIS 0.010 0.001 HIS K 198 PHE 0.013 0.001 PHE A 499 TYR 0.021 0.001 TYR B 50 ARG 0.006 0.000 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 246 time to evaluate : 3.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 PHE cc_start: 0.6661 (OUTLIER) cc_final: 0.5987 (t80) REVERT: A 398 LEU cc_start: 0.9119 (tp) cc_final: 0.8801 (tt) REVERT: A 487 SER cc_start: 0.2385 (OUTLIER) cc_final: 0.1734 (p) REVERT: B 37 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7856 (tp30) REVERT: B 61 ASN cc_start: 0.8693 (t0) cc_final: 0.8471 (t0) REVERT: B 169 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8302 (tpp80) REVERT: H 128 SER cc_start: 0.5166 (OUTLIER) cc_final: 0.4958 (p) REVERT: H 163 ASN cc_start: 0.6444 (m-40) cc_final: 0.5911 (t0) REVERT: C 237 PHE cc_start: 0.6660 (OUTLIER) cc_final: 0.5988 (t80) REVERT: C 398 LEU cc_start: 0.9120 (tp) cc_final: 0.8802 (tt) REVERT: C 487 SER cc_start: 0.2387 (OUTLIER) cc_final: 0.1736 (p) REVERT: D 37 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7854 (tp30) REVERT: D 61 ASN cc_start: 0.8693 (t0) cc_final: 0.8471 (t0) REVERT: D 169 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8299 (tpp80) REVERT: I 128 SER cc_start: 0.5163 (OUTLIER) cc_final: 0.4952 (p) REVERT: I 163 ASN cc_start: 0.6441 (m-40) cc_final: 0.5907 (t0) outliers start: 82 outliers final: 52 residues processed: 322 average time/residue: 0.3765 time to fit residues: 199.2332 Evaluate side-chains 276 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 214 time to evaluate : 3.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 99 TRP Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 762 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 99 TRP Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 332 optimal weight: 4.9990 chunk 38 optimal weight: 0.3980 chunk 196 optimal weight: 9.9990 chunk 251 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 289 optimal weight: 7.9990 chunk 192 optimal weight: 0.0670 chunk 343 optimal weight: 9.9990 chunk 214 optimal weight: 10.0000 chunk 209 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 overall best weight: 2.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN B 175 GLN H 32 HIS H 39 GLN K 38 GLN ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 175 GLN I 39 GLN M 38 GLN ** M 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 29844 Z= 0.260 Angle : 0.654 11.439 40616 Z= 0.328 Chirality : 0.044 0.361 4564 Planarity : 0.004 0.059 5114 Dihedral : 5.469 59.767 4676 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.79 % Favored : 92.10 % Rotamer: Outliers : 2.64 % Allowed : 17.31 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3570 helix: 0.43 (0.13), residues: 1660 sheet: 0.55 (0.23), residues: 460 loop : -1.93 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 99 HIS 0.009 0.001 HIS K 198 PHE 0.014 0.001 PHE M 94 TYR 0.016 0.001 TYR A 578 ARG 0.016 0.001 ARG K 45 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 220 time to evaluate : 3.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 PHE cc_start: 0.6714 (OUTLIER) cc_final: 0.5933 (t80) REVERT: A 398 LEU cc_start: 0.9133 (tp) cc_final: 0.8852 (tt) REVERT: A 487 SER cc_start: 0.2327 (OUTLIER) cc_final: 0.1741 (p) REVERT: B 37 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7889 (tp30) REVERT: B 61 ASN cc_start: 0.8742 (t0) cc_final: 0.8462 (t0) REVERT: B 169 ARG cc_start: 0.9293 (OUTLIER) cc_final: 0.8337 (tpp80) REVERT: H 106 TRP cc_start: 0.6845 (OUTLIER) cc_final: 0.5495 (m-90) REVERT: H 128 SER cc_start: 0.5180 (OUTLIER) cc_final: 0.4940 (p) REVERT: H 163 ASN cc_start: 0.6491 (m-40) cc_final: 0.5982 (t0) REVERT: C 237 PHE cc_start: 0.6715 (OUTLIER) cc_final: 0.5937 (t80) REVERT: C 398 LEU cc_start: 0.9134 (tp) cc_final: 0.8853 (tt) REVERT: C 487 SER cc_start: 0.2328 (OUTLIER) cc_final: 0.1742 (p) REVERT: D 37 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7889 (tp30) REVERT: D 61 ASN cc_start: 0.8741 (t0) cc_final: 0.8461 (t0) REVERT: D 169 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.8336 (tpp80) REVERT: I 106 TRP cc_start: 0.6841 (OUTLIER) cc_final: 0.5495 (m-90) REVERT: I 128 SER cc_start: 0.5174 (OUTLIER) cc_final: 0.4932 (p) REVERT: I 163 ASN cc_start: 0.6488 (m-40) cc_final: 0.5982 (t0) outliers start: 83 outliers final: 57 residues processed: 297 average time/residue: 0.3648 time to fit residues: 180.8285 Evaluate side-chains 281 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 212 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 99 TRP Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 680 SER Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 762 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 99 TRP Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain I residue 192 VAL Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 212 optimal weight: 4.9990 chunk 137 optimal weight: 20.0000 chunk 204 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 67 optimal weight: 0.0980 chunk 66 optimal weight: 3.9990 chunk 218 optimal weight: 0.7980 chunk 233 optimal weight: 9.9990 chunk 169 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 269 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN D 175 GLN ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 29844 Z= 0.234 Angle : 0.640 9.008 40616 Z= 0.321 Chirality : 0.044 0.350 4564 Planarity : 0.004 0.056 5114 Dihedral : 5.391 56.278 4676 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.56 % Favored : 92.32 % Rotamer: Outliers : 2.60 % Allowed : 17.38 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3570 helix: 0.55 (0.13), residues: 1658 sheet: 0.72 (0.24), residues: 436 loop : -1.83 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 99 HIS 0.009 0.001 HIS K 198 PHE 0.013 0.001 PHE D 684 TYR 0.016 0.001 TYR D 50 ARG 0.003 0.000 ARG D 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 219 time to evaluate : 3.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 PHE cc_start: 0.6771 (OUTLIER) cc_final: 0.5914 (t80) REVERT: A 398 LEU cc_start: 0.9116 (tp) cc_final: 0.8850 (tt) REVERT: A 487 SER cc_start: 0.2850 (OUTLIER) cc_final: 0.2341 (p) REVERT: B 37 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7874 (tp30) REVERT: B 61 ASN cc_start: 0.8777 (t0) cc_final: 0.8471 (t0) REVERT: B 169 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.8374 (tpp80) REVERT: H 31 ASN cc_start: 0.8340 (t0) cc_final: 0.8022 (t0) REVERT: H 128 SER cc_start: 0.5289 (OUTLIER) cc_final: 0.5033 (p) REVERT: H 163 ASN cc_start: 0.6431 (m-40) cc_final: 0.5936 (t0) REVERT: C 237 PHE cc_start: 0.6770 (OUTLIER) cc_final: 0.5914 (t80) REVERT: C 398 LEU cc_start: 0.9117 (tp) cc_final: 0.8851 (tt) REVERT: C 487 SER cc_start: 0.2852 (OUTLIER) cc_final: 0.2342 (p) REVERT: D 37 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7876 (tp30) REVERT: D 61 ASN cc_start: 0.8776 (t0) cc_final: 0.8469 (t0) REVERT: D 169 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8372 (tpp80) REVERT: I 31 ASN cc_start: 0.8352 (t0) cc_final: 0.8038 (t0) REVERT: I 128 SER cc_start: 0.5286 (OUTLIER) cc_final: 0.5030 (p) REVERT: I 163 ASN cc_start: 0.6464 (m-40) cc_final: 0.5964 (t0) outliers start: 82 outliers final: 58 residues processed: 293 average time/residue: 0.3632 time to fit residues: 177.9278 Evaluate side-chains 276 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 208 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 99 TRP Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 128 SER Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 762 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 99 TRP Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 312 optimal weight: 0.3980 chunk 328 optimal weight: 1.9990 chunk 299 optimal weight: 0.0970 chunk 319 optimal weight: 0.9990 chunk 192 optimal weight: 0.4980 chunk 139 optimal weight: 3.9990 chunk 251 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 288 optimal weight: 0.8980 chunk 302 optimal weight: 5.9990 chunk 318 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 GLN B 175 GLN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN D 175 GLN ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 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 : 0.002 0.036 29844 Z= 0.157 Angle : 0.621 11.607 40616 Z= 0.308 Chirality : 0.042 0.339 4564 Planarity : 0.004 0.054 5114 Dihedral : 5.156 58.885 4676 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.17 % Favored : 92.72 % Rotamer: Outliers : 2.10 % Allowed : 17.98 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3570 helix: 0.73 (0.13), residues: 1658 sheet: 0.64 (0.24), residues: 440 loop : -1.70 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 99 HIS 0.011 0.001 HIS K 198 PHE 0.019 0.001 PHE H 25 TYR 0.027 0.001 TYR A 578 ARG 0.003 0.000 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 225 time to evaluate : 3.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 PHE cc_start: 0.6741 (OUTLIER) cc_final: 0.5973 (t80) REVERT: A 398 LEU cc_start: 0.9045 (tp) cc_final: 0.8811 (tt) REVERT: A 487 SER cc_start: 0.2967 (OUTLIER) cc_final: 0.2527 (p) REVERT: B 37 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7842 (tp30) REVERT: B 61 ASN cc_start: 0.8720 (t0) cc_final: 0.8421 (t0) REVERT: H 31 ASN cc_start: 0.8183 (t0) cc_final: 0.7868 (t0) REVERT: H 106 TRP cc_start: 0.6647 (OUTLIER) cc_final: 0.5501 (m-90) REVERT: H 163 ASN cc_start: 0.6464 (m-40) cc_final: 0.5953 (t0) REVERT: H 202 TYR cc_start: 0.0053 (m-80) cc_final: -0.0231 (m-80) REVERT: C 237 PHE cc_start: 0.6742 (OUTLIER) cc_final: 0.5977 (t80) REVERT: C 398 LEU cc_start: 0.9045 (tp) cc_final: 0.8810 (tt) REVERT: C 487 SER cc_start: 0.2967 (OUTLIER) cc_final: 0.2526 (p) REVERT: D 37 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7840 (tp30) REVERT: D 61 ASN cc_start: 0.8718 (t0) cc_final: 0.8419 (t0) REVERT: I 31 ASN cc_start: 0.8185 (t0) cc_final: 0.7872 (t0) REVERT: I 106 TRP cc_start: 0.6649 (OUTLIER) cc_final: 0.5504 (m-90) REVERT: I 163 ASN cc_start: 0.6466 (m-40) cc_final: 0.5954 (t0) REVERT: I 202 TYR cc_start: 0.0048 (m-80) cc_final: -0.0235 (m-80) outliers start: 66 outliers final: 42 residues processed: 281 average time/residue: 0.3515 time to fit residues: 167.9327 Evaluate side-chains 260 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 210 time to evaluate : 3.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 237 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 183 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 487 SER Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 209 optimal weight: 0.8980 chunk 338 optimal weight: 10.0000 chunk 206 optimal weight: 20.0000 chunk 160 optimal weight: 10.0000 chunk 235 optimal weight: 0.0870 chunk 354 optimal weight: 40.0000 chunk 326 optimal weight: 40.0000 chunk 282 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 218 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 overall best weight: 4.5966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 175 GLN H 63 ASN K 147 GLN ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN D 139 GLN D 175 GLN I 63 ASN M 147 GLN ** M 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 29844 Z= 0.447 Angle : 0.745 10.562 40616 Z= 0.376 Chirality : 0.049 0.358 4564 Planarity : 0.005 0.054 5114 Dihedral : 5.762 55.426 4676 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.68 % Favored : 92.21 % Rotamer: Outliers : 1.84 % Allowed : 18.46 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3570 helix: 0.35 (0.13), residues: 1656 sheet: 0.59 (0.23), residues: 440 loop : -1.87 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP I 99 HIS 0.010 0.002 HIS K 198 PHE 0.027 0.002 PHE K 94 TYR 0.023 0.002 TYR D 183 ARG 0.007 0.001 ARG B 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 228 time to evaluate : 3.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 LEU cc_start: 0.9149 (tp) cc_final: 0.8894 (tt) REVERT: B 37 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7932 (tp30) REVERT: H 31 ASN cc_start: 0.8292 (t0) cc_final: 0.7826 (t0) REVERT: H 163 ASN cc_start: 0.6537 (m-40) cc_final: 0.6050 (t0) REVERT: C 398 LEU cc_start: 0.9150 (tp) cc_final: 0.8894 (tt) REVERT: D 37 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7935 (tp30) REVERT: I 31 ASN cc_start: 0.8250 (t0) cc_final: 0.7870 (t0) REVERT: I 163 ASN cc_start: 0.6539 (m-40) cc_final: 0.6052 (t0) outliers start: 58 outliers final: 42 residues processed: 278 average time/residue: 0.3433 time to fit residues: 162.5722 Evaluate side-chains 248 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 204 time to evaluate : 3.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 99 TRP Chi-restraints excluded: chain H residue 106 TRP Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 680 SER Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 762 PHE Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 99 TRP Chi-restraints excluded: chain I residue 106 TRP Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 224 optimal weight: 9.9990 chunk 300 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 260 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 282 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 290 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN B 61 ASN B 175 GLN ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 608 ASN D 61 ASN D 175 GLN ** M 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.146512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.095436 restraints weight = 63509.222| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.15 r_work: 0.3023 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.5125 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: