Starting phenix.real_space_refine on Fri Mar 22 07:02:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abj_15323/03_2024/8abj_15323_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abj_15323/03_2024/8abj_15323.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abj_15323/03_2024/8abj_15323_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abj_15323/03_2024/8abj_15323_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abj_15323/03_2024/8abj_15323_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abj_15323/03_2024/8abj_15323.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abj_15323/03_2024/8abj_15323.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abj_15323/03_2024/8abj_15323_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abj_15323/03_2024/8abj_15323_updated.pdb" } resolution = 3.7 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 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 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 GLU 213": "OE1" <-> "OE2" 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 263": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "A GLU 457": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" 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 "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 PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 321": "NH1" <-> "NH2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 37": "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 PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 354": "OE1" <-> "OE2" Residue "L ARG 384": "NH1" <-> "NH2" Residue "L GLU 424": "OE1" <-> "OE2" Residue "L GLU 457": "OE1" <-> "OE2" Residue "L TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M GLU 78": "OE1" <-> "OE2" 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 "M PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 "T GLU 34": "OE1" <-> "OE2" Residue "U TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32548 Number of models: 1 Model: "" Number of chains: 32 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: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 252 Unusual residues: {'AWB': 1, 'CDL': 1, 'HEM': 2, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 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: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 302 Unusual residues: {'AWB': 1, 'CDL': 2, 'HEM': 2, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 127 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: 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: "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 35.274 46.579 24.022 1.00215.57 S ATOM 4207 SG CYS P 187 37.469 45.714 20.914 1.00234.09 S Time building chain proxies: 18.37, per 1000 atoms: 0.56 Number of scatterers: 32548 At special positions: 0 Unit cell: (118.017, 128.898, 165.726, 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=2.06 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=2.07 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=2.06 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: 13.23 Conformation dependent library (CDL) restraints added in 5.2 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 168 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 187 " 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: 184 helices and 15 sheets defined 54.3% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.67 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: 4.138A pdb=" N GLY C 33 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR C 46 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.642A 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 103 removed outlier: 3.731A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 135 removed outlier: 4.130A pdb=" N VAL C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 153 removed outlier: 4.039A pdb=" N VAL C 151 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER C 152 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 4.269A 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: 4.181A pdb=" N THR C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 246 removed outlier: 6.792A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.791A 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: 3.817A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N LEU C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 4.004A 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: 4.092A 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: 3.615A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN P 90 " --> pdb=" O ASP P 86 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N MET P 91 " --> pdb=" O PHE P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 100 No H-bonds generated for 'chain 'P' and resid 97 through 100' 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 61 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: 3.586A 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: 3.551A pdb=" N HIS A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 4.167A 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: 3.839A pdb=" N VAL A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Proline residue: A 124 - end of helix removed outlier: 3.888A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 154 removed outlier: 3.995A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.778A 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: 3.585A 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 removed outlier: 3.528A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.977A 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: 3.654A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 395 removed outlier: 3.593A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.433A 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: 3.607A pdb=" N ASP A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.931A 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: 3.582A pdb=" N LYS B 116 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 4.246A 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: 3.514A pdb=" N THR B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.738A 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: 3.697A 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: 3.549A 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: 4.338A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.769A 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: 5.042A pdb=" N HIS I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LYS I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 49 removed outlier: 3.548A 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: 3.929A pdb=" N PHE N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY N 33 " --> pdb=" O TRP N 30 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR N 46 " --> pdb=" O GLN N 43 " (cutoff:3.500A) removed outlier: 3.631A 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 103 removed outlier: 3.740A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 135 removed outlier: 3.502A pdb=" N LEU N 134 " --> pdb=" O MET N 130 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 138 through 153 removed outlier: 4.169A pdb=" N VAL N 151 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER N 152 " --> pdb=" O CYS N 148 " (cutoff:3.500A) removed outlier: 4.248A 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: 4.166A pdb=" N THR N 203 " --> pdb=" O ILE N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 246 removed outlier: 6.777A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.788A 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: 3.801A pdb=" N ILE N 299 " --> pdb=" O MET N 295 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU N 302 " --> pdb=" O ALA N 298 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU N 303 " --> pdb=" O ILE N 299 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE N 304 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 3.999A 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: 4.085A 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: 3.624A pdb=" N SER E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 4.889A 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: 3.681A 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: 3.594A 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: 3.522A 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: 3.841A pdb=" N VAL L 123 " --> pdb=" O LYS L 120 " (cutoff:3.500A) Proline residue: L 124 - end of helix removed outlier: 3.883A pdb=" N VAL L 127 " --> pdb=" O PRO L 124 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU L 134 " --> pdb=" O ALA L 131 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN L 135 " --> pdb=" O ASP L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 156 removed outlier: 4.000A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) removed outlier: 4.067A 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 193 removed outlier: 3.590A pdb=" N THR L 193 " --> pdb=" O GLU L 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 205 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: 3.517A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 312 through 316 removed outlier: 4.019A 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: 3.659A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 395 removed outlier: 3.637A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.345A 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: 3.613A pdb=" N ASP L 468 " --> pdb=" O ARG L 464 " (cutoff:3.500A) removed outlier: 3.930A 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: 3.636A pdb=" N VAL M 108 " --> pdb=" O PRO M 105 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS M 116 " --> pdb=" O ASN M 113 " (cutoff:3.500A) removed outlier: 4.242A 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: 3.515A pdb=" N THR M 209 " --> pdb=" O GLN M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 263 removed outlier: 3.739A 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: 3.879A 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: 3.556A 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 319 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 40 through 80 removed outlier: 4.332A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.778A 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: 5.026A pdb=" N HIS T 55 " --> pdb=" O LYS T 51 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS T 56 " --> pdb=" O ASP T 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 49 removed outlier: 3.549A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.557A 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 Processing sheet with id= C, first strand: chain 'P' and resid 114 through 120 removed outlier: 3.911A 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: 4.109A 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: 3.600A 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: 4.104A 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: 3.596A 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 1584 hydrogen bonds defined for protein. 4326 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: 11.35 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: 13547 1.40 - 1.61: 19598 1.61 - 1.81: 162 1.81 - 2.02: 50 2.02 - 2.23: 18 Bond restraints: 33375 Sorted by residual: bond pdb=" N ALA I 4 " pdb=" CA ALA I 4 " ideal model delta sigma weight residual 1.458 1.619 -0.161 1.90e-02 2.77e+03 7.16e+01 bond pdb=" N ALA T 4 " pdb=" CA ALA T 4 " ideal model delta sigma weight residual 1.458 1.608 -0.150 1.90e-02 2.77e+03 6.22e+01 bond pdb=" C2C HEC D 401 " pdb=" C3C HEC D 401 " ideal model delta sigma weight residual 1.334 1.475 -0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" C2C HEC O 401 " pdb=" C3C HEC O 401 " ideal model delta sigma weight residual 1.334 1.459 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" CE LYS N 6 " pdb=" NZ LYS N 6 " ideal model delta sigma weight residual 1.489 1.675 -0.186 3.00e-02 1.11e+03 3.82e+01 ... (remaining 33370 not shown) Histogram of bond angle deviations from ideal: 85.29 - 103.92: 755 103.92 - 122.55: 38935 122.55 - 141.18: 5664 141.18 - 159.80: 0 159.80 - 178.43: 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 91.33 13.00 1.14e+00 7.69e-01 1.30e+02 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 91.24 13.09 1.20e+00 6.94e-01 1.19e+02 angle pdb=" CG ARG M 90 " pdb=" CD ARG M 90 " pdb=" NE ARG M 90 " ideal model delta sigma weight residual 112.00 92.21 19.79 2.20e+00 2.07e-01 8.10e+01 angle pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " pdb="FE2 FES P 301 " ideal model delta sigma weight residual 75.66 85.76 -10.10 1.14e+00 7.69e-01 7.85e+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 93.08 18.92 2.20e+00 2.07e-01 7.39e+01 ... (remaining 45361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.33: 18808 32.33 - 64.66: 1027 64.66 - 96.99: 98 96.99 - 129.32: 1 129.32 - 161.65: 3 Dihedral angle restraints: 19937 sinusoidal: 8318 harmonic: 11619 Sorted by residual: 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 -106.38 -16.22 0 2.50e+00 1.60e-01 4.21e+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 -106.92 -15.68 0 2.50e+00 1.60e-01 3.94e+01 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 -107.10 -15.50 0 2.50e+00 1.60e-01 3.85e+01 ... (remaining 19934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.264: 4766 0.264 - 0.529: 177 0.529 - 0.793: 5 0.793 - 1.058: 2 1.058 - 1.322: 2 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 -1.25 -1.32 2.00e-01 2.50e+01 4.37e+01 chirality pdb=" CB4 CDL N 506 " pdb=" CB3 CDL N 506 " pdb=" CB6 CDL N 506 " pdb=" OB6 CDL N 506 " both_signs ideal model delta sigma weight residual False -2.57 -1.50 -1.07 2.00e-01 2.50e+01 2.89e+01 chirality pdb=" CB4 CDL O 402 " pdb=" CB3 CDL O 402 " pdb=" CB6 CDL O 402 " pdb=" OB6 CDL O 402 " both_signs ideal model delta sigma weight residual False -2.57 -1.61 -0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 4949 not shown) Planarity restraints: 5712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 AWB C 506 " 0.009 2.00e-02 2.50e+03 2.40e-01 5.78e+02 pdb=" C21 AWB C 506 " -0.395 2.00e-02 2.50e+03 pdb=" N1 AWB C 506 " 0.170 2.00e-02 2.50e+03 pdb=" O5 AWB C 506 " 0.215 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 AWB N 507 " -0.007 2.00e-02 2.50e+03 2.38e-01 5.65e+02 pdb=" C21 AWB N 507 " 0.390 2.00e-02 2.50e+03 pdb=" N1 AWB N 507 " -0.173 2.00e-02 2.50e+03 pdb=" O5 AWB N 507 " -0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 101 " -0.074 2.00e-02 2.50e+03 3.97e-02 3.15e+01 pdb=" CG TYR G 101 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR G 101 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR G 101 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR G 101 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR G 101 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR G 101 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR G 101 " -0.059 2.00e-02 2.50e+03 ... (remaining 5709 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 6 2.23 - 2.90: 12394 2.90 - 3.57: 47327 3.57 - 4.23: 86806 4.23 - 4.90: 137984 Nonbonded interactions: 284517 Sorted by model distance: nonbonded pdb=" O CYS P 189 " pdb=" CE MET D 235 " model vdw 1.563 3.460 nonbonded pdb=" NE2 HIS C 82 " pdb="FE HEM C 501 " model vdw 2.048 3.080 nonbonded pdb=" NE2 HIS N 183 " pdb="FE HEM N 501 " model vdw 2.058 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.116 2.520 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.187 3.080 ... (remaining 284512 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 503)) selection = (chain 'N' and (resid 1 through 383 or resid 501 through 503)) } ncs_group { reference = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = (chain 'H' and resid 9 through 93) 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 11.950 Check model and map are aligned: 0.550 Set scattering table: 0.300 Process input model: 94.340 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 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 0.223 33375 Z= 0.778 Angle : 1.928 19.795 45366 Z= 1.199 Chirality : 0.126 1.322 4952 Planarity : 0.009 0.240 5712 Dihedral : 18.565 161.654 12436 Min Nonbonded Distance : 1.563 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.76 % Favored : 97.17 % Rotamer: Outliers : 4.36 % Allowed : 8.39 % Favored : 87.25 % Cbeta Deviations : 2.03 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -1.58 (0.12), residues: 3955 helix: -1.22 (0.09), residues: 2139 sheet: -0.11 (0.25), residues: 351 loop : -0.70 (0.16), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.010 TRP N 30 HIS 0.024 0.005 HIS Q 92 PHE 0.055 0.009 PHE B 107 TYR 0.074 0.009 TYR G 101 ARG 0.025 0.003 ARG C 283 *********************** 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 428 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 283 time to evaluate : 4.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 MET cc_start: 0.9105 (mtm) cc_final: 0.8819 (mmm) REVERT: C 272 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8715 (mt-10) REVERT: C 295 MET cc_start: 0.9130 (ttp) cc_final: 0.8792 (tmm) REVERT: P 68 MET cc_start: 0.8592 (mmm) cc_final: 0.8246 (mmt) REVERT: G 17 SER cc_start: 0.7635 (OUTLIER) cc_final: 0.7390 (p) REVERT: G 50 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8944 (pm20) REVERT: F 113 ASP cc_start: 0.8872 (m-30) cc_final: 0.8606 (t0) REVERT: F 125 GLU cc_start: 0.9348 (OUTLIER) cc_final: 0.9022 (mp0) REVERT: F 140 ASP cc_start: 0.8933 (m-30) cc_final: 0.8063 (t0) REVERT: A 29 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8641 (mmtt) REVERT: A 59 ASP cc_start: 0.9245 (t0) cc_final: 0.8971 (p0) REVERT: A 94 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8533 (tp) REVERT: B 19 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8573 (mm-30) REVERT: B 58 GLU cc_start: 0.9356 (OUTLIER) cc_final: 0.8910 (tm-30) REVERT: B 60 PHE cc_start: 0.9297 (OUTLIER) cc_final: 0.8966 (m-80) REVERT: D 186 GLN cc_start: 0.8943 (mp10) cc_final: 0.8708 (mp10) REVERT: D 193 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7938 (pp30) REVERT: D 283 GLU cc_start: 0.9385 (OUTLIER) cc_final: 0.9105 (pm20) REVERT: H 51 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.7356 (ptm-80) REVERT: H 75 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8890 (tm-30) REVERT: H 78 GLU cc_start: 0.9127 (tt0) cc_final: 0.8689 (tm-30) REVERT: J 11 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8297 (tmtt) REVERT: J 74 GLU cc_start: 0.8176 (mp0) cc_final: 0.7916 (pm20) REVERT: N 264 VAL cc_start: 0.8384 (t) cc_final: 0.8183 (p) REVERT: N 272 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8706 (mt-10) REVERT: N 369 MET cc_start: 0.9131 (mmm) cc_final: 0.8904 (mtp) REVERT: E 96 ASP cc_start: 0.8933 (p0) cc_final: 0.8710 (p0) REVERT: R 55 MET cc_start: 0.9250 (mmm) cc_final: 0.9006 (tpt) REVERT: Q 95 LYS cc_start: 0.9351 (tptt) cc_final: 0.8925 (ttpt) REVERT: Q 140 ASP cc_start: 0.9442 (m-30) cc_final: 0.9241 (t0) REVERT: L 51 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8656 (m) REVERT: L 397 LEU cc_start: 0.5734 (OUTLIER) cc_final: 0.5225 (mt) REVERT: M 292 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8661 (p) REVERT: M 386 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9160 (tp) REVERT: S 51 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.7337 (ptm160) REVERT: S 57 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8406 (tp) REVERT: T 31 MET cc_start: 0.9014 (mmp) cc_final: 0.8493 (mmt) outliers start: 145 outliers final: 22 residues processed: 408 average time/residue: 0.5142 time to fit residues: 321.2609 Evaluate side-chains 192 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 152 time to evaluate : 4.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 22 LYS Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain F residue 125 GLU Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 109 PRO Chi-restraints excluded: chain N residue 178 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 378 SER Chi-restraints excluded: chain L residue 397 LEU Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 272 SER Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain O residue 324 ILE Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 57 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 0.5980 chunk 297 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 158 optimal weight: 8.9990 chunk 307 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 228 optimal weight: 40.0000 chunk 355 optimal weight: 20.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN C 173 ASN C 177 GLN C 332 ASN F 92 HIS F 132 HIS F 135 ASN A 74 HIS A 135 GLN A 177 ASN A 222 HIS A 332 ASN A 371 ASN B 87 HIS ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 HIS N 14 ASN N 332 ASN E 57 ASN E 90 ASN R 84 HIS Q 135 ASN L 135 GLN L 332 ASN L 371 ASN M 87 HIS M 92 HIS M 215 GLN M 295 ASN M 316 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33375 Z= 0.228 Angle : 0.649 19.132 45366 Z= 0.313 Chirality : 0.043 0.227 4952 Planarity : 0.004 0.058 5712 Dihedral : 14.408 159.511 5331 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.89 % Allowed : 10.44 % Favored : 87.67 % 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: 0.56 (0.13), residues: 3955 helix: 0.73 (0.11), residues: 2145 sheet: 0.55 (0.27), residues: 357 loop : -0.01 (0.17), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 156 HIS 0.005 0.001 HIS N 197 PHE 0.019 0.002 PHE L 334 TYR 0.018 0.002 TYR D 237 ARG 0.007 0.001 ARG E 62 *********************** 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 228 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 165 time to evaluate : 3.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 MET cc_start: 0.8916 (mtm) cc_final: 0.8554 (mmm) REVERT: C 272 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8528 (mp0) REVERT: C 295 MET cc_start: 0.9116 (ttp) cc_final: 0.8757 (tmm) REVERT: P 68 MET cc_start: 0.8543 (mmm) cc_final: 0.8261 (mpp) REVERT: P 150 GLN cc_start: 0.7549 (mp10) cc_final: 0.7198 (mp10) REVERT: F 88 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8267 (pp20) REVERT: F 113 ASP cc_start: 0.8856 (m-30) cc_final: 0.8613 (t0) REVERT: F 125 GLU cc_start: 0.9374 (mt-10) cc_final: 0.9163 (tp30) REVERT: F 137 ASN cc_start: 0.9049 (m-40) cc_final: 0.8769 (m-40) REVERT: F 140 ASP cc_start: 0.8857 (m-30) cc_final: 0.7877 (t0) REVERT: F 144 ARG cc_start: 0.9423 (mtp85) cc_final: 0.9021 (mtm180) REVERT: A 94 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8549 (tp) REVERT: B 60 PHE cc_start: 0.9345 (OUTLIER) cc_final: 0.8837 (m-80) REVERT: B 269 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8247 (ptp) REVERT: D 186 GLN cc_start: 0.8839 (mp10) cc_final: 0.8556 (mp10) REVERT: D 193 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7679 (pp30) REVERT: D 283 GLU cc_start: 0.9377 (OUTLIER) cc_final: 0.9064 (pm20) REVERT: H 78 GLU cc_start: 0.9211 (tt0) cc_final: 0.8709 (tm-30) REVERT: J 11 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8434 (tmtt) REVERT: J 74 GLU cc_start: 0.8230 (mp0) cc_final: 0.7996 (pm20) REVERT: N 264 VAL cc_start: 0.8225 (t) cc_final: 0.7980 (p) REVERT: R 31 TYR cc_start: 0.9196 (t80) cc_final: 0.8976 (t80) REVERT: R 55 MET cc_start: 0.9223 (mmm) cc_final: 0.8972 (tpt) REVERT: Q 95 LYS cc_start: 0.9392 (tptt) cc_final: 0.9005 (ttpt) REVERT: Q 140 ASP cc_start: 0.9440 (m-30) cc_final: 0.9163 (t0) REVERT: L 51 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8788 (m) REVERT: L 378 SER cc_start: 0.9266 (OUTLIER) cc_final: 0.9045 (t) REVERT: O 235 MET cc_start: 0.8545 (mmt) cc_final: 0.8310 (mmt) REVERT: S 51 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.7157 (ptm160) REVERT: S 57 LEU cc_start: 0.9002 (mt) cc_final: 0.8588 (tp) REVERT: T 31 MET cc_start: 0.8952 (mmp) cc_final: 0.8474 (mmt) outliers start: 63 outliers final: 22 residues processed: 216 average time/residue: 0.4413 time to fit residues: 155.3097 Evaluate side-chains 176 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 145 time to evaluate : 3.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 215 ASP Chi-restraints excluded: chain P residue 218 ASP Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain F residue 92 HIS Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 249 ASP Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain Q residue 99 ASP Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 378 SER Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain O residue 85 MET 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: 9.9990 chunk 110 optimal weight: 9.9990 chunk 296 optimal weight: 10.0000 chunk 242 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 356 optimal weight: 20.0000 chunk 385 optimal weight: 10.0000 chunk 317 optimal weight: 0.6980 chunk 353 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 286 optimal weight: 3.9990 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 85 GLN P 90 ASN G 84 HIS ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN I 39 ASN J 70 HIS N 22 GLN Q 132 HIS L 91 GLN M 295 ASN O 236 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 33375 Z= 0.403 Angle : 0.683 18.451 45366 Z= 0.325 Chirality : 0.044 0.179 4952 Planarity : 0.004 0.039 5712 Dihedral : 13.256 147.438 5272 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.86 % Allowed : 11.64 % Favored : 86.50 % 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: 1.09 (0.13), residues: 3955 helix: 1.18 (0.11), residues: 2129 sheet: 0.69 (0.27), residues: 352 loop : 0.23 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 142 HIS 0.033 0.002 HIS F 92 PHE 0.019 0.002 PHE G 42 TYR 0.018 0.002 TYR A 444 ARG 0.006 0.001 ARG E 62 *********************** 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 200 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 138 time to evaluate : 3.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 MET cc_start: 0.8898 (mtm) cc_final: 0.8443 (mmm) REVERT: C 272 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8460 (mp0) REVERT: C 295 MET cc_start: 0.9136 (ttp) cc_final: 0.8809 (tmm) REVERT: P 68 MET cc_start: 0.8576 (mmm) cc_final: 0.8250 (mpp) REVERT: P 150 GLN cc_start: 0.7773 (mp10) cc_final: 0.7350 (mp10) REVERT: F 125 GLU cc_start: 0.9425 (mt-10) cc_final: 0.9175 (tp30) REVERT: F 140 ASP cc_start: 0.8858 (m-30) cc_final: 0.8033 (t0) REVERT: B 19 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8469 (mm-30) REVERT: D 283 GLU cc_start: 0.9383 (OUTLIER) cc_final: 0.9115 (pm20) REVERT: H 16 MET cc_start: 0.8696 (tpp) cc_final: 0.8183 (tpp) REVERT: H 78 GLU cc_start: 0.9207 (tt0) cc_final: 0.8815 (tm-30) REVERT: J 11 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8487 (tmtt) REVERT: N 264 VAL cc_start: 0.8275 (t) cc_final: 0.8003 (p) REVERT: Q 95 LYS cc_start: 0.9380 (tptt) cc_final: 0.9054 (ttpt) REVERT: Q 99 ASP cc_start: 0.9366 (OUTLIER) cc_final: 0.9024 (t0) REVERT: Q 103 GLU cc_start: 0.9289 (pt0) cc_final: 0.9052 (pt0) REVERT: Q 140 ASP cc_start: 0.9389 (m-30) cc_final: 0.9113 (t0) REVERT: L 51 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8898 (m) REVERT: M 292 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8783 (p) REVERT: O 163 ASP cc_start: 0.8523 (m-30) cc_final: 0.8188 (p0) REVERT: S 57 LEU cc_start: 0.8973 (mt) cc_final: 0.8568 (tp) REVERT: T 31 MET cc_start: 0.8972 (mmp) cc_final: 0.8498 (mmt) outliers start: 62 outliers final: 30 residues processed: 189 average time/residue: 0.4393 time to fit residues: 139.1698 Evaluate side-chains 166 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 130 time to evaluate : 3.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain P residue 90 ASN Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 164 MET Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 249 ASP Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain Q residue 99 ASP Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 68 TYR Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain M residue 377 ASN Chi-restraints excluded: chain O residue 85 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 4.9990 chunk 268 optimal weight: 8.9990 chunk 185 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 170 optimal weight: 0.2980 chunk 239 optimal weight: 1.9990 chunk 357 optimal weight: 7.9990 chunk 378 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 339 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 90 ASN A 91 GLN A 364 HIS ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 ASN J 70 HIS E 57 ASN M 295 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 33375 Z= 0.251 Angle : 0.562 16.121 45366 Z= 0.267 Chirality : 0.041 0.172 4952 Planarity : 0.004 0.040 5712 Dihedral : 12.670 148.446 5253 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.74 % Allowed : 12.12 % Favored : 86.14 % 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: 1.33 (0.13), residues: 3955 helix: 1.42 (0.11), residues: 2121 sheet: 0.60 (0.27), residues: 356 loop : 0.31 (0.17), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 142 HIS 0.005 0.001 HIS C 197 PHE 0.016 0.001 PHE L 334 TYR 0.014 0.001 TYR E 66 ARG 0.005 0.000 ARG H 86 *********************** 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 194 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 136 time to evaluate : 3.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 MET cc_start: 0.8865 (mtm) cc_final: 0.8401 (mmm) REVERT: C 272 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8421 (mp0) REVERT: C 295 MET cc_start: 0.9149 (ttp) cc_final: 0.8810 (tmm) REVERT: P 68 MET cc_start: 0.8542 (mmm) cc_final: 0.8196 (mpp) REVERT: P 150 GLN cc_start: 0.7725 (mp10) cc_final: 0.7362 (mp10) REVERT: F 100 GLU cc_start: 0.9314 (pt0) cc_final: 0.8955 (pp20) REVERT: F 125 GLU cc_start: 0.9419 (mt-10) cc_final: 0.9185 (tp30) REVERT: F 140 ASP cc_start: 0.8787 (m-30) cc_final: 0.8029 (t0) REVERT: A 351 LEU cc_start: 0.9667 (OUTLIER) cc_final: 0.9427 (mt) REVERT: B 19 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8454 (mm-30) REVERT: D 193 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7773 (pp30) REVERT: D 283 GLU cc_start: 0.9370 (OUTLIER) cc_final: 0.9127 (pm20) REVERT: H 78 GLU cc_start: 0.9202 (tt0) cc_final: 0.8789 (tm-30) REVERT: J 11 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8531 (tmtt) REVERT: J 69 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7724 (pm20) REVERT: R 31 TYR cc_start: 0.9082 (t80) cc_final: 0.8828 (t80) REVERT: Q 95 LYS cc_start: 0.9370 (tptt) cc_final: 0.9039 (ttpt) REVERT: Q 99 ASP cc_start: 0.9336 (OUTLIER) cc_final: 0.8940 (t0) REVERT: Q 103 GLU cc_start: 0.9250 (pt0) cc_final: 0.8995 (pt0) REVERT: Q 140 ASP cc_start: 0.9372 (m-30) cc_final: 0.9102 (t0) REVERT: M 292 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8843 (p) REVERT: O 163 ASP cc_start: 0.8535 (m-30) cc_final: 0.8166 (p0) REVERT: O 235 MET cc_start: 0.8672 (mmt) cc_final: 0.8424 (mmt) REVERT: S 57 LEU cc_start: 0.9000 (mt) cc_final: 0.8605 (tp) REVERT: T 31 MET cc_start: 0.8967 (mmp) cc_final: 0.8484 (mmt) outliers start: 58 outliers final: 33 residues processed: 186 average time/residue: 0.4007 time to fit residues: 127.4892 Evaluate side-chains 171 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 130 time to evaluate : 3.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 249 ASP Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain Q residue 99 ASP Chi-restraints excluded: chain L residue 68 TYR Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain O residue 85 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 282 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 chunk 323 optimal weight: 0.0770 chunk 261 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 10.0000 chunk 340 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 overall best weight: 5.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 253 HIS ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN M 295 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 33375 Z= 0.344 Angle : 0.599 17.293 45366 Z= 0.282 Chirality : 0.042 0.169 4952 Planarity : 0.004 0.045 5712 Dihedral : 12.305 149.217 5250 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.77 % Allowed : 12.69 % Favored : 85.53 % 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: 1.40 (0.13), residues: 3955 helix: 1.53 (0.11), residues: 2113 sheet: 0.52 (0.27), residues: 354 loop : 0.30 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 142 HIS 0.008 0.001 HIS C 96 PHE 0.016 0.002 PHE N 77 TYR 0.015 0.001 TYR N 225 ARG 0.005 0.000 ARG H 86 *********************** 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 191 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 132 time to evaluate : 3.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 12 MET cc_start: 0.8881 (mtm) cc_final: 0.8379 (mmm) REVERT: C 272 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8429 (mp0) REVERT: P 68 MET cc_start: 0.8571 (mmm) cc_final: 0.8214 (mpp) REVERT: P 150 GLN cc_start: 0.7847 (mp10) cc_final: 0.7478 (mp10) REVERT: F 100 GLU cc_start: 0.9284 (pt0) cc_final: 0.8910 (pp20) REVERT: F 125 GLU cc_start: 0.9414 (mt-10) cc_final: 0.9143 (tp30) REVERT: F 140 ASP cc_start: 0.8734 (m-30) cc_final: 0.7961 (t0) REVERT: A 351 LEU cc_start: 0.9676 (OUTLIER) cc_final: 0.9432 (mt) REVERT: B 19 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8454 (mm-30) REVERT: D 193 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7551 (pp30) REVERT: D 283 GLU cc_start: 0.9393 (OUTLIER) cc_final: 0.9185 (pm20) REVERT: H 78 GLU cc_start: 0.9188 (tt0) cc_final: 0.8754 (tm-30) REVERT: I 42 ASP cc_start: 0.9190 (OUTLIER) cc_final: 0.8900 (p0) REVERT: J 11 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8577 (tmtt) REVERT: J 69 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7758 (pm20) REVERT: R 31 TYR cc_start: 0.9045 (t80) cc_final: 0.8776 (t80) REVERT: Q 95 LYS cc_start: 0.9327 (tptt) cc_final: 0.9000 (ttpt) REVERT: Q 122 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7856 (m-30) REVERT: Q 140 ASP cc_start: 0.9379 (m-30) cc_final: 0.9110 (t0) REVERT: M 292 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8809 (p) REVERT: O 163 ASP cc_start: 0.8554 (m-30) cc_final: 0.8193 (p0) REVERT: S 57 LEU cc_start: 0.9003 (mt) cc_final: 0.8606 (tp) REVERT: T 31 MET cc_start: 0.8952 (mmp) cc_final: 0.8478 (mmp) outliers start: 59 outliers final: 39 residues processed: 184 average time/residue: 0.4220 time to fit residues: 131.7501 Evaluate side-chains 180 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 132 time to evaluate : 3.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 201 ARG Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 249 ASP Chi-restraints excluded: chain N residue 253 HIS Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain Q residue 122 ASP Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 68 TYR Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 371 SER Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 86 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 6.9990 chunk 341 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 222 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 379 optimal weight: 7.9990 chunk 314 optimal weight: 10.0000 chunk 175 optimal weight: 20.0000 chunk 31 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 199 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN L 192 GLN L 332 ASN T 55 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 33375 Z= 0.404 Angle : 0.648 18.519 45366 Z= 0.300 Chirality : 0.043 0.228 4952 Planarity : 0.004 0.051 5712 Dihedral : 12.279 150.848 5250 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.11 % Allowed : 12.90 % Favored : 84.99 % 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: 1.31 (0.13), residues: 3955 helix: 1.47 (0.11), residues: 2114 sheet: 0.36 (0.27), residues: 356 loop : 0.27 (0.17), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 142 HIS 0.008 0.001 HIS C 96 PHE 0.016 0.002 PHE N 77 TYR 0.017 0.002 TYR O 221 ARG 0.006 0.000 ARG H 86 *********************** 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 199 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 129 time to evaluate : 3.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 272 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8464 (mp0) REVERT: C 295 MET cc_start: 0.9171 (ttp) cc_final: 0.8687 (tmm) REVERT: P 68 MET cc_start: 0.8553 (mmm) cc_final: 0.8202 (mpp) REVERT: P 150 GLN cc_start: 0.7914 (mp10) cc_final: 0.7512 (mp10) REVERT: F 100 GLU cc_start: 0.9305 (pt0) cc_final: 0.9073 (pp20) REVERT: F 140 ASP cc_start: 0.8690 (m-30) cc_final: 0.7880 (t70) REVERT: A 351 LEU cc_start: 0.9682 (OUTLIER) cc_final: 0.9451 (mt) REVERT: B 19 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8344 (mm-30) REVERT: D 193 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7501 (pp30) REVERT: H 78 GLU cc_start: 0.9179 (tt0) cc_final: 0.8798 (tm-30) REVERT: I 42 ASP cc_start: 0.9206 (OUTLIER) cc_final: 0.8949 (p0) REVERT: J 69 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7736 (pm20) REVERT: Q 95 LYS cc_start: 0.9395 (tptt) cc_final: 0.9026 (ttpt) REVERT: Q 113 ASP cc_start: 0.8959 (t0) cc_final: 0.8471 (t0) REVERT: Q 122 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8090 (m-30) REVERT: Q 140 ASP cc_start: 0.9367 (m-30) cc_final: 0.9085 (t0) REVERT: M 292 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8729 (p) REVERT: T 31 MET cc_start: 0.8919 (mmp) cc_final: 0.8449 (mmp) outliers start: 70 outliers final: 43 residues processed: 188 average time/residue: 0.4072 time to fit residues: 131.4082 Evaluate side-chains 175 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 125 time to evaluate : 3.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 201 ARG Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 90 ASN Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 249 ASP Chi-restraints excluded: chain N residue 265 THR Chi-restraints excluded: chain N residue 270 VAL Chi-restraints excluded: chain N residue 357 ILE Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain Q residue 122 ASP Chi-restraints excluded: chain L residue 68 TYR Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 179 LYS Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 371 SER Chi-restraints excluded: chain M residue 373 ILE Chi-restraints excluded: chain O residue 86 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 216 optimal weight: 5.9990 chunk 276 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 chunk 319 optimal weight: 9.9990 chunk 211 optimal weight: 0.1980 chunk 377 optimal weight: 0.9980 chunk 236 optimal weight: 7.9990 chunk 230 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 192 ASN ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 256 ASN E 57 ASN Q 116 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33375 Z= 0.164 Angle : 0.515 12.985 45366 Z= 0.246 Chirality : 0.039 0.177 4952 Planarity : 0.004 0.052 5712 Dihedral : 11.767 150.583 5243 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.38 % Allowed : 13.74 % Favored : 84.87 % 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: 1.53 (0.14), residues: 3955 helix: 1.63 (0.11), residues: 2131 sheet: 0.46 (0.27), residues: 355 loop : 0.39 (0.17), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 120 HIS 0.006 0.001 HIS Q 116 PHE 0.015 0.001 PHE L 334 TYR 0.013 0.001 TYR O 117 ARG 0.004 0.000 ARG H 86 *********************** 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 180 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 134 time to evaluate : 4.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 272 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8411 (mp0) REVERT: C 295 MET cc_start: 0.9182 (ttp) cc_final: 0.8688 (tmm) REVERT: P 150 GLN cc_start: 0.7792 (mp10) cc_final: 0.7375 (mp10) REVERT: F 100 GLU cc_start: 0.9438 (pt0) cc_final: 0.9102 (pp20) REVERT: F 140 ASP cc_start: 0.8620 (m-30) cc_final: 0.7799 (t0) REVERT: A 351 LEU cc_start: 0.9677 (OUTLIER) cc_final: 0.9471 (mp) REVERT: D 193 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7366 (pp30) REVERT: H 16 MET cc_start: 0.8408 (tpp) cc_final: 0.8183 (tpp) REVERT: H 78 GLU cc_start: 0.9170 (tt0) cc_final: 0.8741 (tm-30) REVERT: I 42 ASP cc_start: 0.9194 (OUTLIER) cc_final: 0.8936 (p0) REVERT: J 56 THR cc_start: 0.9037 (m) cc_final: 0.8721 (p) REVERT: J 69 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7643 (pm20) REVERT: N 256 ASN cc_start: 0.9492 (OUTLIER) cc_final: 0.9276 (t0) REVERT: R 31 TYR cc_start: 0.8964 (t80) cc_final: 0.8696 (t80) REVERT: Q 95 LYS cc_start: 0.9398 (tptt) cc_final: 0.9046 (ttpt) REVERT: Q 103 GLU cc_start: 0.9307 (OUTLIER) cc_final: 0.9014 (pt0) REVERT: Q 113 ASP cc_start: 0.8887 (t0) cc_final: 0.8618 (m-30) REVERT: Q 122 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8157 (m-30) REVERT: Q 140 ASP cc_start: 0.9358 (m-30) cc_final: 0.9072 (t0) REVERT: O 163 ASP cc_start: 0.8478 (m-30) cc_final: 0.8101 (p0) REVERT: S 57 LEU cc_start: 0.9025 (mt) cc_final: 0.8631 (tp) REVERT: T 31 MET cc_start: 0.8949 (mmp) cc_final: 0.8411 (mmp) outliers start: 46 outliers final: 32 residues processed: 173 average time/residue: 0.4099 time to fit residues: 121.3479 Evaluate side-chains 166 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 127 time to evaluate : 3.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 201 ARG Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 249 ASP Chi-restraints excluded: chain N residue 256 ASN Chi-restraints excluded: chain N residue 270 VAL Chi-restraints excluded: chain Q residue 103 GLU Chi-restraints excluded: chain Q residue 122 ASP Chi-restraints excluded: chain L residue 68 TYR Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 179 LYS Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 371 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 225 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 240 optimal weight: 9.9990 chunk 257 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 296 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 55 HIS N 256 ASN E 57 ASN M 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 33375 Z= 0.199 Angle : 0.527 12.735 45366 Z= 0.247 Chirality : 0.040 0.178 4952 Planarity : 0.004 0.050 5712 Dihedral : 11.570 149.964 5243 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.50 % Allowed : 13.77 % Favored : 84.72 % 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: 1.63 (0.14), residues: 3955 helix: 1.70 (0.11), residues: 2130 sheet: 0.55 (0.27), residues: 355 loop : 0.45 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 120 HIS 0.004 0.001 HIS C 96 PHE 0.015 0.001 PHE L 334 TYR 0.021 0.001 TYR F 114 ARG 0.004 0.000 ARG H 86 *********************** 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 178 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 128 time to evaluate : 3.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 272 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8388 (mp0) REVERT: C 295 MET cc_start: 0.9188 (ttp) cc_final: 0.8702 (tmm) REVERT: P 130 ARG cc_start: 0.6578 (OUTLIER) cc_final: 0.6300 (ptp-170) REVERT: P 150 GLN cc_start: 0.7830 (mp10) cc_final: 0.7440 (mp10) REVERT: F 100 GLU cc_start: 0.9454 (pt0) cc_final: 0.9128 (pp20) REVERT: F 140 ASP cc_start: 0.8652 (m-30) cc_final: 0.7836 (t0) REVERT: A 351 LEU cc_start: 0.9680 (OUTLIER) cc_final: 0.9462 (mt) REVERT: B 19 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8410 (mm-30) REVERT: D 193 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7377 (pp30) REVERT: D 248 MET cc_start: 0.7890 (tpp) cc_final: 0.6781 (tpp) REVERT: H 78 GLU cc_start: 0.9176 (tt0) cc_final: 0.8752 (tm-30) REVERT: I 42 ASP cc_start: 0.9180 (OUTLIER) cc_final: 0.8912 (p0) REVERT: J 56 THR cc_start: 0.9015 (m) cc_final: 0.8733 (p) REVERT: J 69 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7608 (pm20) REVERT: N 256 ASN cc_start: 0.9498 (OUTLIER) cc_final: 0.9219 (t0) REVERT: R 14 ILE cc_start: 0.9387 (mm) cc_final: 0.9173 (tt) REVERT: R 31 TYR cc_start: 0.9007 (t80) cc_final: 0.8707 (t80) REVERT: Q 95 LYS cc_start: 0.9389 (tptt) cc_final: 0.9030 (ttpt) REVERT: Q 103 GLU cc_start: 0.9323 (OUTLIER) cc_final: 0.9035 (pt0) REVERT: Q 113 ASP cc_start: 0.8830 (t0) cc_final: 0.8517 (m-30) REVERT: Q 122 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8162 (m-30) REVERT: Q 140 ASP cc_start: 0.9361 (m-30) cc_final: 0.9074 (t0) REVERT: O 163 ASP cc_start: 0.8478 (m-30) cc_final: 0.8101 (p0) REVERT: S 57 LEU cc_start: 0.9018 (mt) cc_final: 0.8624 (tp) REVERT: T 31 MET cc_start: 0.8939 (mmp) cc_final: 0.8395 (mmp) outliers start: 50 outliers final: 35 residues processed: 172 average time/residue: 0.4053 time to fit residues: 118.9092 Evaluate side-chains 172 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 128 time to evaluate : 3.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 201 ARG Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 ASP Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 249 ASP Chi-restraints excluded: chain N residue 256 ASN Chi-restraints excluded: chain N residue 270 VAL Chi-restraints excluded: chain Q residue 103 GLU Chi-restraints excluded: chain Q residue 122 ASP Chi-restraints excluded: chain L residue 68 TYR Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 179 LYS Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 371 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 0.6980 chunk 361 optimal weight: 0.9990 chunk 330 optimal weight: 20.0000 chunk 352 optimal weight: 9.9990 chunk 211 optimal weight: 0.9990 chunk 153 optimal weight: 8.9990 chunk 276 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 318 optimal weight: 5.9990 chunk 332 optimal weight: 1.9990 chunk 350 optimal weight: 10.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 256 ASN B 121 GLN L 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33375 Z= 0.171 Angle : 0.508 13.380 45366 Z= 0.241 Chirality : 0.039 0.167 4952 Planarity : 0.004 0.050 5712 Dihedral : 11.321 149.821 5243 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.38 % Allowed : 14.08 % Favored : 84.54 % 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: 1.74 (0.14), residues: 3955 helix: 1.78 (0.11), residues: 2126 sheet: 0.59 (0.27), residues: 357 loop : 0.51 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 120 HIS 0.004 0.001 HIS O 128 PHE 0.015 0.001 PHE L 334 TYR 0.030 0.001 TYR F 114 ARG 0.003 0.000 ARG H 86 *********************** 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 178 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 132 time to evaluate : 3.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 272 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8348 (mp0) REVERT: C 295 MET cc_start: 0.9192 (ttp) cc_final: 0.8858 (tmm) REVERT: P 130 ARG cc_start: 0.6512 (OUTLIER) cc_final: 0.6235 (ptp-170) REVERT: P 150 GLN cc_start: 0.7813 (mp10) cc_final: 0.7426 (mp10) REVERT: F 100 GLU cc_start: 0.9445 (pt0) cc_final: 0.9131 (pp20) REVERT: F 140 ASP cc_start: 0.8632 (m-30) cc_final: 0.7826 (t0) REVERT: A 351 LEU cc_start: 0.9679 (OUTLIER) cc_final: 0.9472 (mt) REVERT: D 193 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7405 (pp30) REVERT: H 78 GLU cc_start: 0.9174 (tt0) cc_final: 0.8756 (tm-30) REVERT: I 42 ASP cc_start: 0.9187 (OUTLIER) cc_final: 0.8915 (p0) REVERT: J 56 THR cc_start: 0.8975 (m) cc_final: 0.8754 (p) REVERT: J 69 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7548 (pm20) REVERT: R 14 ILE cc_start: 0.9397 (mm) cc_final: 0.9189 (tt) REVERT: R 31 TYR cc_start: 0.9025 (t80) cc_final: 0.8796 (t80) REVERT: Q 95 LYS cc_start: 0.9388 (tptt) cc_final: 0.9031 (ttpt) REVERT: Q 103 GLU cc_start: 0.9346 (OUTLIER) cc_final: 0.9053 (pt0) REVERT: Q 113 ASP cc_start: 0.8767 (t0) cc_final: 0.8420 (m-30) REVERT: Q 122 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8199 (m-30) REVERT: Q 140 ASP cc_start: 0.9361 (m-30) cc_final: 0.9079 (t0) REVERT: O 163 ASP cc_start: 0.8495 (m-30) cc_final: 0.8132 (p0) REVERT: S 57 LEU cc_start: 0.9011 (mt) cc_final: 0.8614 (tp) REVERT: T 31 MET cc_start: 0.8963 (mmp) cc_final: 0.8439 (mmp) outliers start: 46 outliers final: 32 residues processed: 171 average time/residue: 0.4341 time to fit residues: 125.5418 Evaluate side-chains 164 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 125 time to evaluate : 3.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 201 ARG Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 249 ASP Chi-restraints excluded: chain N residue 270 VAL Chi-restraints excluded: chain Q residue 103 GLU Chi-restraints excluded: chain Q residue 122 ASP Chi-restraints excluded: chain L residue 68 TYR Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 179 LYS Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 371 SER Chi-restraints excluded: chain O residue 85 MET 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: 5.9990 chunk 227 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 258 optimal weight: 0.1980 chunk 390 optimal weight: 0.9980 chunk 359 optimal weight: 0.9980 chunk 310 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 240 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 256 ASN L 323 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 33375 Z= 0.145 Angle : 0.493 13.627 45366 Z= 0.232 Chirality : 0.039 0.164 4952 Planarity : 0.003 0.051 5712 Dihedral : 10.957 149.848 5243 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.05 % Allowed : 14.35 % Favored : 84.60 % 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: 1.88 (0.14), residues: 3955 helix: 1.87 (0.11), residues: 2136 sheet: 0.67 (0.27), residues: 357 loop : 0.60 (0.18), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 120 HIS 0.004 0.001 HIS M 87 PHE 0.027 0.001 PHE P 64 TYR 0.030 0.001 TYR F 114 ARG 0.003 0.000 ARG H 86 ********************** 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 168 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 133 time to evaluate : 3.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 272 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8283 (mp0) REVERT: C 295 MET cc_start: 0.9190 (ttp) cc_final: 0.8856 (tmm) REVERT: P 150 GLN cc_start: 0.7763 (mp10) cc_final: 0.7417 (mp10) REVERT: F 100 GLU cc_start: 0.9429 (pt0) cc_final: 0.9118 (pp20) REVERT: F 140 ASP cc_start: 0.8663 (m-30) cc_final: 0.7850 (t0) REVERT: D 193 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7424 (pp30) REVERT: H 78 GLU cc_start: 0.9157 (tt0) cc_final: 0.8732 (tm-30) REVERT: I 42 ASP cc_start: 0.9179 (OUTLIER) cc_final: 0.8893 (p0) REVERT: J 69 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7501 (pm20) REVERT: N 264 VAL cc_start: 0.8388 (t) cc_final: 0.8112 (p) REVERT: R 14 ILE cc_start: 0.9385 (mm) cc_final: 0.9181 (tt) REVERT: R 31 TYR cc_start: 0.8996 (t80) cc_final: 0.8782 (t80) REVERT: Q 95 LYS cc_start: 0.9389 (tptt) cc_final: 0.9030 (ttpt) REVERT: Q 103 GLU cc_start: 0.9350 (OUTLIER) cc_final: 0.8835 (pt0) REVERT: Q 107 LYS cc_start: 0.9194 (tttt) cc_final: 0.8978 (mmtt) REVERT: Q 113 ASP cc_start: 0.8694 (t0) cc_final: 0.8279 (m-30) REVERT: Q 122 ASP cc_start: 0.8535 (p0) cc_final: 0.8246 (m-30) REVERT: Q 140 ASP cc_start: 0.9369 (m-30) cc_final: 0.9091 (t0) REVERT: O 163 ASP cc_start: 0.8518 (m-30) cc_final: 0.8192 (p0) REVERT: S 57 LEU cc_start: 0.9011 (mt) cc_final: 0.8628 (tp) REVERT: T 31 MET cc_start: 0.8959 (mmp) cc_final: 0.8411 (mmp) outliers start: 35 outliers final: 27 residues processed: 164 average time/residue: 0.4090 time to fit residues: 114.4989 Evaluate side-chains 156 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 125 time to evaluate : 3.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain P residue 201 ARG Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 249 ASP Chi-restraints excluded: chain N residue 253 HIS Chi-restraints excluded: chain N residue 270 VAL Chi-restraints excluded: chain Q residue 103 GLU Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 179 LYS Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain O residue 85 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 0.4980 chunk 331 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 286 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 311 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 319 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 375 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 = 0.3064 r_free = 0.3064 target = 0.046291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.038096 restraints weight = 162807.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.039322 restraints weight = 77403.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.040102 restraints weight = 47569.288| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 33375 Z= 0.139 Angle : 0.482 13.786 45366 Z= 0.229 Chirality : 0.039 0.165 4952 Planarity : 0.003 0.050 5712 Dihedral : 10.709 149.902 5241 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.87 % Allowed : 14.74 % Favored : 84.39 % 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: 1.97 (0.14), residues: 3955 helix: 1.93 (0.11), residues: 2143 sheet: 0.90 (0.27), residues: 351 loop : 0.61 (0.18), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 120 HIS 0.004 0.000 HIS B 87 PHE 0.026 0.001 PHE P 64 TYR 0.028 0.001 TYR F 114 ARG 0.002 0.000 ARG H 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4850.25 seconds wall clock time: 91 minutes 8.24 seconds (5468.24 seconds total)