Starting phenix.real_space_refine on Tue Feb 20 23:20:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v61_31732/02_2024/7v61_31732.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v61_31732/02_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_31732/02_2024/7v61_31732.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v61_31732/02_2024/7v61_31732.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v61_31732/02_2024/7v61_31732.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v61_31732/02_2024/7v61_31732.pdb" } 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-5238/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: 15.62, 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: 11.61 Conformation dependent library (CDL) restraints added in 5.3 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: 3.06 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: 9.85 Time building geometry restraints manager: 12.55 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 2.520 nonbonded pdb=" O ASN I 31 " pdb=" ND1 HIS I 32 " model vdw 1.986 2.520 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 2.440 ... (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 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.660 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 73.950 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.340 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.260 ------------------------------------------------------------------------------- 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 : 3.358 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: 0.4133 time to fit residues: 432.6217 Evaluate side-chains 319 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 279 time to evaluate : 3.133 ------------------------------------------------------------------------------- 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: 0.0570 chunk 149 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 182 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 279 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 207 optimal weight: 20.0000 chunk 323 optimal weight: 4.9990 overall best weight: 2.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 GLN A 293 ASN A 297 ASN ** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 GLN A 364 GLN A 574 GLN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN B 49 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 GLN C 293 ASN C 297 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 GLN C 364 GLN C 574 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 49 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: 0.7591 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 29844 Z= 0.301 Angle : 0.761 11.475 40616 Z= 0.389 Chirality : 0.048 0.445 4564 Planarity : 0.006 0.048 5114 Dihedral : 8.350 70.905 4744 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.28 % Favored : 92.32 % Rotamer: Outliers : 3.68 % Allowed : 13.53 % Favored : 82.78 % 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: -3.20 (0.12), residues: 3570 helix: -1.99 (0.11), residues: 1676 sheet: -0.51 (0.22), residues: 480 loop : -2.74 (0.15), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 99 HIS 0.005 0.001 HIS I 33 PHE 0.020 0.002 PHE I 29 TYR 0.017 0.002 TYR B 385 ARG 0.006 0.001 ARG D 169 *********************** 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 414 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 298 time to evaluate : 3.251 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: 0.8131 (OUTLIER) cc_final: 0.7748 (m-80) REVERT: B 171 GLU cc_start: 0.5703 (OUTLIER) cc_final: 0.5173 (mm-30) REVERT: B 325 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7769 (tm-30) REVERT: H 31 ASN cc_start: 0.8056 (t0) cc_final: 0.7715 (t0) REVERT: H 37 MET cc_start: 0.7497 (mpp) cc_final: 0.6843 (mpp) REVERT: H 163 ASN cc_start: 0.6080 (m-40) cc_final: 0.5662 (t0) REVERT: H 174 PHE cc_start: -0.0876 (m-80) cc_final: -0.1120 (m-80) REVERT: H 202 TYR cc_start: 0.0540 (m-80) cc_final: 0.0056 (m-80) REVERT: K 61 ARG cc_start: 0.5639 (ptp90) cc_final: 0.5274 (mtm110) REVERT: K 70 ASP cc_start: 0.6335 (m-30) cc_final: 0.6115 (p0) REVERT: K 98 PHE cc_start: 0.5993 (m-80) cc_final: 0.5676 (m-80) REVERT: C 403 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7751 (m-80) REVERT: D 171 GLU cc_start: 0.5702 (OUTLIER) cc_final: 0.5174 (mm-30) REVERT: D 325 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7772 (tm-30) REVERT: I 31 ASN cc_start: 0.8059 (t0) cc_final: 0.7719 (t0) REVERT: I 37 MET cc_start: 0.7495 (mpp) cc_final: 0.6841 (mpp) REVERT: I 163 ASN cc_start: 0.6079 (m-40) cc_final: 0.5658 (t0) REVERT: I 174 PHE cc_start: -0.0869 (m-80) cc_final: -0.1120 (m-80) REVERT: I 202 TYR cc_start: 0.0531 (m-80) cc_final: 0.0046 (m-80) REVERT: M 61 ARG cc_start: 0.5640 (ptp90) cc_final: 0.5275 (mtm110) REVERT: M 70 ASP cc_start: 0.6338 (m-30) cc_final: 0.6116 (p0) REVERT: M 98 PHE cc_start: 0.5989 (m-80) cc_final: 0.5671 (m-80) outliers start: 116 outliers final: 62 residues processed: 394 average time/residue: 0.4016 time to fit residues: 256.4007 Evaluate side-chains 308 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 242 time to evaluate : 3.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 238 LEU 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 304 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 A residue 527 ASN Chi-restraints excluded: chain B residue 34 HIS 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 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 186 LEU 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 101 LEU Chi-restraints excluded: chain C residue 238 LEU 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 304 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 C residue 527 ASN Chi-restraints excluded: chain D residue 34 HIS 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 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 186 LEU 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: 0.6980 chunk 100 optimal weight: 0.0870 chunk 269 optimal weight: 0.9990 chunk 220 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 323 optimal weight: 7.9990 chunk 349 optimal weight: 30.0000 chunk 288 optimal weight: 1.9990 chunk 321 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 130 ASN A 340 ASN ** B 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN ** H 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN C 130 ASN C 340 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29844 Z= 0.184 Angle : 0.656 11.969 40616 Z= 0.331 Chirality : 0.044 0.388 4564 Planarity : 0.004 0.050 5114 Dihedral : 7.099 67.867 4708 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.23 % Favored : 92.44 % Rotamer: Outliers : 3.05 % Allowed : 15.31 % Favored : 81.64 % 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: -1.94 (0.13), residues: 3570 helix: -0.66 (0.12), residues: 1654 sheet: -0.17 (0.23), residues: 494 loop : -2.42 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 99 HIS 0.008 0.001 HIS C 108 PHE 0.022 0.001 PHE H 154 TYR 0.033 0.001 TYR C 578 ARG 0.011 0.000 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 367 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 271 time to evaluate : 3.246 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: 0.8189 (OUTLIER) cc_final: 0.7894 (m-80) REVERT: B 297 MET cc_start: 0.7521 (mtm) cc_final: 0.7245 (mtm) REVERT: H 31 ASN cc_start: 0.8078 (t0) cc_final: 0.7720 (t0) REVERT: H 154 PHE cc_start: 0.6123 (t80) cc_final: 0.5361 (t80) REVERT: H 163 ASN cc_start: 0.6276 (m-40) cc_final: 0.5765 (t0) REVERT: H 174 PHE cc_start: -0.0784 (m-80) cc_final: -0.1027 (m-80) REVERT: K 61 ARG cc_start: 0.5787 (OUTLIER) cc_final: 0.5333 (mtm110) REVERT: K 70 ASP cc_start: 0.6394 (m-30) cc_final: 0.6187 (p0) REVERT: K 98 PHE cc_start: 0.6066 (m-80) cc_final: 0.5604 (m-80) REVERT: C 403 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7893 (m-80) REVERT: D 297 MET cc_start: 0.7516 (mtm) cc_final: 0.7245 (mtm) REVERT: I 31 ASN cc_start: 0.8076 (t0) cc_final: 0.7719 (t0) REVERT: I 154 PHE cc_start: 0.6129 (t80) cc_final: 0.5366 (t80) REVERT: I 163 ASN cc_start: 0.6274 (m-40) cc_final: 0.5765 (t0) REVERT: I 174 PHE cc_start: -0.0784 (m-80) cc_final: -0.1029 (m-80) REVERT: M 61 ARG cc_start: 0.5786 (OUTLIER) cc_final: 0.5332 (mtm110) REVERT: M 70 ASP cc_start: 0.6392 (m-30) cc_final: 0.6189 (p0) REVERT: M 98 PHE cc_start: 0.6064 (m-80) cc_final: 0.5601 (m-80) outliers start: 96 outliers final: 50 residues processed: 347 average time/residue: 0.4183 time to fit residues: 235.0746 Evaluate side-chains 288 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 234 time to evaluate : 3.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 101 LEU 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 466 THR Chi-restraints excluded: chain A residue 527 ASN 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 100 ARG 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 150 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 101 LEU 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 466 THR Chi-restraints excluded: chain C residue 527 ASN 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 100 ARG 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 150 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain M residue 61 ARG Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 319 optimal weight: 8.9990 chunk 243 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 154 optimal weight: 30.0000 chunk 217 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 chunk 344 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 chunk 308 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN B 175 GLN ** H 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 ASN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN D 175 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 205 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29844 Z= 0.211 Angle : 0.640 9.962 40616 Z= 0.322 Chirality : 0.044 0.377 4564 Planarity : 0.004 0.052 5114 Dihedral : 6.348 66.061 4682 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.28 % Favored : 92.49 % Rotamer: Outliers : 3.30 % Allowed : 15.53 % Favored : 81.16 % 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: -1.33 (0.14), residues: 3570 helix: -0.08 (0.13), residues: 1656 sheet: 0.08 (0.23), residues: 494 loop : -2.19 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 99 HIS 0.015 0.001 HIS K 198 PHE 0.017 0.001 PHE C 499 TYR 0.014 0.001 TYR A 567 ARG 0.005 0.000 ARG I 13 *********************** 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 349 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 245 time to evaluate : 3.625 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 237 PHE cc_start: 0.6955 (OUTLIER) cc_final: 0.6028 (t80) REVERT: B 169 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8399 (tpp80) REVERT: H 154 PHE cc_start: 0.6172 (t80) cc_final: 0.5949 (t80) REVERT: K 30 ARG cc_start: 0.8030 (ptm160) cc_final: 0.7694 (tmm-80) REVERT: K 61 ARG cc_start: 0.5970 (OUTLIER) cc_final: 0.5320 (mtm110) REVERT: C 237 PHE cc_start: 0.6955 (OUTLIER) cc_final: 0.6029 (t80) REVERT: D 169 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8399 (tpp80) REVERT: I 154 PHE cc_start: 0.6171 (t80) cc_final: 0.5955 (t80) REVERT: M 30 ARG cc_start: 0.8030 (ptm160) cc_final: 0.7693 (tmm-80) REVERT: M 61 ARG cc_start: 0.5975 (OUTLIER) cc_final: 0.5323 (mtm110) outliers start: 104 outliers final: 60 residues processed: 329 average time/residue: 0.4021 time to fit residues: 216.6824 Evaluate side-chains 294 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 228 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 232 VAL 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 320 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 169 ARG 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 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 99 TRP 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 146 LEU Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 232 VAL 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 320 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 527 ASN Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain D residue 169 ARG 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 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 99 TRP 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 146 LEU Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 61 ARG 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: 1.9990 chunk 195 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 256 optimal weight: 0.6980 chunk 141 optimal weight: 0.0970 chunk 293 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 175 optimal weight: 8.9990 chunk 308 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 24 GLN ** 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** ** 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** ** D 24 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29844 Z= 0.168 Angle : 0.615 9.673 40616 Z= 0.307 Chirality : 0.042 0.359 4564 Planarity : 0.004 0.052 5114 Dihedral : 5.910 57.200 4682 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.00 % Favored : 92.83 % Rotamer: Outliers : 2.73 % Allowed : 15.79 % Favored : 81.48 % 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: -0.99 (0.14), residues: 3570 helix: 0.26 (0.13), residues: 1662 sheet: 0.15 (0.23), residues: 472 loop : -2.03 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 99 HIS 0.013 0.001 HIS K 198 PHE 0.013 0.001 PHE A 499 TYR 0.026 0.001 TYR C 578 ARG 0.006 0.000 ARG M 142 *********************** 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 337 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 251 time to evaluate : 3.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.6463 (OUTLIER) cc_final: 0.5791 (p0) REVERT: A 237 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.5942 (t80) REVERT: A 543 LEU cc_start: 0.7387 (mt) cc_final: 0.7033 (pp) REVERT: H 163 ASN cc_start: 0.6285 (m-40) cc_final: 0.5835 (t0) REVERT: K 30 ARG cc_start: 0.7980 (ptm160) cc_final: 0.7633 (tmm-80) REVERT: K 61 ARG cc_start: 0.5922 (OUTLIER) cc_final: 0.5581 (ptp90) REVERT: K 79 GLU cc_start: 0.3070 (mt-10) cc_final: 0.2322 (mt-10) REVERT: C 156 ASN cc_start: 0.6462 (OUTLIER) cc_final: 0.5665 (p0) REVERT: C 237 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.5943 (t80) REVERT: C 543 LEU cc_start: 0.7389 (mt) cc_final: 0.7034 (pp) REVERT: I 163 ASN cc_start: 0.6282 (m-40) cc_final: 0.5830 (t0) REVERT: M 30 ARG cc_start: 0.7983 (ptm160) cc_final: 0.7632 (tmm-80) REVERT: M 61 ARG cc_start: 0.5922 (OUTLIER) cc_final: 0.5582 (ptp90) REVERT: M 79 GLU cc_start: 0.3061 (mt-10) cc_final: 0.2320 (mt-10) outliers start: 86 outliers final: 54 residues processed: 319 average time/residue: 0.3987 time to fit residues: 214.1209 Evaluate side-chains 278 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 218 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN 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 403 PHE Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 368 ASP 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 743 LEU 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 103 ASP Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 146 LEU Chi-restraints excluded: chain H residue 150 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain C residue 156 ASN 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 403 PHE Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 527 ASN Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 368 ASP 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 743 LEU 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 103 ASP Chi-restraints excluded: chain I residue 135 SER Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 150 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 61 ARG 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: 0.9990 chunk 309 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 202 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 344 optimal weight: 6.9990 chunk 285 optimal weight: 3.9990 chunk 159 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 58 ASN B 61 ASN B 175 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29844 Z= 0.221 Angle : 0.631 9.526 40616 Z= 0.315 Chirality : 0.044 0.356 4564 Planarity : 0.004 0.053 5114 Dihedral : 5.435 49.667 4676 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.45 % Favored : 92.44 % Rotamer: Outliers : 2.80 % Allowed : 16.71 % Favored : 80.50 % 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: 0.41 (0.13), residues: 1670 sheet: 0.40 (0.23), residues: 480 loop : -1.99 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 99 HIS 0.013 0.002 HIS K 198 PHE 0.013 0.001 PHE B 684 TYR 0.015 0.001 TYR D 183 ARG 0.004 0.000 ARG M 142 *********************** 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 322 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 234 time to evaluate : 3.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.6420 (OUTLIER) cc_final: 0.5594 (p0) REVERT: A 237 PHE cc_start: 0.6665 (OUTLIER) cc_final: 0.5973 (t80) REVERT: A 398 LEU cc_start: 0.9134 (tp) cc_final: 0.8844 (tt) REVERT: B 169 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8422 (tpp80) REVERT: H 106 TRP cc_start: 0.6626 (OUTLIER) cc_final: 0.5541 (m-90) REVERT: H 163 ASN cc_start: 0.6387 (m-40) cc_final: 0.5949 (t0) REVERT: K 61 ARG cc_start: 0.5952 (OUTLIER) cc_final: 0.5540 (ptp90) REVERT: K 79 GLU cc_start: 0.3175 (mt-10) cc_final: 0.2548 (mt-10) REVERT: C 156 ASN cc_start: 0.6421 (OUTLIER) cc_final: 0.5594 (p0) REVERT: C 237 PHE cc_start: 0.6663 (OUTLIER) cc_final: 0.5970 (t80) REVERT: C 398 LEU cc_start: 0.9135 (tp) cc_final: 0.8844 (tt) REVERT: D 169 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8410 (tpp80) REVERT: I 106 TRP cc_start: 0.6629 (OUTLIER) cc_final: 0.5548 (m-90) REVERT: I 163 ASN cc_start: 0.6387 (m-40) cc_final: 0.5946 (t0) REVERT: M 61 ARG cc_start: 0.5953 (OUTLIER) cc_final: 0.5545 (ptp90) REVERT: M 79 GLU cc_start: 0.3166 (mt-10) cc_final: 0.2542 (mt-10) outliers start: 88 outliers final: 62 residues processed: 306 average time/residue: 0.3783 time to fit residues: 191.5109 Evaluate side-chains 279 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 207 time to evaluate : 3.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN 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 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 501 GLU Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 578 TYR Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 169 ARG 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 692 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 759 ILE Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain H residue 6 GLU 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 H residue 150 VAL Chi-restraints excluded: chain H residue 186 LEU Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 61 ARG 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 156 ASN 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 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 501 GLU Chi-restraints excluded: chain C residue 527 ASN Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 578 TYR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 169 ARG 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 692 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 759 ILE Chi-restraints excluded: chain D residue 762 PHE Chi-restraints excluded: chain I residue 6 GLU 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 I residue 150 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 61 ARG 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: 20.0000 chunk 38 optimal weight: 7.9990 chunk 196 optimal weight: 20.0000 chunk 251 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 289 optimal weight: 4.9990 chunk 192 optimal weight: 0.7980 chunk 343 optimal weight: 9.9990 chunk 214 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 158 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN H 39 GLN K 38 GLN ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 GLN I 39 GLN I 63 ASN M 38 GLN ** M 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 29844 Z= 0.374 Angle : 0.695 10.043 40616 Z= 0.350 Chirality : 0.046 0.357 4564 Planarity : 0.004 0.057 5114 Dihedral : 5.696 53.038 4676 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.04 % Favored : 91.85 % Rotamer: Outliers : 3.02 % Allowed : 17.41 % Favored : 79.57 % 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: -0.87 (0.14), residues: 3570 helix: 0.30 (0.13), residues: 1654 sheet: 0.47 (0.24), residues: 456 loop : -1.96 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 99 HIS 0.012 0.002 HIS K 198 PHE 0.021 0.002 PHE B 684 TYR 0.022 0.002 TYR D 183 ARG 0.007 0.001 ARG D 169 *********************** 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 325 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 230 time to evaluate : 3.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.6422 (OUTLIER) cc_final: 0.5596 (p0) REVERT: A 302 ASP cc_start: 0.4713 (m-30) cc_final: 0.4344 (t0) REVERT: A 398 LEU cc_start: 0.9176 (tp) cc_final: 0.8910 (tt) REVERT: B 37 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: B 61 ASN cc_start: 0.8825 (t0) cc_final: 0.8593 (t0) REVERT: B 169 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.8392 (tpp80) REVERT: B 325 GLN cc_start: 0.8361 (tm-30) cc_final: 0.8097 (tm-30) REVERT: H 37 MET cc_start: 0.7982 (mpp) cc_final: 0.7681 (mpp) REVERT: H 74 ARG cc_start: 0.6167 (OUTLIER) cc_final: 0.5555 (mtm180) REVERT: H 106 TRP cc_start: 0.6805 (OUTLIER) cc_final: 0.5779 (m-90) REVERT: H 163 ASN cc_start: 0.6374 (m-40) cc_final: 0.5955 (t0) REVERT: K 61 ARG cc_start: 0.5928 (OUTLIER) cc_final: 0.5460 (ptp90) REVERT: K 79 GLU cc_start: 0.3649 (mt-10) cc_final: 0.3179 (mt-10) REVERT: C 156 ASN cc_start: 0.6421 (OUTLIER) cc_final: 0.5594 (p0) REVERT: C 302 ASP cc_start: 0.4718 (m-30) cc_final: 0.4345 (t0) REVERT: C 398 LEU cc_start: 0.9176 (tp) cc_final: 0.8909 (tt) REVERT: D 37 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: D 169 ARG cc_start: 0.9308 (OUTLIER) cc_final: 0.8395 (tpp80) REVERT: D 325 GLN cc_start: 0.8361 (tm-30) cc_final: 0.8097 (tm-30) REVERT: I 37 MET cc_start: 0.7982 (mpp) cc_final: 0.7679 (mpp) REVERT: I 74 ARG cc_start: 0.6165 (OUTLIER) cc_final: 0.5556 (mtm180) REVERT: I 106 TRP cc_start: 0.6802 (OUTLIER) cc_final: 0.5777 (m-90) REVERT: I 163 ASN cc_start: 0.6368 (m-40) cc_final: 0.5949 (t0) REVERT: M 61 ARG cc_start: 0.5930 (OUTLIER) cc_final: 0.5463 (ptp90) REVERT: M 79 GLU cc_start: 0.3650 (mt-10) cc_final: 0.3181 (mt-10) outliers start: 95 outliers final: 66 residues processed: 311 average time/residue: 0.3766 time to fit residues: 194.4363 Evaluate side-chains 282 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 204 time to evaluate : 3.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN 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 315 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 527 ASN 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 91 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 170 SER 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 692 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain H residue 74 ARG 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 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 K residue 32 TYR Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain C residue 156 ASN 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 315 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 527 ASN 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 91 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 170 SER 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 692 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 762 PHE Chi-restraints excluded: chain I residue 74 ARG 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 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 M residue 32 TYR Chi-restraints excluded: chain M residue 61 ARG 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: 2.9990 chunk 137 optimal weight: 1.9990 chunk 204 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 218 optimal weight: 0.8980 chunk 233 optimal weight: 0.0570 chunk 169 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 269 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 58 ASN B 61 ASN B 139 GLN B 175 GLN ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN D 175 GLN ** M 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4734 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= 0.156 Angle : 0.610 9.658 40616 Z= 0.306 Chirality : 0.042 0.340 4564 Planarity : 0.004 0.051 5114 Dihedral : 5.272 49.626 4672 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.95 % Favored : 92.89 % Rotamer: Outliers : 1.97 % Allowed : 18.68 % Favored : 79.35 % 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: -0.54 (0.14), residues: 3570 helix: 0.60 (0.13), residues: 1660 sheet: 0.49 (0.24), residues: 438 loop : -1.77 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 111 HIS 0.013 0.001 HIS C 108 PHE 0.012 0.001 PHE B 683 TYR 0.021 0.001 TYR C 578 ARG 0.003 0.000 ARG H 13 *********************** 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 275 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 213 time to evaluate : 3.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.6296 (OUTLIER) cc_final: 0.5483 (p0) REVERT: A 302 ASP cc_start: 0.4574 (m-30) cc_final: 0.4330 (t0) REVERT: A 398 LEU cc_start: 0.9066 (tp) cc_final: 0.8812 (tt) REVERT: B 37 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7550 (tm-30) REVERT: B 61 ASN cc_start: 0.8811 (t0) cc_final: 0.8546 (t0) REVERT: B 169 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8196 (tpp80) REVERT: H 31 ASN cc_start: 0.8120 (t0) cc_final: 0.7777 (t0) REVERT: H 74 ARG cc_start: 0.6116 (OUTLIER) cc_final: 0.5571 (mtm180) REVERT: H 106 TRP cc_start: 0.6656 (OUTLIER) cc_final: 0.5629 (m-90) REVERT: H 163 ASN cc_start: 0.6457 (m-40) cc_final: 0.6007 (t0) REVERT: K 24 ARG cc_start: 0.7061 (mmm-85) cc_final: 0.6819 (tpp-160) REVERT: K 61 ARG cc_start: 0.5793 (OUTLIER) cc_final: 0.5436 (ptp90) REVERT: K 79 GLU cc_start: 0.3259 (mt-10) cc_final: 0.2781 (mt-10) REVERT: C 156 ASN cc_start: 0.6293 (OUTLIER) cc_final: 0.5481 (p0) REVERT: C 302 ASP cc_start: 0.4580 (m-30) cc_final: 0.4334 (t0) REVERT: C 398 LEU cc_start: 0.9066 (tp) cc_final: 0.8812 (tt) REVERT: D 37 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: D 169 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8196 (tpp80) REVERT: I 31 ASN cc_start: 0.8120 (t0) cc_final: 0.7778 (t0) REVERT: I 74 ARG cc_start: 0.6149 (OUTLIER) cc_final: 0.5576 (mtm180) REVERT: I 106 TRP cc_start: 0.6665 (OUTLIER) cc_final: 0.5637 (m-90) REVERT: I 163 ASN cc_start: 0.6457 (m-40) cc_final: 0.6006 (t0) REVERT: M 24 ARG cc_start: 0.7063 (mmm-85) cc_final: 0.6821 (tpp-160) REVERT: M 61 ARG cc_start: 0.5784 (OUTLIER) cc_final: 0.5432 (ptp90) REVERT: M 79 GLU cc_start: 0.3257 (mt-10) cc_final: 0.2777 (mt-10) outliers start: 62 outliers final: 36 residues processed: 263 average time/residue: 0.3926 time to fit residues: 169.0983 Evaluate side-chains 250 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 202 time to evaluate : 3.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 354 ASN 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 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 74 ARG 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 K residue 32 TYR Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 354 ASN 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 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 74 ARG 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 M residue 32 TYR Chi-restraints excluded: chain M residue 61 ARG 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: 5.9990 chunk 328 optimal weight: 7.9990 chunk 299 optimal weight: 0.4980 chunk 319 optimal weight: 6.9990 chunk 192 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 288 optimal weight: 0.9980 chunk 302 optimal weight: 6.9990 chunk 318 optimal weight: 3.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- 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 139 GLN B 175 GLN H 63 ASN ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN D 175 GLN ** 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: 0.7677 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29844 Z= 0.254 Angle : 0.641 9.813 40616 Z= 0.322 Chirality : 0.044 0.347 4564 Planarity : 0.004 0.056 5114 Dihedral : 5.304 51.349 4672 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.70 % Favored : 92.13 % Rotamer: Outliers : 2.03 % Allowed : 18.74 % Favored : 79.22 % 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: -0.55 (0.14), residues: 3570 helix: 0.60 (0.13), residues: 1658 sheet: 0.51 (0.24), residues: 438 loop : -1.79 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP I 99 HIS 0.014 0.002 HIS A 108 PHE 0.016 0.001 PHE B 684 TYR 0.017 0.001 TYR C 41 ARG 0.005 0.000 ARG B 169 *********************** 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 279 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 215 time to evaluate : 3.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.6271 (OUTLIER) cc_final: 0.5471 (p0) REVERT: A 302 ASP cc_start: 0.4727 (m-30) cc_final: 0.4373 (t0) REVERT: A 398 LEU cc_start: 0.9118 (tp) cc_final: 0.8883 (tt) REVERT: B 37 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7760 (mm-30) REVERT: B 61 ASN cc_start: 0.8867 (t0) cc_final: 0.8610 (t0) REVERT: B 169 ARG cc_start: 0.9261 (OUTLIER) cc_final: 0.8346 (tpp80) REVERT: B 325 GLN cc_start: 0.8305 (tm-30) cc_final: 0.8085 (tm-30) REVERT: H 31 ASN cc_start: 0.8158 (t0) cc_final: 0.7797 (t0) REVERT: H 106 TRP cc_start: 0.6621 (OUTLIER) cc_final: 0.5722 (m-90) REVERT: H 163 ASN cc_start: 0.6493 (m-40) cc_final: 0.6059 (t0) REVERT: K 61 ARG cc_start: 0.5860 (OUTLIER) cc_final: 0.5462 (ptp90) REVERT: K 79 GLU cc_start: 0.3422 (mt-10) cc_final: 0.2941 (mt-10) REVERT: C 156 ASN cc_start: 0.6274 (OUTLIER) cc_final: 0.5471 (p0) REVERT: C 302 ASP cc_start: 0.4732 (m-30) cc_final: 0.4380 (t0) REVERT: C 398 LEU cc_start: 0.9118 (tp) cc_final: 0.8882 (tt) REVERT: D 37 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7761 (mm-30) REVERT: D 169 ARG cc_start: 0.9261 (OUTLIER) cc_final: 0.8344 (tpp80) REVERT: D 325 GLN cc_start: 0.8302 (tm-30) cc_final: 0.8082 (tm-30) REVERT: I 31 ASN cc_start: 0.8156 (t0) cc_final: 0.7798 (t0) REVERT: I 106 TRP cc_start: 0.6623 (OUTLIER) cc_final: 0.5727 (m-90) REVERT: I 163 ASN cc_start: 0.6492 (m-40) cc_final: 0.6057 (t0) REVERT: M 61 ARG cc_start: 0.5849 (OUTLIER) cc_final: 0.5458 (ptp90) REVERT: M 79 GLU cc_start: 0.3422 (mt-10) cc_final: 0.2943 (mt-10) outliers start: 64 outliers final: 42 residues processed: 267 average time/residue: 0.3929 time to fit residues: 172.9471 Evaluate side-chains 261 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 209 time to evaluate : 3.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 361 VAL 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 283 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 743 LEU Chi-restraints excluded: chain B residue 762 PHE 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 150 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 361 VAL 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 283 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 743 LEU Chi-restraints excluded: chain D residue 762 PHE 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 150 VAL Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 61 ARG 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: 1.9990 chunk 338 optimal weight: 8.9990 chunk 206 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 chunk 354 optimal weight: 8.9990 chunk 326 optimal weight: 10.0000 chunk 282 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 218 optimal weight: 0.9990 chunk 173 optimal weight: 20.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN ** H 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 HIS ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 ASN D 175 GLN ** I 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 147 GLN ** M 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 29844 Z= 0.373 Angle : 0.694 9.339 40616 Z= 0.351 Chirality : 0.047 0.350 4564 Planarity : 0.004 0.054 5114 Dihedral : 5.691 59.221 4672 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.54 % Favored : 91.29 % Rotamer: Outliers : 2.00 % Allowed : 19.19 % Favored : 78.81 % 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: -0.74 (0.14), residues: 3570 helix: 0.41 (0.13), residues: 1654 sheet: 0.52 (0.24), residues: 430 loop : -1.86 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP I 99 HIS 0.014 0.002 HIS C 108 PHE 0.023 0.002 PHE K 94 TYR 0.021 0.002 TYR B 183 ARG 0.007 0.001 ARG I 104 ********************** 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 280 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 217 time to evaluate : 3.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 ASN cc_start: 0.6269 (OUTLIER) cc_final: 0.5474 (p0) REVERT: A 398 LEU cc_start: 0.9137 (tp) cc_final: 0.8900 (tt) REVERT: B 61 ASN cc_start: 0.8898 (t0) cc_final: 0.8631 (t0) REVERT: B 169 ARG cc_start: 0.9287 (OUTLIER) cc_final: 0.8303 (tpp80) REVERT: B 630 ASP cc_start: 0.7538 (t0) cc_final: 0.7265 (t0) REVERT: H 31 ASN cc_start: 0.8206 (t0) cc_final: 0.7706 (t0) REVERT: H 106 TRP cc_start: 0.6856 (OUTLIER) cc_final: 0.5718 (m-90) REVERT: H 163 ASN cc_start: 0.6505 (m-40) cc_final: 0.6114 (t0) REVERT: K 61 ARG cc_start: 0.5937 (OUTLIER) cc_final: 0.5357 (ptp90) REVERT: K 79 GLU cc_start: 0.3714 (mt-10) cc_final: 0.3213 (mt-10) REVERT: C 156 ASN cc_start: 0.6266 (OUTLIER) cc_final: 0.5470 (p0) REVERT: C 398 LEU cc_start: 0.9137 (tp) cc_final: 0.8899 (tt) REVERT: D 169 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.8302 (tpp80) REVERT: D 630 ASP cc_start: 0.7539 (t0) cc_final: 0.7266 (t0) REVERT: I 31 ASN cc_start: 0.8207 (t0) cc_final: 0.7708 (t0) REVERT: I 106 TRP cc_start: 0.6855 (OUTLIER) cc_final: 0.5717 (m-90) REVERT: I 163 ASN cc_start: 0.6503 (m-40) cc_final: 0.6110 (t0) REVERT: M 61 ARG cc_start: 0.5930 (OUTLIER) cc_final: 0.5351 (ptp90) REVERT: M 79 GLU cc_start: 0.3714 (mt-10) cc_final: 0.3214 (mt-10) outliers start: 63 outliers final: 46 residues processed: 267 average time/residue: 0.3787 time to fit residues: 167.0503 Evaluate side-chains 254 residues out of total 3156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 200 time to evaluate : 3.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 501 GLU Chi-restraints excluded: chain A residue 522 ILE Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 169 ARG Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 558 LEU 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 74 ARG 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 150 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 61 ARG Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 501 GLU Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 169 ARG Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 558 LEU 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 74 ARG 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 150 VAL Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain M residue 61 ARG 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: 8.9990 chunk 300 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 260 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 282 optimal weight: 0.5980 chunk 118 optimal weight: 0.7980 chunk 290 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 139 GLN B 175 GLN ** K 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 61 ASN D 139 GLN 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 = 0.4232 r_free = 0.4232 target = 0.145800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.095363 restraints weight = 63761.693| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 3.46 r_work: 0.3004 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.5161 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= 0.171 Angle : 0.623 8.829 40616 Z= 0.313 Chirality : 0.043 0.337 4564 Planarity : 0.004 0.054 5114 Dihedral : 5.326 54.073 4672 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.45 % Favored : 92.38 % Rotamer: Outliers : 1.75 % Allowed : 19.50 % Favored : 78.75 % 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: -0.49 (0.14), residues: 3570 helix: 0.61 (0.13), residues: 1664 sheet: 0.50 (0.24), residues: 430 loop : -1.67 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 99 HIS 0.012 0.001 HIS M 198 PHE 0.012 0.001 PHE B 684 TYR 0.014 0.001 TYR C 567 ARG 0.004 0.000 ARG M 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7264.12 seconds wall clock time: 132 minutes 12.55 seconds (7932.55 seconds total)