Starting phenix.real_space_refine on Thu Feb 22 02:02:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abh_15321/02_2024/8abh_15321_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abh_15321/02_2024/8abh_15321.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abh_15321/02_2024/8abh_15321_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abh_15321/02_2024/8abh_15321_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abh_15321/02_2024/8abh_15321_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abh_15321/02_2024/8abh_15321.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abh_15321/02_2024/8abh_15321.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abh_15321/02_2024/8abh_15321_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abh_15321/02_2024/8abh_15321_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 8 7.16 5 P 30 5.49 5 S 102 5.16 5 C 21039 2.51 5 N 5300 2.21 5 O 6069 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 4": "NH1" <-> "NH2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P GLU 137": "OE1" <-> "OE2" Residue "P GLU 178": "OE1" <-> "OE2" Residue "P PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 213": "OE1" <-> "OE2" Residue "P PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 220": "OE1" <-> "OE2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G ARG 61": "NH1" <-> "NH2" Residue "G GLU 66": "OE1" <-> "OE2" Residue "G ARG 70": "NH1" <-> "NH2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G GLU 96": "OE1" <-> "OE2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F GLU 121": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B GLU 350": "OE1" <-> "OE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "D ARG 189": "NH1" <-> "NH2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "D TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D ARG 321": "NH1" <-> "NH2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "N ARG 4": "NH1" <-> "NH2" Residue "N ARG 70": "NH1" <-> "NH2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "N ARG 110": "NH1" <-> "NH2" Residue "N PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 283": "NH1" <-> "NH2" Residue "N ARG 310": "NH1" <-> "NH2" Residue "N ARG 314": "NH1" <-> "NH2" Residue "N TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "R GLU 12": "OE1" <-> "OE2" Residue "R GLU 50": "OE1" <-> "OE2" Residue "R GLU 51": "OE1" <-> "OE2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R ARG 61": "NH1" <-> "NH2" Residue "R GLU 66": "OE1" <-> "OE2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R ARG 73": "NH1" <-> "NH2" Residue "R ARG 76": "NH1" <-> "NH2" Residue "R GLU 96": "OE1" <-> "OE2" Residue "R GLU 110": "OE1" <-> "OE2" Residue "R GLU 123": "OE1" <-> "OE2" Residue "Q GLU 88": "OE1" <-> "OE2" Residue "Q GLU 118": "OE1" <-> "OE2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "Q GLU 126": "OE1" <-> "OE2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "L GLU 141": "OE1" <-> "OE2" Residue "L ARG 188": "NH1" <-> "NH2" Residue "L GLU 354": "OE1" <-> "OE2" Residue "L ARG 384": "NH1" <-> "NH2" Residue "L GLU 424": "OE1" <-> "OE2" Residue "L TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M GLU 78": "OE1" <-> "OE2" Residue "M TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 117": "OE1" <-> "OE2" Residue "M ARG 140": "NH1" <-> "NH2" Residue "M GLU 150": "OE1" <-> "OE2" Residue "M ARG 234": "NH1" <-> "NH2" Residue "M GLU 313": "OE1" <-> "OE2" Residue "M GLU 350": "OE1" <-> "OE2" Residue "M GLU 376": "OE1" <-> "OE2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "O ARG 132": "NH1" <-> "NH2" Residue "O ARG 136": "NH1" <-> "NH2" Residue "O GLU 164": "OE1" <-> "OE2" Residue "O ARG 170": "NH1" <-> "NH2" Residue "O TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 189": "NH1" <-> "NH2" Residue "O ARG 207": "NH1" <-> "NH2" Residue "O TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 250": "NH1" <-> "NH2" Residue "O GLU 260": "OE1" <-> "OE2" Residue "O ARG 289": "NH1" <-> "NH2" Residue "O PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 321": "NH1" <-> "NH2" Residue "S PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 34": "OE1" <-> "OE2" Residue "U TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32548 Number of models: 1 Model: "" Number of chains: 33 Chain: "C" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "P" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1445 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 11, 'TRANS': 174} Chain: "G" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "A" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "B" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "D" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "I" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "J" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "N" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "E" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "R" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "Q" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "L" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "M" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "O" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "S" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "T" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "U" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "C" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 300 Unusual residues: {'AWB': 1, 'CDL': 2, 'HEM': 2, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 129 Chain: "P" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {'FES': 1, 'LMT': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "J" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 243 Unusual residues: {'AWB': 1, 'CDL': 1, 'HEM': 2, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 86 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 30.295 50.168 35.049 1.00152.11 S ATOM 4207 SG CYS P 187 32.756 47.305 34.080 1.00117.87 S Time building chain proxies: 16.91, per 1000 atoms: 0.52 Number of scatterers: 32548 At special positions: 0 Unit cell: (118.002, 129.636, 163.707, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 8 26.01 S 102 16.00 P 30 15.00 O 6069 8.00 N 5300 7.00 C 21039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS P 173 " - pdb=" SG CYS P 189 " distance=2.04 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.06 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.06 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.06 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.07 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.34 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 301 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 170 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 190 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 187 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 168 " Number of angles added : 3 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7486 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 185 helices and 15 sheets defined 54.3% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.05 Creating SS restraints... Processing helix chain 'C' and resid 3 through 6 No H-bonds generated for 'chain 'C' and resid 3 through 6' Processing helix chain 'C' and resid 8 through 17 Processing helix chain 'C' and resid 28 through 52 removed outlier: 3.903A pdb=" N PHE C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY C 33 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR C 46 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 70 Processing helix chain 'C' and resid 75 through 102 removed outlier: 3.758A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 135 removed outlier: 4.157A pdb=" N VAL C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 153 removed outlier: 3.977A pdb=" N VAL C 151 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER C 152 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA C 153 " --> pdb=" O ASN C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 166 Processing helix chain 'C' and resid 173 through 203 Proline residue: C 187 - end of helix removed outlier: 4.170A pdb=" N THR C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 246 removed outlier: 6.814A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 257 Processing helix chain 'C' and resid 273 through 284 Proline residue: C 277 - end of helix Processing helix chain 'C' and resid 288 through 308 removed outlier: 3.795A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEU C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Proline residue: C 306 - end of helix Processing helix chain 'C' and resid 320 through 340 Processing helix chain 'C' and resid 348 through 364 removed outlier: 4.094A pdb=" N PHE C 363 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 382 Processing helix chain 'P' and resid 59 through 91 removed outlier: 3.632A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN P 90 " --> pdb=" O ASP P 86 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N MET P 91 " --> pdb=" O PHE P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 100 removed outlier: 3.617A pdb=" N MET P 100 " --> pdb=" O ASP P 96 " (cutoff:3.500A) Processing helix chain 'P' and resid 132 through 138 Processing helix chain 'P' and resid 152 through 155 No H-bonds generated for 'chain 'P' and resid 152 through 155' Processing helix chain 'G' and resid 4 through 16 Processing helix chain 'G' and resid 18 through 35 Proline residue: G 26 - end of helix Processing helix chain 'G' and resid 37 through 40 Processing helix chain 'G' and resid 44 through 47 Processing helix chain 'G' and resid 53 through 60 Processing helix chain 'G' and resid 64 through 83 Processing helix chain 'G' and resid 89 through 91 No H-bonds generated for 'chain 'G' and resid 89 through 91' Processing helix chain 'G' and resid 95 through 97 No H-bonds generated for 'chain 'G' and resid 95 through 97' Processing helix chain 'G' and resid 103 through 121 removed outlier: 3.666A pdb=" N ASN G 121 " --> pdb=" O ASP G 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 88 Processing helix chain 'F' and resid 92 through 110 Processing helix chain 'F' and resid 124 through 137 Processing helix chain 'F' and resid 139 through 145 removed outlier: 3.601A pdb=" N VAL F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.529A pdb=" N HIS A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 99 Processing helix chain 'A' and resid 120 through 135 removed outlier: 3.848A pdb=" N VAL A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Proline residue: A 124 - end of helix removed outlier: 3.883A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 154 removed outlier: 3.997A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.609A pdb=" N THR A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 206 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.969A pdb=" N ARG A 315 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'A' and resid 359 through 375 removed outlier: 3.669A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 395 removed outlier: 3.560A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 413 Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 432 through 442 Processing helix chain 'A' and resid 462 through 469 removed outlier: 3.612A pdb=" N ASP A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET A 469 " --> pdb=" O ILE A 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 70 through 79 Processing helix chain 'B' and resid 101 through 117 Proline residue: B 105 - end of helix removed outlier: 3.583A pdb=" N LYS B 116 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU B 117 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 129 through 141 Processing helix chain 'B' and resid 144 through 157 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 200 through 210 removed outlier: 3.527A pdb=" N THR B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.747A pdb=" N LEU B 263 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 311 through 330 Processing helix chain 'B' and resid 334 through 353 Processing helix chain 'B' and resid 355 through 367 removed outlier: 3.715A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 383 through 394 Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'D' and resid 87 through 90 No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 124 through 126 No H-bonds generated for 'chain 'D' and resid 124 through 126' Processing helix chain 'D' and resid 135 through 138 Processing helix chain 'D' and resid 145 through 153 Processing helix chain 'D' and resid 185 through 192 Processing helix chain 'D' and resid 210 through 218 removed outlier: 3.531A pdb=" N PHE D 215 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 282 Processing helix chain 'D' and resid 286 through 319 Proline residue: D 317 - end of helix Processing helix chain 'H' and resid 40 through 80 removed outlier: 4.331A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) Proline residue: H 62 - end of helix Processing helix chain 'H' and resid 86 through 92 Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 44 Processing helix chain 'I' and resid 50 through 56 removed outlier: 5.022A pdb=" N HIS I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LYS I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 49 removed outlier: 3.539A pdb=" N LYS J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP J 31 " --> pdb=" O THR J 27 " (cutoff:3.500A) Proline residue: J 33 - end of helix Processing helix chain 'J' and resid 54 through 59 Processing helix chain 'J' and resid 61 through 63 No H-bonds generated for 'chain 'J' and resid 61 through 63' Processing helix chain 'J' and resid 67 through 71 Processing helix chain 'J' and resid 77 through 79 No H-bonds generated for 'chain 'J' and resid 77 through 79' Processing helix chain 'N' and resid 3 through 6 No H-bonds generated for 'chain 'N' and resid 3 through 6' Processing helix chain 'N' and resid 8 through 17 Processing helix chain 'N' and resid 28 through 52 removed outlier: 3.894A pdb=" N PHE N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY N 33 " --> pdb=" O TRP N 30 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR N 46 " --> pdb=" O GLN N 43 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE N 48 " --> pdb=" O ALA N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 70 Processing helix chain 'N' and resid 75 through 102 removed outlier: 3.756A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 135 removed outlier: 4.177A pdb=" N VAL N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 138 through 153 removed outlier: 4.088A pdb=" N VAL N 151 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER N 152 " --> pdb=" O CYS N 148 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA N 153 " --> pdb=" O ASN N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 166 Processing helix chain 'N' and resid 173 through 203 Proline residue: N 187 - end of helix removed outlier: 4.188A pdb=" N THR N 203 " --> pdb=" O ILE N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 246 removed outlier: 6.826A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR N 232 " --> pdb=" O LYS N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 254 through 257 Processing helix chain 'N' and resid 273 through 284 Proline residue: N 277 - end of helix Processing helix chain 'N' and resid 288 through 308 removed outlier: 3.791A pdb=" N ILE N 299 " --> pdb=" O MET N 295 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU N 302 " --> pdb=" O ALA N 298 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU N 303 " --> pdb=" O ILE N 299 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ILE N 304 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU N 305 " --> pdb=" O ILE N 301 " (cutoff:3.500A) Proline residue: N 306 - end of helix Processing helix chain 'N' and resid 320 through 340 Processing helix chain 'N' and resid 348 through 364 removed outlier: 4.086A pdb=" N PHE N 363 " --> pdb=" O TYR N 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 366 through 382 Processing helix chain 'E' and resid 59 through 91 removed outlier: 3.631A pdb=" N SER E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N MET E 91 " --> pdb=" O PHE E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 98 No H-bonds generated for 'chain 'E' and resid 95 through 98' Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 35 Proline residue: R 26 - end of helix Processing helix chain 'R' and resid 37 through 40 Processing helix chain 'R' and resid 44 through 47 Processing helix chain 'R' and resid 53 through 61 Processing helix chain 'R' and resid 64 through 83 Processing helix chain 'R' and resid 89 through 91 No H-bonds generated for 'chain 'R' and resid 89 through 91' Processing helix chain 'R' and resid 95 through 97 No H-bonds generated for 'chain 'R' and resid 95 through 97' Processing helix chain 'R' and resid 103 through 121 removed outlier: 3.673A pdb=" N ASN R 121 " --> pdb=" O ASP R 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 88 Processing helix chain 'Q' and resid 92 through 110 Processing helix chain 'Q' and resid 124 through 137 Processing helix chain 'Q' and resid 139 through 145 removed outlier: 3.599A pdb=" N VAL Q 145 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 72 through 79 removed outlier: 3.509A pdb=" N HIS L 78 " --> pdb=" O HIS L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 99 Processing helix chain 'L' and resid 120 through 135 removed outlier: 3.842A pdb=" N VAL L 123 " --> pdb=" O LYS L 120 " (cutoff:3.500A) Proline residue: L 124 - end of helix removed outlier: 3.881A pdb=" N VAL L 127 " --> pdb=" O PRO L 124 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU L 134 " --> pdb=" O ALA L 131 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN L 135 " --> pdb=" O ASP L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 156 removed outlier: 3.993A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU L 156 " --> pdb=" O THR L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 160 No H-bonds generated for 'chain 'L' and resid 158 through 160' Processing helix chain 'L' and resid 162 through 174 Processing helix chain 'L' and resid 179 through 181 No H-bonds generated for 'chain 'L' and resid 179 through 181' Processing helix chain 'L' and resid 188 through 191 No H-bonds generated for 'chain 'L' and resid 188 through 191' Processing helix chain 'L' and resid 196 through 206 Processing helix chain 'L' and resid 209 through 211 No H-bonds generated for 'chain 'L' and resid 209 through 211' Processing helix chain 'L' and resid 222 through 232 Processing helix chain 'L' and resid 294 through 304 removed outlier: 3.504A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 312 through 316 removed outlier: 3.977A pdb=" N ARG L 315 " --> pdb=" O GLY L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 320 through 327 Processing helix chain 'L' and resid 359 through 375 removed outlier: 3.662A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 395 removed outlier: 3.623A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU L 394 " --> pdb=" O LYS L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 413 Processing helix chain 'L' and resid 420 through 428 Processing helix chain 'L' and resid 432 through 442 Processing helix chain 'L' and resid 462 through 469 removed outlier: 3.603A pdb=" N ASP L 468 " --> pdb=" O ARG L 464 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET L 469 " --> pdb=" O ILE L 465 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 47 No H-bonds generated for 'chain 'M' and resid 45 through 47' Processing helix chain 'M' and resid 53 through 59 Processing helix chain 'M' and resid 70 through 79 Processing helix chain 'M' and resid 101 through 117 Proline residue: M 105 - end of helix removed outlier: 3.579A pdb=" N VAL M 108 " --> pdb=" O PRO M 105 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS M 116 " --> pdb=" O ASN M 113 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU M 117 " --> pdb=" O VAL M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 127 Processing helix chain 'M' and resid 129 through 141 Processing helix chain 'M' and resid 144 through 157 Processing helix chain 'M' and resid 160 through 162 No H-bonds generated for 'chain 'M' and resid 160 through 162' Processing helix chain 'M' and resid 175 through 185 Processing helix chain 'M' and resid 188 through 190 No H-bonds generated for 'chain 'M' and resid 188 through 190' Processing helix chain 'M' and resid 200 through 210 removed outlier: 3.529A pdb=" N THR M 209 " --> pdb=" O GLN M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 263 removed outlier: 3.744A pdb=" N LEU M 263 " --> pdb=" O ALA M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 280 through 282 No H-bonds generated for 'chain 'M' and resid 280 through 282' Processing helix chain 'M' and resid 311 through 330 Processing helix chain 'M' and resid 334 through 353 Processing helix chain 'M' and resid 355 through 367 removed outlier: 3.839A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 375 through 377 No H-bonds generated for 'chain 'M' and resid 375 through 377' Processing helix chain 'M' and resid 383 through 394 Processing helix chain 'M' and resid 407 through 409 No H-bonds generated for 'chain 'M' and resid 407 through 409' Processing helix chain 'M' and resid 413 through 415 No H-bonds generated for 'chain 'M' and resid 413 through 415' Processing helix chain 'O' and resid 87 through 90 No H-bonds generated for 'chain 'O' and resid 87 through 90' Processing helix chain 'O' and resid 110 through 122 Processing helix chain 'O' and resid 124 through 126 No H-bonds generated for 'chain 'O' and resid 124 through 126' Processing helix chain 'O' and resid 135 through 138 Processing helix chain 'O' and resid 145 through 153 Processing helix chain 'O' and resid 185 through 192 Processing helix chain 'O' and resid 210 through 219 removed outlier: 3.529A pdb=" N PHE O 215 " --> pdb=" O ASP O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 267 through 282 Processing helix chain 'O' and resid 286 through 314 Processing helix chain 'O' and resid 316 through 319 No H-bonds generated for 'chain 'O' and resid 316 through 319' Processing helix chain 'S' and resid 40 through 80 removed outlier: 4.319A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL S 59 " --> pdb=" O GLN S 55 " (cutoff:3.500A) Proline residue: S 62 - end of helix Processing helix chain 'S' and resid 86 through 92 Processing helix chain 'T' and resid 5 through 11 Processing helix chain 'T' and resid 15 through 44 Processing helix chain 'T' and resid 50 through 56 removed outlier: 5.002A pdb=" N HIS T 55 " --> pdb=" O LYS T 51 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LYS T 56 " --> pdb=" O ASP T 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 49 removed outlier: 3.559A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP U 31 " --> pdb=" O THR U 27 " (cutoff:3.500A) Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 54 through 59 Processing helix chain 'U' and resid 61 through 63 No H-bonds generated for 'chain 'U' and resid 61 through 63' Processing helix chain 'U' and resid 67 through 71 Processing helix chain 'U' and resid 77 through 79 No H-bonds generated for 'chain 'U' and resid 77 through 79' Processing sheet with id= A, first strand: chain 'C' and resid 21 through 23 Processing sheet with id= B, first strand: chain 'P' and resid 103 through 106 removed outlier: 3.526A pdb=" N VAL P 103 " --> pdb=" O ILE P 224 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'P' and resid 114 through 120 removed outlier: 3.905A pdb=" N LYS P 114 " --> pdb=" O HIS P 129 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'P' and resid 185 through 187 Processing sheet with id= E, first strand: chain 'A' and resid 31 through 34 Processing sheet with id= F, first strand: chain 'A' and resid 266 through 271 Processing sheet with id= G, first strand: chain 'B' and resid 16 through 20 removed outlier: 4.089A pdb=" N LYS B 24 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 231 through 235 removed outlier: 3.605A pdb=" N ASN B 241 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 156 through 158 Processing sheet with id= J, first strand: chain 'N' and resid 21 through 23 Processing sheet with id= K, first strand: chain 'L' and resid 31 through 34 Processing sheet with id= L, first strand: chain 'L' and resid 266 through 271 Processing sheet with id= M, first strand: chain 'M' and resid 16 through 20 removed outlier: 4.085A pdb=" N LYS M 24 " --> pdb=" O VAL M 191 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'M' and resid 231 through 235 removed outlier: 3.597A pdb=" N ASN M 241 " --> pdb=" O GLY M 308 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'O' and resid 156 through 158 1580 hydrogen bonds defined for protein. 4317 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: 11.56 Time building geometry restraints manager: 14.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.40: 13620 1.40 - 1.61: 19543 1.61 - 1.82: 170 1.82 - 2.03: 25 2.03 - 2.24: 17 Bond restraints: 33375 Sorted by residual: bond pdb=" C14 CDL S 701 " pdb=" C15 CDL S 701 " ideal model delta sigma weight residual 1.517 1.790 -0.273 2.70e-02 1.37e+03 1.02e+02 bond pdb=" N ALA T 4 " pdb=" CA ALA T 4 " ideal model delta sigma weight residual 1.458 1.609 -0.151 1.90e-02 2.77e+03 6.35e+01 bond pdb=" N ALA I 4 " pdb=" CA ALA I 4 " ideal model delta sigma weight residual 1.458 1.606 -0.148 1.90e-02 2.77e+03 6.11e+01 bond pdb=" C76 CDL A3001 " pdb=" C77 CDL A3001 " ideal model delta sigma weight residual 1.517 1.725 -0.208 2.70e-02 1.37e+03 5.94e+01 bond pdb=" N TYR S 9 " pdb=" CA TYR S 9 " ideal model delta sigma weight residual 1.458 1.578 -0.120 1.90e-02 2.77e+03 3.99e+01 ... (remaining 33370 not shown) Histogram of bond angle deviations from ideal: 83.28 - 102.39: 381 102.39 - 121.50: 37208 121.50 - 140.61: 7765 140.61 - 159.72: 0 159.72 - 178.83: 12 Bond angle restraints: 45366 Sorted by residual: angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 94.21 10.12 1.14e+00 7.69e-01 7.89e+01 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 94.03 10.30 1.20e+00 6.94e-01 7.36e+01 angle pdb=" C MET P 100 " pdb=" N ALA P 101 " pdb=" CA ALA P 101 " ideal model delta sigma weight residual 121.54 105.39 16.15 1.91e+00 2.74e-01 7.15e+01 angle pdb=" CG ARG M 90 " pdb=" CD ARG M 90 " pdb=" NE ARG M 90 " ideal model delta sigma weight residual 112.00 93.60 18.40 2.20e+00 2.07e-01 6.99e+01 angle pdb=" CG ARG B 90 " pdb=" CD ARG B 90 " pdb=" NE ARG B 90 " ideal model delta sigma weight residual 112.00 93.95 18.05 2.20e+00 2.07e-01 6.73e+01 ... (remaining 45361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.21: 18816 32.21 - 64.43: 1018 64.43 - 96.64: 99 96.64 - 128.85: 1 128.85 - 161.06: 3 Dihedral angle restraints: 19937 sinusoidal: 8318 harmonic: 11619 Sorted by residual: dihedral pdb=" C GLN M 215 " pdb=" N GLN M 215 " pdb=" CA GLN M 215 " pdb=" CB GLN M 215 " ideal model delta harmonic sigma weight residual -122.60 -106.05 -16.55 0 2.50e+00 1.60e-01 4.38e+01 dihedral pdb=" C GLN B 215 " pdb=" N GLN B 215 " pdb=" CA GLN B 215 " pdb=" CB GLN B 215 " ideal model delta harmonic sigma weight residual -122.60 -106.21 -16.39 0 2.50e+00 1.60e-01 4.30e+01 dihedral pdb=" C GLU O 283 " pdb=" N GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta harmonic sigma weight residual -122.60 -106.78 -15.82 0 2.50e+00 1.60e-01 4.01e+01 ... (remaining 19934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.213: 4603 0.213 - 0.425: 331 0.425 - 0.638: 14 0.638 - 0.850: 0 0.850 - 1.063: 4 Chirality restraints: 4952 Sorted by residual: chirality pdb=" CB4 CDL C 505 " pdb=" CB3 CDL C 505 " pdb=" CB6 CDL C 505 " pdb=" OB6 CDL C 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.51 -1.06 2.00e-01 2.50e+01 2.82e+01 chirality pdb=" CB4 CDL D 402 " pdb=" CB3 CDL D 402 " pdb=" CB6 CDL D 402 " pdb=" OB6 CDL D 402 " both_signs ideal model delta sigma weight residual False -2.57 -1.59 -0.99 2.00e-01 2.50e+01 2.43e+01 chirality pdb=" CB4 CDL C 507 " pdb=" CB3 CDL C 507 " pdb=" CB6 CDL C 507 " pdb=" OB6 CDL C 507 " both_signs ideal model delta sigma weight residual False -2.57 -1.62 -0.96 2.00e-01 2.50e+01 2.30e+01 ... (remaining 4949 not shown) Planarity restraints: 5712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 AWB C 506 " -0.046 2.00e-02 2.50e+03 2.46e-01 6.06e+02 pdb=" C21 AWB C 506 " -0.382 2.00e-02 2.50e+03 pdb=" N1 AWB C 506 " 0.249 2.00e-02 2.50e+03 pdb=" O5 AWB C 506 " 0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 AWB N 505 " -0.029 2.00e-02 2.50e+03 2.43e-01 5.93e+02 pdb=" C21 AWB N 505 " 0.403 2.00e-02 2.50e+03 pdb=" N1 AWB N 505 " -0.145 2.00e-02 2.50e+03 pdb=" O5 AWB N 505 " -0.230 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEC D 401 " -0.020 2.00e-02 2.50e+03 3.50e-02 2.75e+01 pdb=" C2A HEC D 401 " -0.013 2.00e-02 2.50e+03 pdb=" C3A HEC D 401 " -0.027 2.00e-02 2.50e+03 pdb=" C4A HEC D 401 " -0.046 2.00e-02 2.50e+03 pdb=" CAA HEC D 401 " 0.052 2.00e-02 2.50e+03 pdb=" CHA HEC D 401 " 0.005 2.00e-02 2.50e+03 pdb=" CHB HEC D 401 " 0.067 2.00e-02 2.50e+03 pdb=" CMA HEC D 401 " -0.018 2.00e-02 2.50e+03 pdb=" NA HEC D 401 " 0.000 2.00e-02 2.50e+03 ... (remaining 5709 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 217 2.61 - 3.18: 28575 3.18 - 3.76: 53821 3.76 - 4.33: 80719 4.33 - 4.90: 123153 Nonbonded interactions: 286485 Sorted by model distance: nonbonded pdb=" NE2 HIS C 82 " pdb="FE HEM C 501 " model vdw 2.040 3.080 nonbonded pdb=" NE2 HIS N 183 " pdb="FE HEM N 501 " model vdw 2.062 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.084 2.520 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.154 3.080 nonbonded pdb=" NE2 HIS C 96 " pdb="FE HEM C 502 " model vdw 2.211 3.080 ... (remaining 286480 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 'L' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = (chain 'C' and (resid 1 through 383 or resid 501 through 504)) selection = (chain 'N' and (resid 1 through 383 or resid 501 through 504)) } ncs_group { reference = (chain 'D' and (resid 85 through 328 or resid 401)) selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = chain 'H' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = (chain 'J' and resid 8 through 82) selection = chain 'U' } 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: 2.080 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: 0.030 Extract box with map and model: 11.500 Check model and map are aligned: 0.520 Set scattering table: 0.310 Process input model: 92.180 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 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 : 0.012 0.273 33375 Z= 0.811 Angle : 1.850 18.396 45366 Z= 1.154 Chirality : 0.121 1.063 4952 Planarity : 0.009 0.246 5712 Dihedral : 18.492 161.065 12436 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.58 % Favored : 97.37 % Rotamer: Outliers : 4.03 % Allowed : 8.06 % Favored : 87.91 % Cbeta Deviations : 1.47 % Peptide Plane: Cis-proline : 2.84 % 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: -1.61 (0.12), residues: 3955 helix: -1.27 (0.09), residues: 2116 sheet: -0.05 (0.26), residues: 357 loop : -0.70 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.009 TRP L 474 HIS 0.025 0.004 HIS N 96 PHE 0.053 0.008 PHE B 107 TYR 0.053 0.008 TYR R 101 ARG 0.060 0.003 ARG B 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 412 time to evaluate : 3.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 160 ASP cc_start: 0.9311 (m-30) cc_final: 0.9045 (m-30) REVERT: C 255 ASP cc_start: 0.8516 (m-30) cc_final: 0.8298 (p0) REVERT: C 369 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8658 (mtp) REVERT: P 104 GLU cc_start: 0.9322 (mt-10) cc_final: 0.8955 (tp30) REVERT: P 137 GLU cc_start: 0.9001 (tt0) cc_final: 0.8696 (tt0) REVERT: P 176 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8491 (pp) REVERT: G 66 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8973 (mp0) REVERT: G 123 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8274 (tm-30) REVERT: F 84 GLU cc_start: 0.8784 (tt0) cc_final: 0.8329 (tp30) REVERT: F 145 VAL cc_start: 0.9328 (m) cc_final: 0.9110 (p) REVERT: A 91 GLN cc_start: 0.9021 (tp40) cc_final: 0.8812 (tp40) REVERT: A 144 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8222 (mt) REVERT: B 31 GLN cc_start: 0.8842 (mt0) cc_final: 0.8508 (mm-40) REVERT: B 334 GLU cc_start: 0.9104 (tp30) cc_final: 0.8676 (pp20) REVERT: D 85 MET cc_start: 0.8360 (mtt) cc_final: 0.8065 (mtt) REVERT: D 164 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8288 (tp30) REVERT: D 166 ASN cc_start: 0.8511 (m110) cc_final: 0.8229 (m110) REVERT: D 235 MET cc_start: 0.8135 (mmt) cc_final: 0.7815 (mmm) REVERT: D 301 SER cc_start: 0.9402 (m) cc_final: 0.9200 (p) REVERT: H 41 VAL cc_start: 0.9046 (t) cc_final: 0.8661 (m) REVERT: H 75 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8355 (tm-30) REVERT: H 87 HIS cc_start: 0.8147 (m-70) cc_final: 0.7842 (m-70) REVERT: I 30 ASP cc_start: 0.8780 (t70) cc_final: 0.8270 (t0) REVERT: I 38 ASP cc_start: 0.8962 (m-30) cc_final: 0.8746 (m-30) REVERT: I 43 ARG cc_start: 0.8304 (mtm110) cc_final: 0.7824 (ptm160) REVERT: J 11 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7766 (tptp) REVERT: J 55 ARG cc_start: 0.8430 (ttm-80) cc_final: 0.7913 (ttm-80) REVERT: N 197 HIS cc_start: 0.9516 (OUTLIER) cc_final: 0.8445 (p-80) REVERT: R 50 GLU cc_start: 0.8916 (pt0) cc_final: 0.8703 (pm20) REVERT: R 94 LYS cc_start: 0.9097 (mttm) cc_final: 0.8880 (mmmt) REVERT: L 164 GLU cc_start: 0.9284 (mt-10) cc_final: 0.9047 (tp30) REVERT: L 227 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8859 (pp20) REVERT: L 228 LEU cc_start: 0.8124 (mt) cc_final: 0.7643 (mt) REVERT: L 397 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6759 (mp) REVERT: L 403 VAL cc_start: 0.8673 (t) cc_final: 0.8472 (m) REVERT: M 19 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8284 (mm-30) REVERT: M 31 GLN cc_start: 0.9003 (mt0) cc_final: 0.8585 (mm-40) REVERT: M 170 TYR cc_start: 0.8379 (p90) cc_final: 0.7966 (p90) REVERT: T 35 THR cc_start: 0.9113 (m) cc_final: 0.8716 (p) REVERT: T 38 ASP cc_start: 0.8803 (m-30) cc_final: 0.8489 (m-30) REVERT: U 10 LYS cc_start: 0.9175 (tttm) cc_final: 0.8973 (tptt) REVERT: U 13 SER cc_start: 0.8744 (t) cc_final: 0.8490 (p) REVERT: U 69 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8996 (pp20) outliers start: 134 outliers final: 17 residues processed: 514 average time/residue: 1.5501 time to fit residues: 933.0715 Evaluate side-chains 241 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 216 time to evaluate : 3.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain L residue 378 SER Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain S residue 51 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 30.0000 chunk 297 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 200 optimal weight: 0.0980 chunk 158 optimal weight: 1.9990 chunk 307 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 186 optimal weight: 0.9990 chunk 228 optimal weight: 30.0000 chunk 355 optimal weight: 2.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN C 22 GLN C 173 ASN C 177 GLN C 332 ASN P 85 GLN G 54 ASN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 ASN A 74 HIS ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN A 222 HIS ** A 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN A 371 ASN B 87 HIS ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN B 316 GLN I 39 ASN N 14 ASN N 177 GLN N 332 ASN E 90 ASN Q 135 ASN L 135 GLN L 332 ASN L 371 ASN M 87 HIS M 92 HIS M 98 GLN M 215 GLN M 316 GLN O 102 ASN O 118 GLN O 193 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33375 Z= 0.214 Angle : 0.651 16.803 45366 Z= 0.321 Chirality : 0.042 0.160 4952 Planarity : 0.004 0.043 5712 Dihedral : 14.206 156.720 5287 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.59 % Allowed : 12.84 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.13), residues: 3955 helix: 0.64 (0.11), residues: 2126 sheet: 0.65 (0.27), residues: 356 loop : 0.02 (0.17), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 156 HIS 0.016 0.001 HIS F 96 PHE 0.020 0.002 PHE L 334 TYR 0.022 0.002 TYR B 341 ARG 0.007 0.001 ARG P 202 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 240 time to evaluate : 3.753 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: C 139 MET cc_start: 0.9162 (tpt) cc_final: 0.8667 (tpt) REVERT: P 118 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8696 (pp) REVERT: G 66 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8984 (mp0) REVERT: G 110 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8689 (mt-10) REVERT: G 124 VAL cc_start: 0.9196 (t) cc_final: 0.8841 (m) REVERT: F 84 GLU cc_start: 0.8787 (tt0) cc_final: 0.8184 (tp30) REVERT: F 88 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8467 (mm-30) REVERT: F 103 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8396 (tm-30) REVERT: F 125 GLU cc_start: 0.8742 (tp30) cc_final: 0.8503 (tp30) REVERT: A 91 GLN cc_start: 0.9056 (tp40) cc_final: 0.8797 (tp40) REVERT: A 120 LYS cc_start: 0.8835 (tttt) cc_final: 0.8447 (tptp) REVERT: B 31 GLN cc_start: 0.8766 (mt0) cc_final: 0.8468 (mm-40) REVERT: B 334 GLU cc_start: 0.9071 (tp30) cc_final: 0.8765 (tp30) REVERT: D 164 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8180 (tp30) REVERT: D 166 ASN cc_start: 0.8506 (m110) cc_final: 0.8140 (m110) REVERT: H 51 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.6038 (ptm-80) REVERT: H 75 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8564 (tm-30) REVERT: J 11 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7811 (tptp) REVERT: J 13 SER cc_start: 0.8709 (t) cc_final: 0.8350 (p) REVERT: E 54 LYS cc_start: 0.9136 (tppt) cc_final: 0.8906 (mmmt) REVERT: E 62 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7789 (mtm110) REVERT: Q 88 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8216 (mm-30) REVERT: Q 104 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7815 (ptp90) REVERT: Q 137 ASN cc_start: 0.7936 (m-40) cc_final: 0.7491 (m-40) REVERT: L 164 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8909 (tp30) REVERT: L 228 LEU cc_start: 0.8249 (mt) cc_final: 0.7768 (mt) REVERT: L 403 VAL cc_start: 0.8766 (t) cc_final: 0.8559 (m) REVERT: M 31 GLN cc_start: 0.8966 (mt0) cc_final: 0.8561 (mm-40) REVERT: M 251 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8656 (pm20) REVERT: S 51 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.5955 (ptm-80) REVERT: S 75 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8947 (pt0) REVERT: S 88 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8764 (tm-30) REVERT: T 31 MET cc_start: 0.8518 (mmm) cc_final: 0.8076 (mmm) REVERT: U 69 GLU cc_start: 0.9318 (mt-10) cc_final: 0.9034 (pp20) outliers start: 86 outliers final: 19 residues processed: 304 average time/residue: 1.5287 time to fit residues: 548.9703 Evaluate side-chains 221 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 196 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 140 GLU Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain P residue 215 ASP Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 90 ASN Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain Q residue 104 ARG Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 378 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain S residue 51 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 296 optimal weight: 8.9990 chunk 242 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 356 optimal weight: 9.9990 chunk 385 optimal weight: 0.0670 chunk 317 optimal weight: 4.9990 chunk 353 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 286 optimal weight: 30.0000 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 341 GLN F 132 HIS A 91 GLN ** A 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 22 GLN Q 132 HIS M 408 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.158 33375 Z= 0.355 Angle : 0.728 40.192 45366 Z= 0.328 Chirality : 0.045 0.213 4952 Planarity : 0.005 0.056 5712 Dihedral : 13.148 149.246 5260 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.62 % Allowed : 13.83 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.13), residues: 3955 helix: 0.84 (0.11), residues: 2129 sheet: 0.66 (0.27), residues: 355 loop : 0.23 (0.17), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 142 HIS 0.031 0.002 HIS C 343 PHE 0.024 0.002 PHE F 94 TYR 0.018 0.002 TYR C 16 ARG 0.006 0.001 ARG P 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 203 time to evaluate : 3.712 Fit side-chains revert: symmetry clash REVERT: C 341 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.8986 (pp30) REVERT: P 118 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8643 (pt) REVERT: G 23 ILE cc_start: 0.8947 (tp) cc_final: 0.8689 (mp) REVERT: G 66 GLU cc_start: 0.9368 (mm-30) cc_final: 0.9109 (mp0) REVERT: G 96 GLU cc_start: 0.9033 (pp20) cc_final: 0.8606 (pp20) REVERT: G 97 GLU cc_start: 0.9030 (tt0) cc_final: 0.8338 (mt-10) REVERT: G 110 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8686 (mt-10) REVERT: G 124 VAL cc_start: 0.9268 (OUTLIER) cc_final: 0.9039 (m) REVERT: F 84 GLU cc_start: 0.9005 (tt0) cc_final: 0.8505 (tp30) REVERT: F 88 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8606 (mm-30) REVERT: F 103 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8432 (tm-30) REVERT: F 107 LYS cc_start: 0.9104 (pttt) cc_final: 0.8616 (mmtt) REVERT: A 120 LYS cc_start: 0.9083 (tttt) cc_final: 0.8617 (tptp) REVERT: A 212 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8521 (mtm) REVERT: B 334 GLU cc_start: 0.9054 (tp30) cc_final: 0.8744 (tm-30) REVERT: D 85 MET cc_start: 0.8580 (mtp) cc_final: 0.8298 (mtp) REVERT: D 166 ASN cc_start: 0.8680 (m110) cc_final: 0.8448 (m110) REVERT: H 75 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8844 (tp30) REVERT: I 30 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.8543 (t0) REVERT: J 11 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7956 (tptp) REVERT: J 13 SER cc_start: 0.8843 (t) cc_final: 0.8485 (p) REVERT: N 142 TRP cc_start: 0.8825 (m100) cc_final: 0.8606 (m100) REVERT: N 239 MET cc_start: 0.8760 (ptt) cc_final: 0.8077 (tpp) REVERT: E 62 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8045 (mtm110) REVERT: Q 84 GLU cc_start: 0.9046 (tt0) cc_final: 0.8835 (mm-30) REVERT: Q 116 HIS cc_start: 0.8521 (OUTLIER) cc_final: 0.8159 (m-70) REVERT: Q 121 GLU cc_start: 0.7885 (tt0) cc_final: 0.7551 (tp30) REVERT: Q 131 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8134 (mp10) REVERT: Q 137 ASN cc_start: 0.8242 (m-40) cc_final: 0.8013 (m-40) REVERT: M 31 GLN cc_start: 0.9102 (mt0) cc_final: 0.8692 (mm-40) REVERT: U 69 GLU cc_start: 0.9341 (mt-10) cc_final: 0.9065 (pp20) outliers start: 87 outliers final: 18 residues processed: 267 average time/residue: 1.5472 time to fit residues: 488.2813 Evaluate side-chains 198 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 171 time to evaluate : 3.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 341 GLN Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain P residue 215 ASP Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 90 ASN Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain Q residue 116 HIS Chi-restraints excluded: chain Q residue 131 GLN Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 40 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 170 optimal weight: 9.9990 chunk 239 optimal weight: 0.8980 chunk 357 optimal weight: 0.0270 chunk 378 optimal weight: 8.9990 chunk 186 optimal weight: 7.9990 chunk 339 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 overall best weight: 1.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 341 GLN ** P 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 HIS ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 HIS B 377 ASN E 85 GLN R 84 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33375 Z= 0.186 Angle : 0.551 15.197 45366 Z= 0.264 Chirality : 0.040 0.222 4952 Planarity : 0.004 0.057 5712 Dihedral : 12.529 150.045 5249 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.74 % Allowed : 15.07 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 1.11 (0.13), residues: 3955 helix: 1.15 (0.11), residues: 2141 sheet: 0.56 (0.27), residues: 358 loop : 0.35 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 156 HIS 0.008 0.001 HIS F 96 PHE 0.017 0.001 PHE A 334 TYR 0.016 0.001 TYR B 341 ARG 0.004 0.000 ARG U 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 187 time to evaluate : 3.435 Fit side-chains REVERT: C 341 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8631 (pp30) REVERT: P 68 MET cc_start: 0.8992 (tpp) cc_final: 0.8753 (mmp) REVERT: P 118 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8785 (pt) REVERT: G 23 ILE cc_start: 0.8921 (tp) cc_final: 0.8658 (mp) REVERT: G 66 GLU cc_start: 0.9359 (mm-30) cc_final: 0.9102 (mp0) REVERT: G 110 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8635 (mt-10) REVERT: F 84 GLU cc_start: 0.9018 (tt0) cc_final: 0.8467 (tm-30) REVERT: F 88 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8637 (mm-30) REVERT: F 103 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8472 (pp20) REVERT: F 104 ARG cc_start: 0.8210 (ptp90) cc_final: 0.7855 (ptm-80) REVERT: F 107 LYS cc_start: 0.9093 (pttt) cc_final: 0.8592 (mmtt) REVERT: F 116 HIS cc_start: 0.8690 (m90) cc_final: 0.8409 (m90) REVERT: A 99 MET cc_start: 0.8909 (tmm) cc_final: 0.8672 (tmm) REVERT: A 120 LYS cc_start: 0.9120 (tttt) cc_final: 0.8668 (tptp) REVERT: B 268 SER cc_start: 0.8445 (m) cc_final: 0.8098 (p) REVERT: B 334 GLU cc_start: 0.9005 (tp30) cc_final: 0.8679 (tm-30) REVERT: D 85 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8463 (mtp) REVERT: D 166 ASN cc_start: 0.8793 (m110) cc_final: 0.8590 (m110) REVERT: H 75 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8884 (tp30) REVERT: I 30 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8579 (t0) REVERT: J 13 SER cc_start: 0.8795 (t) cc_final: 0.8435 (p) REVERT: N 142 TRP cc_start: 0.8783 (m100) cc_final: 0.8578 (m100) REVERT: N 239 MET cc_start: 0.8688 (ptt) cc_final: 0.8056 (tpp) REVERT: E 54 LYS cc_start: 0.9101 (mmmt) cc_final: 0.8742 (tppt) REVERT: E 62 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8007 (mtm110) REVERT: R 12 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8960 (mt-10) REVERT: Q 80 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8561 (pp) REVERT: Q 116 HIS cc_start: 0.8543 (OUTLIER) cc_final: 0.8183 (m-70) REVERT: Q 121 GLU cc_start: 0.8145 (tt0) cc_final: 0.7764 (tp30) REVERT: Q 131 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8284 (mp10) REVERT: M 31 GLN cc_start: 0.9102 (mt0) cc_final: 0.8676 (mm-40) REVERT: M 60 PHE cc_start: 0.9545 (OUTLIER) cc_final: 0.8879 (t80) REVERT: S 75 GLU cc_start: 0.9299 (mt-10) cc_final: 0.9044 (pt0) REVERT: U 69 GLU cc_start: 0.9364 (mt-10) cc_final: 0.9050 (pp20) outliers start: 58 outliers final: 17 residues processed: 230 average time/residue: 1.5005 time to fit residues: 409.2526 Evaluate side-chains 201 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 175 time to evaluate : 3.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 341 GLN Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 215 ASP Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain R residue 90 ASN Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 116 HIS Chi-restraints excluded: chain Q residue 131 GLN Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 396 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain S residue 93 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 282 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 323 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 8.9990 chunk 340 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 341 GLN ** P 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 ASN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN B 92 HIS ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 332 ASN Q 135 ASN M 184 GLN O 193 GLN S 87 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.114 33375 Z= 0.514 Angle : 0.755 21.226 45366 Z= 0.350 Chirality : 0.046 0.218 4952 Planarity : 0.005 0.060 5712 Dihedral : 12.760 151.135 5239 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.62 % Allowed : 15.04 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 0.92 (0.13), residues: 3955 helix: 0.95 (0.11), residues: 2148 sheet: 0.24 (0.27), residues: 358 loop : 0.40 (0.17), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 142 HIS 0.016 0.002 HIS C 343 PHE 0.027 0.002 PHE C 240 TYR 0.024 0.002 TYR C 16 ARG 0.004 0.001 ARG U 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 178 time to evaluate : 3.644 Fit side-chains REVERT: C 295 MET cc_start: 0.8755 (ttt) cc_final: 0.8498 (ttp) REVERT: P 118 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8723 (pt) REVERT: P 216 PHE cc_start: 0.8556 (m-80) cc_final: 0.8102 (m-80) REVERT: G 23 ILE cc_start: 0.8940 (tp) cc_final: 0.8721 (mp) REVERT: G 69 ASP cc_start: 0.9403 (OUTLIER) cc_final: 0.9141 (m-30) REVERT: G 97 GLU cc_start: 0.8949 (tt0) cc_final: 0.8396 (mt-10) REVERT: G 110 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8666 (mt-10) REVERT: G 112 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8868 (tt0) REVERT: F 84 GLU cc_start: 0.9209 (tt0) cc_final: 0.8761 (tm-30) REVERT: F 88 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8644 (mm-30) REVERT: F 100 GLU cc_start: 0.8801 (pp20) cc_final: 0.8114 (pt0) REVERT: F 104 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8084 (ptm-80) REVERT: F 107 LYS cc_start: 0.9247 (pttt) cc_final: 0.8826 (mmtt) REVERT: F 122 ASP cc_start: 0.8125 (p0) cc_final: 0.7652 (p0) REVERT: F 144 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8854 (ttm110) REVERT: A 99 MET cc_start: 0.9103 (tmm) cc_final: 0.8690 (tmm) REVERT: B 334 GLU cc_start: 0.8891 (tp30) cc_final: 0.8656 (tm-30) REVERT: H 75 GLU cc_start: 0.9325 (mt-10) cc_final: 0.9060 (tm-30) REVERT: I 30 ASP cc_start: 0.8993 (OUTLIER) cc_final: 0.8603 (t0) REVERT: J 13 SER cc_start: 0.8899 (t) cc_final: 0.8555 (p) REVERT: N 239 MET cc_start: 0.8838 (ptt) cc_final: 0.8209 (tpt) REVERT: N 255 ASP cc_start: 0.9199 (p0) cc_final: 0.8994 (p0) REVERT: E 62 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8051 (mtm110) REVERT: R 12 GLU cc_start: 0.9417 (mm-30) cc_final: 0.8995 (mt-10) REVERT: Q 121 GLU cc_start: 0.8551 (tt0) cc_final: 0.8055 (tp30) REVERT: Q 140 ASP cc_start: 0.9167 (m-30) cc_final: 0.8725 (t70) REVERT: M 60 PHE cc_start: 0.9558 (OUTLIER) cc_final: 0.8891 (t80) REVERT: M 339 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8526 (ttp80) REVERT: S 75 GLU cc_start: 0.9323 (mt-10) cc_final: 0.8692 (tm-30) REVERT: S 78 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8726 (pp20) REVERT: U 58 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8792 (tp40) REVERT: U 69 GLU cc_start: 0.9318 (mt-10) cc_final: 0.9110 (pp20) outliers start: 87 outliers final: 27 residues processed: 245 average time/residue: 1.5166 time to fit residues: 440.2941 Evaluate side-chains 197 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 160 time to evaluate : 3.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 104 ARG Chi-restraints excluded: chain F residue 144 ARG Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 90 ASN Chi-restraints excluded: chain R residue 92 ILE Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 396 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 339 ARG Chi-restraints excluded: chain M residue 371 SER Chi-restraints excluded: chain O residue 235 MET Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 93 LEU Chi-restraints excluded: chain U residue 58 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 0.7980 chunk 341 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 222 optimal weight: 0.9980 chunk 93 optimal weight: 8.9990 chunk 379 optimal weight: 8.9990 chunk 314 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 chunk 199 optimal weight: 20.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9058 moved from start: 0.5360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33375 Z= 0.182 Angle : 0.552 14.818 45366 Z= 0.263 Chirality : 0.040 0.149 4952 Planarity : 0.004 0.058 5712 Dihedral : 12.147 150.101 5239 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.80 % Allowed : 16.27 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 1.17 (0.14), residues: 3955 helix: 1.23 (0.11), residues: 2150 sheet: 0.16 (0.27), residues: 358 loop : 0.46 (0.18), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 156 HIS 0.007 0.001 HIS F 96 PHE 0.017 0.001 PHE A 334 TYR 0.015 0.001 TYR D 117 ARG 0.006 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 178 time to evaluate : 3.829 Fit side-chains REVERT: C 295 MET cc_start: 0.8722 (ttt) cc_final: 0.8487 (ttp) REVERT: P 118 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8740 (pt) REVERT: G 23 ILE cc_start: 0.8881 (tp) cc_final: 0.8674 (mp) REVERT: G 110 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8641 (mt-10) REVERT: F 84 GLU cc_start: 0.9198 (tt0) cc_final: 0.8728 (tm-30) REVERT: F 88 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8654 (mm-30) REVERT: F 100 GLU cc_start: 0.8928 (pp20) cc_final: 0.8405 (pt0) REVERT: F 107 LYS cc_start: 0.9179 (pttt) cc_final: 0.8818 (mmtt) REVERT: F 122 ASP cc_start: 0.8154 (p0) cc_final: 0.7720 (p0) REVERT: B 334 GLU cc_start: 0.8821 (tp30) cc_final: 0.8594 (tm-30) REVERT: H 75 GLU cc_start: 0.9287 (mt-10) cc_final: 0.9037 (tm-30) REVERT: I 30 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8658 (t0) REVERT: J 13 SER cc_start: 0.8810 (t) cc_final: 0.8478 (p) REVERT: N 239 MET cc_start: 0.8762 (ptt) cc_final: 0.8087 (tpp) REVERT: E 54 LYS cc_start: 0.9087 (mmmt) cc_final: 0.8757 (tppt) REVERT: E 62 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7963 (mtm110) REVERT: E 76 SER cc_start: 0.9380 (m) cc_final: 0.9070 (p) REVERT: R 12 GLU cc_start: 0.9407 (mm-30) cc_final: 0.8991 (mt-10) REVERT: Q 121 GLU cc_start: 0.8586 (tt0) cc_final: 0.8001 (tp30) REVERT: Q 140 ASP cc_start: 0.9100 (m-30) cc_final: 0.8637 (t70) REVERT: M 31 GLN cc_start: 0.9105 (mt0) cc_final: 0.8879 (mt0) REVERT: M 60 PHE cc_start: 0.9521 (OUTLIER) cc_final: 0.8876 (t80) REVERT: S 75 GLU cc_start: 0.9283 (mt-10) cc_final: 0.8622 (tm-30) REVERT: S 78 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8739 (pp20) REVERT: U 69 GLU cc_start: 0.9382 (mt-10) cc_final: 0.9134 (pp20) outliers start: 60 outliers final: 21 residues processed: 225 average time/residue: 1.4424 time to fit residues: 387.5387 Evaluate side-chains 189 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 218 ASP Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 90 ASN Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 396 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain S residue 40 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 216 optimal weight: 10.0000 chunk 276 optimal weight: 7.9990 chunk 214 optimal weight: 4.9990 chunk 319 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 chunk 377 optimal weight: 7.9990 chunk 236 optimal weight: 1.9990 chunk 230 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN L 323 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9087 moved from start: 0.5561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 33375 Z= 0.310 Angle : 0.597 18.012 45366 Z= 0.278 Chirality : 0.042 0.186 4952 Planarity : 0.004 0.058 5712 Dihedral : 12.036 149.782 5239 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.62 % Allowed : 16.75 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 1.27 (0.14), residues: 3955 helix: 1.30 (0.11), residues: 2150 sheet: 0.15 (0.27), residues: 357 loop : 0.52 (0.18), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 142 HIS 0.013 0.001 HIS D 90 PHE 0.018 0.002 PHE L 334 TYR 0.025 0.002 TYR P 214 ARG 0.003 0.000 ARG U 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 170 time to evaluate : 3.722 Fit side-chains revert: symmetry clash REVERT: C 295 MET cc_start: 0.8773 (ttt) cc_final: 0.8541 (ttp) REVERT: P 118 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8710 (pt) REVERT: G 23 ILE cc_start: 0.8880 (tp) cc_final: 0.8675 (mp) REVERT: G 69 ASP cc_start: 0.9385 (OUTLIER) cc_final: 0.9184 (m-30) REVERT: G 110 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8660 (mt-10) REVERT: F 84 GLU cc_start: 0.9232 (tt0) cc_final: 0.8813 (tm-30) REVERT: F 88 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8726 (mm-30) REVERT: F 100 GLU cc_start: 0.8874 (pp20) cc_final: 0.8418 (mp0) REVERT: F 107 LYS cc_start: 0.9226 (pttt) cc_final: 0.8932 (mmtt) REVERT: F 122 ASP cc_start: 0.8432 (p0) cc_final: 0.7976 (p0) REVERT: B 334 GLU cc_start: 0.8788 (tp30) cc_final: 0.8587 (tm-30) REVERT: H 75 GLU cc_start: 0.9303 (mt-10) cc_final: 0.9071 (tm-30) REVERT: I 30 ASP cc_start: 0.8909 (OUTLIER) cc_final: 0.8634 (t0) REVERT: J 13 SER cc_start: 0.8854 (t) cc_final: 0.8536 (p) REVERT: N 239 MET cc_start: 0.8773 (ptt) cc_final: 0.8151 (tpt) REVERT: E 54 LYS cc_start: 0.9084 (mmmt) cc_final: 0.8753 (tppt) REVERT: E 62 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.7997 (mtm110) REVERT: E 76 SER cc_start: 0.9381 (m) cc_final: 0.9076 (p) REVERT: R 12 GLU cc_start: 0.9418 (mm-30) cc_final: 0.9013 (mt-10) REVERT: Q 126 GLU cc_start: 0.8946 (mp0) cc_final: 0.8607 (mp0) REVERT: Q 140 ASP cc_start: 0.9109 (m-30) cc_final: 0.8708 (t0) REVERT: L 270 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9235 (mt) REVERT: M 60 PHE cc_start: 0.9528 (OUTLIER) cc_final: 0.8981 (t80) REVERT: S 75 GLU cc_start: 0.9293 (mt-10) cc_final: 0.8706 (tm-30) REVERT: S 78 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8750 (pp20) REVERT: U 69 GLU cc_start: 0.9407 (mt-10) cc_final: 0.9153 (pp20) outliers start: 54 outliers final: 25 residues processed: 211 average time/residue: 1.5323 time to fit residues: 384.3251 Evaluate side-chains 196 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 165 time to evaluate : 3.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 218 ASP Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 90 ASN Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 270 LEU Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 396 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain O residue 235 MET Chi-restraints excluded: chain S residue 40 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 225 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 240 optimal weight: 0.5980 chunk 257 optimal weight: 6.9990 chunk 186 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 296 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 33375 Z= 0.285 Angle : 0.575 15.845 45366 Z= 0.272 Chirality : 0.041 0.149 4952 Planarity : 0.004 0.058 5712 Dihedral : 11.892 150.025 5239 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.62 % Allowed : 16.90 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 1.34 (0.14), residues: 3955 helix: 1.37 (0.11), residues: 2130 sheet: 0.07 (0.27), residues: 367 loop : 0.58 (0.18), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 142 HIS 0.007 0.001 HIS P 190 PHE 0.017 0.001 PHE L 334 TYR 0.015 0.001 TYR D 117 ARG 0.003 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 167 time to evaluate : 3.687 Fit side-chains REVERT: C 295 MET cc_start: 0.8773 (ttt) cc_final: 0.8542 (ttp) REVERT: P 118 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8718 (pt) REVERT: P 150 GLN cc_start: 0.7569 (mm-40) cc_final: 0.6953 (mm110) REVERT: G 23 ILE cc_start: 0.8879 (tp) cc_final: 0.8679 (mp) REVERT: G 110 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8649 (mt-10) REVERT: F 84 GLU cc_start: 0.9244 (tt0) cc_final: 0.8878 (tm-30) REVERT: F 88 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8749 (mm-30) REVERT: F 100 GLU cc_start: 0.8874 (pp20) cc_final: 0.8462 (mp0) REVERT: F 107 LYS cc_start: 0.9287 (pttt) cc_final: 0.8997 (mmtt) REVERT: F 122 ASP cc_start: 0.8643 (p0) cc_final: 0.8192 (p0) REVERT: A 390 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8710 (mttt) REVERT: H 75 GLU cc_start: 0.9298 (mt-10) cc_final: 0.9079 (tm-30) REVERT: I 30 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8659 (t0) REVERT: J 13 SER cc_start: 0.8818 (t) cc_final: 0.8496 (p) REVERT: N 239 MET cc_start: 0.8766 (ptt) cc_final: 0.8143 (tpt) REVERT: E 54 LYS cc_start: 0.9081 (mmmt) cc_final: 0.8755 (tppt) REVERT: E 62 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.7977 (mtm110) REVERT: E 76 SER cc_start: 0.9377 (m) cc_final: 0.9082 (p) REVERT: R 12 GLU cc_start: 0.9397 (mm-30) cc_final: 0.9014 (mt-10) REVERT: Q 121 GLU cc_start: 0.8701 (tt0) cc_final: 0.8120 (tp30) REVERT: Q 122 ASP cc_start: 0.8324 (p0) cc_final: 0.8061 (p0) REVERT: Q 126 GLU cc_start: 0.8992 (mp0) cc_final: 0.8642 (mp0) REVERT: Q 140 ASP cc_start: 0.9104 (m-30) cc_final: 0.8707 (t0) REVERT: L 270 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9277 (mt) REVERT: M 60 PHE cc_start: 0.9517 (OUTLIER) cc_final: 0.8978 (t80) REVERT: S 75 GLU cc_start: 0.9288 (mt-10) cc_final: 0.8713 (tm-30) REVERT: S 78 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8732 (pp20) REVERT: U 69 GLU cc_start: 0.9398 (mt-10) cc_final: 0.9153 (pp20) outliers start: 54 outliers final: 23 residues processed: 210 average time/residue: 1.5445 time to fit residues: 383.9248 Evaluate side-chains 192 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 163 time to evaluate : 3.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 218 ASP Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain R residue 10 THR Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 90 ASN Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 270 LEU Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 396 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain S residue 40 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 9.9990 chunk 361 optimal weight: 0.7980 chunk 330 optimal weight: 0.0980 chunk 352 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 276 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 318 optimal weight: 0.8980 chunk 332 optimal weight: 3.9990 chunk 350 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.5823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 33375 Z= 0.161 Angle : 0.532 13.395 45366 Z= 0.253 Chirality : 0.040 0.185 4952 Planarity : 0.004 0.059 5712 Dihedral : 11.458 149.475 5239 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.90 % Allowed : 17.74 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 1.48 (0.14), residues: 3955 helix: 1.50 (0.11), residues: 2141 sheet: 0.14 (0.27), residues: 367 loop : 0.62 (0.18), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 41 HIS 0.008 0.001 HIS F 96 PHE 0.015 0.001 PHE A 334 TYR 0.029 0.001 TYR P 214 ARG 0.009 0.000 ARG F 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 175 time to evaluate : 3.617 Fit side-chains REVERT: C 295 MET cc_start: 0.8719 (ttt) cc_final: 0.8483 (ttp) REVERT: P 118 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8659 (pt) REVERT: G 110 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8632 (mt-10) REVERT: G 123 GLU cc_start: 0.9003 (tp30) cc_final: 0.8659 (tm-30) REVERT: F 84 GLU cc_start: 0.9243 (tt0) cc_final: 0.8854 (tm-30) REVERT: F 88 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8742 (mm-30) REVERT: F 100 GLU cc_start: 0.8874 (pp20) cc_final: 0.8517 (mp0) REVERT: F 107 LYS cc_start: 0.9287 (pttt) cc_final: 0.8992 (mmtt) REVERT: F 122 ASP cc_start: 0.8618 (p0) cc_final: 0.8121 (p0) REVERT: H 75 GLU cc_start: 0.9283 (mt-10) cc_final: 0.9045 (tm-30) REVERT: J 13 SER cc_start: 0.8820 (t) cc_final: 0.8503 (p) REVERT: N 239 MET cc_start: 0.8705 (ptt) cc_final: 0.8113 (tpt) REVERT: E 54 LYS cc_start: 0.9059 (mmmt) cc_final: 0.8733 (tppt) REVERT: E 62 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7979 (mtm110) REVERT: E 76 SER cc_start: 0.9372 (m) cc_final: 0.9102 (p) REVERT: R 12 GLU cc_start: 0.9359 (mm-30) cc_final: 0.9008 (mt-10) REVERT: Q 121 GLU cc_start: 0.8711 (tt0) cc_final: 0.8126 (tp30) REVERT: Q 140 ASP cc_start: 0.9087 (m-30) cc_final: 0.8690 (t0) REVERT: M 60 PHE cc_start: 0.9490 (OUTLIER) cc_final: 0.8897 (t80) REVERT: S 75 GLU cc_start: 0.9330 (mt-10) cc_final: 0.8691 (tm-30) REVERT: S 78 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8745 (pp20) REVERT: U 69 GLU cc_start: 0.9390 (mt-10) cc_final: 0.9137 (pp20) outliers start: 30 outliers final: 16 residues processed: 198 average time/residue: 1.5432 time to fit residues: 362.1617 Evaluate side-chains 180 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 161 time to evaluate : 3.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain T residue 30 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 9.9990 chunk 372 optimal weight: 7.9990 chunk 227 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 258 optimal weight: 5.9990 chunk 390 optimal weight: 7.9990 chunk 359 optimal weight: 0.9980 chunk 310 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 240 optimal weight: 0.0060 chunk 190 optimal weight: 6.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9076 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 33375 Z= 0.309 Angle : 0.593 17.098 45366 Z= 0.277 Chirality : 0.041 0.165 4952 Planarity : 0.004 0.068 5712 Dihedral : 11.558 149.677 5237 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.87 % Allowed : 17.71 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % 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: 1.50 (0.14), residues: 3955 helix: 1.52 (0.11), residues: 2122 sheet: 0.14 (0.27), residues: 367 loop : 0.63 (0.18), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 142 HIS 0.010 0.001 HIS C 197 PHE 0.018 0.001 PHE L 334 TYR 0.016 0.001 TYR D 117 ARG 0.014 0.000 ARG F 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 3.654 Fit side-chains REVERT: C 295 MET cc_start: 0.8757 (ttt) cc_final: 0.8525 (ttp) REVERT: P 118 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8629 (pt) REVERT: G 110 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8678 (mt-10) REVERT: G 123 GLU cc_start: 0.9052 (tp30) cc_final: 0.8705 (tm-30) REVERT: F 84 GLU cc_start: 0.9266 (tt0) cc_final: 0.8894 (tm-30) REVERT: F 88 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8726 (mm-30) REVERT: F 100 GLU cc_start: 0.8852 (pp20) cc_final: 0.8516 (mp0) REVERT: F 107 LYS cc_start: 0.9314 (pttt) cc_final: 0.9032 (mmtt) REVERT: F 122 ASP cc_start: 0.8660 (p0) cc_final: 0.8187 (p0) REVERT: D 90 HIS cc_start: 0.9102 (OUTLIER) cc_final: 0.8893 (m170) REVERT: H 75 GLU cc_start: 0.9307 (mt-10) cc_final: 0.9079 (tm-30) REVERT: J 13 SER cc_start: 0.8848 (t) cc_final: 0.8548 (p) REVERT: N 239 MET cc_start: 0.8748 (ptt) cc_final: 0.8154 (tpt) REVERT: E 54 LYS cc_start: 0.9060 (mmmt) cc_final: 0.8730 (tppt) REVERT: E 62 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8001 (mtm110) REVERT: E 76 SER cc_start: 0.9373 (m) cc_final: 0.9087 (p) REVERT: R 12 GLU cc_start: 0.9361 (mm-30) cc_final: 0.8996 (mt-10) REVERT: Q 140 ASP cc_start: 0.9109 (m-30) cc_final: 0.8710 (t0) REVERT: M 60 PHE cc_start: 0.9507 (OUTLIER) cc_final: 0.8895 (t80) REVERT: S 75 GLU cc_start: 0.9296 (mt-10) cc_final: 0.8732 (tm-30) REVERT: S 78 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8757 (pp20) REVERT: U 69 GLU cc_start: 0.9366 (mt-10) cc_final: 0.9144 (pp20) outliers start: 29 outliers final: 17 residues processed: 185 average time/residue: 1.6533 time to fit residues: 362.4826 Evaluate side-chains 179 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 3.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain N residue 233 VAL Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 62 ARG Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain O residue 235 MET Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain S residue 61 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 8.9990 chunk 331 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 286 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 311 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 319 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.058737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.046715 restraints weight = 106664.021| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.33 r_work: 0.2752 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33375 Z= 0.216 Angle : 0.557 15.048 45366 Z= 0.262 Chirality : 0.040 0.158 4952 Planarity : 0.004 0.058 5712 Dihedral : 11.429 149.714 5237 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.84 % Allowed : 17.80 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.55 (0.14), residues: 3955 helix: 1.55 (0.11), residues: 2124 sheet: 0.11 (0.27), residues: 367 loop : 0.69 (0.18), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 142 HIS 0.008 0.001 HIS F 96 PHE 0.016 0.001 PHE L 334 TYR 0.029 0.001 TYR P 214 ARG 0.008 0.000 ARG F 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9053.91 seconds wall clock time: 166 minutes 7.31 seconds (9967.31 seconds total)