Starting phenix.real_space_refine on Thu Feb 22 01:06:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abb_15317/02_2024/8abb_15317_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abb_15317/02_2024/8abb_15317.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abb_15317/02_2024/8abb_15317_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abb_15317/02_2024/8abb_15317_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abb_15317/02_2024/8abb_15317_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abb_15317/02_2024/8abb_15317.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abb_15317/02_2024/8abb_15317.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abb_15317/02_2024/8abb_15317_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abb_15317/02_2024/8abb_15317_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 21031 2.51 5 N 5296 2.21 5 O 6073 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 TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "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 PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 220": "OE1" <-> "OE2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G ARG 61": "NH1" <-> "NH2" Residue "G GLU 66": "OE1" <-> "OE2" Residue "G ARG 70": "NH1" <-> "NH2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G GLU 96": "OE1" <-> "OE2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F GLU 121": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A TYR 115": "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 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 "J TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "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 "M GLU 76": "OE1" <-> "OE2" Residue "M GLU 78": "OE1" <-> "OE2" Residue "M TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 117": "OE1" <-> "OE2" Residue "M ARG 140": "NH1" <-> "NH2" Residue "M GLU 150": "OE1" <-> "OE2" Residue "M ARG 234": "NH1" <-> "NH2" Residue "M GLU 313": "OE1" <-> "OE2" Residue "M GLU 350": "OE1" <-> "OE2" Residue "M GLU 376": "OE1" <-> "OE2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "O ARG 132": "NH1" <-> "NH2" Residue "O ARG 136": "NH1" <-> "NH2" Residue "O GLU 164": "OE1" <-> "OE2" Residue "O ARG 170": "NH1" <-> "NH2" Residue "O 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 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32540 Number of models: 1 Model: "" Number of chains: 33 Chain: "C" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "P" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1445 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 11, 'TRANS': 174} Chain: "G" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "A" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "B" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "D" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "I" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "J" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "N" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "E" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "R" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "Q" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "L" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "M" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "O" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "S" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "T" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "U" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "C" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 248 Unusual residues: {'CDL': 1, 'HEM': 2, 'LMT': 1, '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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 111 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: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 298 Unusual residues: {'CDL': 2, 'HEM': 2, 'LMT': 1, '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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 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 35.287 46.186 23.863 1.00127.29 S ATOM 4207 SG CYS P 187 37.446 45.403 20.721 1.00131.48 S Time building chain proxies: 16.68, per 1000 atoms: 0.51 Number of scatterers: 32540 At special positions: 0 Unit cell: (118.833, 128.805, 165.369, 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 6073 8.00 N 5296 7.00 C 21031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS P 173 " - pdb=" SG CYS P 189 " distance=2.04 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.07 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.06 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.06 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.06 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: 13.38 Conformation dependent library (CDL) restraints added in 5.6 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: 186 helices and 15 sheets defined 54.4% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.52 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: 3.884A pdb=" N PHE C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY C 33 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR C 46 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 70 Processing helix chain 'C' and resid 75 through 102 removed outlier: 3.718A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 135 removed outlier: 4.173A pdb=" N VAL C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 153 removed outlier: 3.604A pdb=" N LEU C 150 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL C 151 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER C 152 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 4.294A 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: 4.056A pdb=" N THR C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 246 removed outlier: 6.831A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.805A 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: 3.822A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.902A 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: 4.039A pdb=" N PHE C 363 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 381 Processing helix chain 'P' and resid 59 through 91 removed outlier: 3.587A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN P 90 " --> pdb=" O ASP P 86 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N MET P 91 " --> pdb=" O PHE P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 99 Processing helix chain 'P' and resid 132 through 138 Processing helix chain 'P' and resid 152 through 155 No H-bonds generated for 'chain 'P' and resid 152 through 155' Processing helix chain 'G' and resid 4 through 16 Processing helix chain 'G' and resid 18 through 35 Proline residue: G 26 - end of helix Processing helix chain 'G' and resid 37 through 40 Processing helix chain 'G' and resid 44 through 47 Processing helix chain 'G' and resid 53 through 60 Processing helix chain 'G' and resid 64 through 83 Processing helix chain 'G' and resid 89 through 91 No H-bonds generated for 'chain 'G' and resid 89 through 91' Processing helix chain 'G' and resid 103 through 121 removed outlier: 3.617A 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: 3.599A 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: 4.189A 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: 3.802A pdb=" N VAL A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Proline residue: A 124 - end of helix removed outlier: 3.843A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 154 removed outlier: 4.006A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.761A 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: 3.551A pdb=" N THR A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 206 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.991A 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: 3.584A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 395 removed outlier: 3.548A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.358A 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: 3.643A pdb=" N ASP A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.968A 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: 3.635A pdb=" N LYS B 116 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 4.254A 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 Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.704A 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: 3.655A 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: 3.513A 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 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 40 through 81 removed outlier: 4.369A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.728A 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: 5.081A pdb=" N HIS I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LYS I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 49 removed outlier: 3.577A 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: 3.897A pdb=" N PHE N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY N 33 " --> pdb=" O TRP N 30 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR N 46 " --> pdb=" O GLN N 43 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE N 48 " --> pdb=" O ALA N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 70 Processing helix chain 'N' and resid 75 through 102 removed outlier: 3.719A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 135 removed outlier: 4.170A pdb=" N VAL N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 138 through 153 removed outlier: 3.587A pdb=" N LEU N 150 " --> pdb=" O VAL N 146 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL N 151 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER N 152 " --> pdb=" O CYS N 148 " (cutoff:3.500A) removed outlier: 4.272A 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: 4.050A pdb=" N THR N 203 " --> pdb=" O ILE N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 246 removed outlier: 6.843A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.824A 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: 3.817A pdb=" N ILE N 299 " --> pdb=" O MET N 295 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LEU N 302 " --> pdb=" O ALA N 298 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU N 303 " --> pdb=" O ILE N 299 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE N 304 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 3.924A 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: 4.040A 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: 3.593A pdb=" N SER E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 4.858A 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 60 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: 3.606A 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: 3.609A 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 Processing helix chain 'L' and resid 89 through 99 Processing helix chain 'L' and resid 120 through 135 removed outlier: 3.804A pdb=" N VAL L 123 " --> pdb=" O LYS L 120 " (cutoff:3.500A) Proline residue: L 124 - end of helix removed outlier: 3.841A pdb=" N VAL L 127 " --> pdb=" O PRO L 124 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU L 134 " --> pdb=" O ALA L 131 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN L 135 " --> pdb=" O ASP L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 156 removed outlier: 3.994A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU L 156 " --> pdb=" O THR L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 160 No H-bonds generated for 'chain 'L' and resid 158 through 160' Processing helix chain 'L' and resid 162 through 174 Processing helix chain 'L' and resid 179 through 181 No H-bonds generated for 'chain 'L' and resid 179 through 181' Processing helix chain 'L' and resid 188 through 191 No H-bonds generated for 'chain 'L' and resid 188 through 191' Processing helix chain 'L' and resid 196 through 206 Processing helix chain 'L' and resid 209 through 211 No H-bonds generated for 'chain 'L' and resid 209 through 211' Processing helix chain 'L' and resid 222 through 232 Processing helix chain 'L' and resid 294 through 304 Processing helix chain 'L' and resid 312 through 316 removed outlier: 3.996A 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: 3.588A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 395 removed outlier: 3.670A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.337A 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: 3.660A pdb=" N ASP L 468 " --> pdb=" O ARG L 464 " (cutoff:3.500A) removed outlier: 3.975A 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: 3.632A pdb=" N VAL M 108 " --> pdb=" O PRO M 105 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS M 116 " --> pdb=" O ASN M 113 " (cutoff:3.500A) removed outlier: 4.269A 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 Processing helix chain 'M' and resid 254 through 263 removed outlier: 3.693A 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 366 removed outlier: 3.902A 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 203 through 206 No H-bonds generated for 'chain 'O' and resid 203 through 206' Processing helix chain 'O' and resid 210 through 218 removed outlier: 3.512A 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 31 through 33 No H-bonds generated for 'chain 'S' and resid 31 through 33' Processing helix chain 'S' and resid 40 through 81 removed outlier: 4.367A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.719A 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: 5.055A pdb=" N HIS T 55 " --> pdb=" O LYS T 51 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LYS T 56 " --> pdb=" O ASP T 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 49 removed outlier: 3.616A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.590A 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: 3.903A 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: 4.054A 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: 3.560A 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: 4.056A 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: 3.532A 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 1589 hydrogen bonds defined for protein. 4338 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.22 Time building geometry restraints manager: 14.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 13594 1.41 - 1.61: 19564 1.61 - 1.82: 167 1.82 - 2.03: 22 2.03 - 2.23: 20 Bond restraints: 33367 Sorted by residual: bond pdb=" N TYR S 9 " pdb=" CA TYR S 9 " ideal model delta sigma weight residual 1.458 1.622 -0.164 1.90e-02 2.77e+03 7.41e+01 bond pdb=" N TYR H 9 " pdb=" CA TYR H 9 " ideal model delta sigma weight residual 1.458 1.615 -0.157 1.90e-02 2.77e+03 6.83e+01 bond pdb=" N ALA T 4 " pdb=" CA ALA T 4 " ideal model delta sigma weight residual 1.458 1.604 -0.146 1.90e-02 2.77e+03 5.93e+01 bond pdb=" N ALA I 4 " pdb=" CA ALA I 4 " ideal model delta sigma weight residual 1.458 1.603 -0.145 1.90e-02 2.77e+03 5.82e+01 bond pdb=" C3B HEC D 401 " pdb=" CAB HEC D 401 " ideal model delta sigma weight residual 1.544 1.426 0.118 2.00e-02 2.50e+03 3.47e+01 ... (remaining 33362 not shown) Histogram of bond angle deviations from ideal: 84.30 - 103.30: 551 103.30 - 122.30: 38695 122.30 - 141.30: 6094 141.30 - 160.30: 0 160.30 - 179.30: 12 Bond angle restraints: 45352 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 91.89 12.44 1.14e+00 7.69e-01 1.19e+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 91.75 12.58 1.20e+00 6.94e-01 1.10e+02 angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.14 97.06 14.08 1.56e+00 4.11e-01 8.15e+01 angle pdb=" CG ARG M 90 " pdb=" CD ARG M 90 " pdb=" NE ARG M 90 " ideal model delta sigma weight residual 112.00 94.47 17.53 2.20e+00 2.07e-01 6.35e+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 94.48 17.52 2.20e+00 2.07e-01 6.34e+01 ... (remaining 45347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.11: 18820 32.11 - 64.22: 1040 64.22 - 96.34: 99 96.34 - 128.45: 1 128.45 - 160.56: 3 Dihedral angle restraints: 19963 sinusoidal: 8344 harmonic: 11619 Sorted by residual: 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 -105.35 -17.25 0 2.50e+00 1.60e-01 4.76e+01 dihedral pdb=" C2B HEC O 401 " pdb=" C3B HEC O 401 " pdb=" CAB HEC O 401 " pdb=" CBB HEC O 401 " ideal model delta sinusoidal sigma weight residual 60.00 -5.62 65.62 2 1.00e+01 1.00e-02 3.98e+01 dihedral pdb=" C2B HEC D 401 " pdb=" C3B HEC D 401 " pdb=" CAB HEC D 401 " pdb=" CBB HEC D 401 " ideal model delta sinusoidal sigma weight residual 60.00 -3.99 63.99 2 1.00e+01 1.00e-02 3.88e+01 ... (remaining 19960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.190: 4561 0.190 - 0.379: 381 0.379 - 0.569: 16 0.569 - 0.759: 0 0.759 - 0.949: 4 Chirality restraints: 4962 Sorted by residual: chirality pdb=" CB4 CDL H 702 " pdb=" CB3 CDL H 702 " pdb=" CB6 CDL H 702 " pdb=" OB6 CDL H 702 " both_signs ideal model delta sigma weight residual False -2.57 -1.63 -0.95 2.00e-01 2.50e+01 2.25e+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 -1.63 -0.94 2.00e-01 2.50e+01 2.22e+01 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 -1.67 -0.91 2.00e-01 2.50e+01 2.07e+01 ... (remaining 4959 not shown) Planarity restraints: 5700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A HEC D 401 " -0.018 2.00e-02 2.50e+03 3.23e-02 2.34e+01 pdb=" C2A HEC D 401 " -0.025 2.00e-02 2.50e+03 pdb=" C3A HEC D 401 " -0.026 2.00e-02 2.50e+03 pdb=" C4A HEC D 401 " -0.047 2.00e-02 2.50e+03 pdb=" CAA HEC D 401 " 0.039 2.00e-02 2.50e+03 pdb=" CHA HEC D 401 " 0.022 2.00e-02 2.50e+03 pdb=" CHB HEC D 401 " 0.059 2.00e-02 2.50e+03 pdb=" CMA HEC D 401 " 0.001 2.00e-02 2.50e+03 pdb=" NA HEC D 401 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEC O 401 " -0.013 2.00e-02 2.50e+03 3.04e-02 2.08e+01 pdb=" C1B HEC O 401 " -0.010 2.00e-02 2.50e+03 pdb=" C2B HEC O 401 " -0.014 2.00e-02 2.50e+03 pdb=" C3B HEC O 401 " -0.033 2.00e-02 2.50e+03 pdb=" C4B HEC O 401 " -0.009 2.00e-02 2.50e+03 pdb=" CAB HEC O 401 " 0.059 2.00e-02 2.50e+03 pdb=" CHB HEC O 401 " 0.050 2.00e-02 2.50e+03 pdb=" CHC HEC O 401 " -0.006 2.00e-02 2.50e+03 pdb=" CMB HEC O 401 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEC O 401 " 0.020 2.00e-02 2.50e+03 2.98e-02 2.00e+01 pdb=" C2A HEC O 401 " 0.017 2.00e-02 2.50e+03 pdb=" C3A HEC O 401 " 0.012 2.00e-02 2.50e+03 pdb=" C4A HEC O 401 " 0.050 2.00e-02 2.50e+03 pdb=" CAA HEC O 401 " -0.032 2.00e-02 2.50e+03 pdb=" CHA HEC O 401 " -0.021 2.00e-02 2.50e+03 pdb=" CHB HEC O 401 " -0.056 2.00e-02 2.50e+03 pdb=" CMA HEC O 401 " 0.006 2.00e-02 2.50e+03 pdb=" NA HEC O 401 " 0.006 2.00e-02 2.50e+03 ... (remaining 5697 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 9 2.28 - 2.94: 14089 2.94 - 3.59: 48861 3.59 - 4.25: 86693 4.25 - 4.90: 137014 Nonbonded interactions: 286666 Sorted by model distance: nonbonded pdb=" O CYS P 189 " pdb=" CE MET D 235 " model vdw 1.629 3.460 nonbonded pdb=" NE2 HIS N 82 " pdb="FE HEM N 501 " model vdw 2.053 3.080 nonbonded pdb=" NE2 HIS C 82 " pdb="FE HEM C 501 " model vdw 2.064 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.100 2.520 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.144 3.080 ... (remaining 286661 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 or (resid 701 and (name CB2 or name OB2 or na \ me CB3 or name OB3 or name C1 or name C11 or name C12 or name C31 or name C71 or \ name C72 or name CA2 or name CA3 or name CA4 or name CA5 or name CA6 or name CA \ 7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or name OA2 or name \ OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 or name OA9 or \ name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name OB9 or name PA1 \ or name PB2)))) selection = (chain 'S' and (resid 9 through 93 or (resid 101 and (name CB2 or name OB2 or na \ me CB3 or name OB3 or name C1 or name C11 or name C12 or name C31 or name C71 or \ name C72 or name CA2 or name CA3 or name CA4 or name CA5 or name CA6 or name CA \ 7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or name OA2 or name \ OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 or name OA9 or \ name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name OB9 or name PA1 \ or name PB2)))) } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = (chain 'J' and resid 8 through 82) selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 11.430 Check model and map are aligned: 0.530 Set scattering table: 0.320 Process input model: 87.960 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9218 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 : 0.011 0.216 33367 Z= 0.707 Angle : 1.779 17.899 45352 Z= 1.114 Chirality : 0.112 0.949 4962 Planarity : 0.007 0.094 5700 Dihedral : 18.415 160.561 12462 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.35 % Favored : 97.62 % Rotamer: Outliers : 3.76 % Allowed : 8.03 % Favored : 88.21 % Cbeta Deviations : 1.23 % 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: -1.54 (0.12), residues: 3955 helix: -1.20 (0.09), residues: 2144 sheet: -0.15 (0.25), residues: 358 loop : -0.66 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.008 TRP L 474 HIS 0.023 0.005 HIS N 96 PHE 0.054 0.007 PHE C 234 TYR 0.051 0.007 TYR D 120 ARG 0.033 0.002 ARG G 76 *********************** 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 579 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 454 time to evaluate : 3.691 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: C 6 LYS cc_start: 0.9435 (tttt) cc_final: 0.9162 (ttpt) REVERT: P 92 SER cc_start: 0.9635 (t) cc_final: 0.9351 (m) REVERT: G 9 LYS cc_start: 0.9065 (mttp) cc_final: 0.8727 (ttpt) REVERT: G 50 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8842 (pm20) REVERT: G 97 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8666 (mt-10) REVERT: G 99 ASP cc_start: 0.8843 (p0) cc_final: 0.8550 (p0) REVERT: G 123 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8883 (tm-30) REVERT: F 84 GLU cc_start: 0.9230 (tt0) cc_final: 0.9018 (pt0) REVERT: F 96 HIS cc_start: 0.9097 (OUTLIER) cc_final: 0.8599 (t70) REVERT: A 87 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7803 (mtp85) REVERT: A 141 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8943 (tp30) REVERT: A 397 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8089 (mt) REVERT: B 251 GLU cc_start: 0.9450 (mt-10) cc_final: 0.9167 (pm20) REVERT: D 303 MET cc_start: 0.9280 (mtp) cc_final: 0.9045 (mtt) REVERT: H 51 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8179 (mtm-85) REVERT: I 30 ASP cc_start: 0.9498 (t70) cc_final: 0.8951 (t0) REVERT: J 10 LYS cc_start: 0.9610 (tttm) cc_final: 0.9350 (tptp) REVERT: J 11 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8772 (pttm) REVERT: J 55 ARG cc_start: 0.8800 (ttm-80) cc_final: 0.8542 (tpp80) REVERT: J 59 ASP cc_start: 0.9541 (m-30) cc_final: 0.9293 (m-30) REVERT: J 73 ARG cc_start: 0.8917 (ptt-90) cc_final: 0.8684 (mtm180) REVERT: J 80 ASN cc_start: 0.9214 (t0) cc_final: 0.8967 (t0) REVERT: N 197 HIS cc_start: 0.9439 (OUTLIER) cc_final: 0.8747 (p-80) REVERT: N 287 ASP cc_start: 0.8435 (t0) cc_final: 0.8045 (t0) REVERT: N 345 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8932 (mt-10) REVERT: N 369 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8762 (mtt) REVERT: E 53 LYS cc_start: 0.9132 (mtpt) cc_final: 0.8764 (mtmt) REVERT: E 55 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8312 (p0) REVERT: E 68 MET cc_start: 0.9389 (mmm) cc_final: 0.9037 (mmm) REVERT: R 50 GLU cc_start: 0.9065 (pt0) cc_final: 0.8710 (pm20) REVERT: R 55 MET cc_start: 0.9482 (mmm) cc_final: 0.9257 (tpp) REVERT: R 117 ASP cc_start: 0.8994 (m-30) cc_final: 0.8683 (t0) REVERT: Q 114 TYR cc_start: 0.8495 (t80) cc_final: 0.8149 (t80) REVERT: Q 115 ASP cc_start: 0.9037 (p0) cc_final: 0.8475 (p0) REVERT: Q 116 HIS cc_start: 0.8828 (m-70) cc_final: 0.8327 (m-70) REVERT: Q 126 GLU cc_start: 0.9479 (mp0) cc_final: 0.8791 (mp0) REVERT: Q 133 CYS cc_start: 0.8936 (t) cc_final: 0.8674 (t) REVERT: Q 140 ASP cc_start: 0.9334 (m-30) cc_final: 0.8831 (t0) REVERT: L 87 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8167 (mtt90) REVERT: M 16 SER cc_start: 0.9541 (OUTLIER) cc_final: 0.9093 (p) REVERT: M 31 GLN cc_start: 0.9065 (mt0) cc_final: 0.8626 (tt0) REVERT: M 309 ASP cc_start: 0.9419 (m-30) cc_final: 0.9053 (t0) REVERT: M 341 TYR cc_start: 0.9202 (t80) cc_final: 0.8930 (t80) REVERT: S 78 GLU cc_start: 0.9349 (tt0) cc_final: 0.9109 (pp20) REVERT: T 30 ASP cc_start: 0.9498 (t70) cc_final: 0.9230 (t0) REVERT: T 43 ARG cc_start: 0.9238 (mtm110) cc_final: 0.8714 (ttp80) REVERT: U 55 ARG cc_start: 0.8821 (ttm-80) cc_final: 0.8592 (tpp80) REVERT: U 58 GLN cc_start: 0.9381 (tp40) cc_final: 0.9019 (mt0) REVERT: U 59 ASP cc_start: 0.9567 (m-30) cc_final: 0.9244 (m-30) REVERT: U 73 ARG cc_start: 0.8863 (ptt-90) cc_final: 0.8624 (ptt180) REVERT: U 80 ASN cc_start: 0.9209 (t0) cc_final: 0.8984 (t0) outliers start: 125 outliers final: 15 residues processed: 538 average time/residue: 0.5047 time to fit residues: 411.5202 Evaluate side-chains 358 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 330 time to evaluate : 3.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain P residue 114 LYS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain F residue 96 HIS Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 369 MET Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 215 GLN Chi-restraints excluded: chain M residue 261 SER Chi-restraints excluded: chain S residue 51 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 20.0000 chunk 297 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 200 optimal weight: 0.5980 chunk 158 optimal weight: 3.9990 chunk 307 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 228 optimal weight: 0.0020 chunk 355 optimal weight: 5.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- 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 202 HIS C 332 ASN P 85 GLN P 90 ASN P 115 ASN P 157 GLN G 54 ASN G 84 HIS F 96 HIS F 109 GLN A 74 HIS A 192 GLN A 222 HIS A 332 ASN A 371 ASN B 87 HIS B 197 ASN N 11 ASN N 14 ASN N 202 HIS N 332 ASN E 85 GLN E 90 ASN R 84 HIS L 332 ASN L 371 ASN M 87 HIS M 197 ASN M 215 GLN M 377 ASN O 93 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9159 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33367 Z= 0.208 Angle : 0.613 17.194 45352 Z= 0.304 Chirality : 0.042 0.230 4962 Planarity : 0.004 0.040 5700 Dihedral : 14.168 155.026 5333 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.32 % Allowed : 10.17 % Favored : 88.51 % 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: 0.61 (0.13), residues: 3955 helix: 0.75 (0.11), residues: 2133 sheet: 0.30 (0.26), residues: 368 loop : 0.14 (0.17), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 156 HIS 0.010 0.001 HIS F 96 PHE 0.021 0.002 PHE L 334 TYR 0.018 0.002 TYR D 237 ARG 0.005 0.000 ARG P 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 388 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 344 time to evaluate : 4.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 92 SER cc_start: 0.9630 (t) cc_final: 0.9373 (m) REVERT: G 9 LYS cc_start: 0.9020 (mttp) cc_final: 0.8679 (tttm) REVERT: G 31 TYR cc_start: 0.9231 (t80) cc_final: 0.8963 (t80) REVERT: G 97 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8728 (mt-10) REVERT: G 123 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8898 (tm-30) REVERT: A 397 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8097 (mt) REVERT: A 433 HIS cc_start: 0.8903 (t70) cc_final: 0.8577 (m90) REVERT: B 154 GLU cc_start: 0.9324 (tp30) cc_final: 0.9113 (pt0) REVERT: B 251 GLU cc_start: 0.9446 (mt-10) cc_final: 0.9231 (pm20) REVERT: D 163 ASP cc_start: 0.9358 (m-30) cc_final: 0.8838 (p0) REVERT: I 7 PHE cc_start: 0.8838 (t80) cc_final: 0.8538 (m-80) REVERT: J 11 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8768 (pttm) REVERT: J 13 SER cc_start: 0.9454 (t) cc_final: 0.9097 (p) REVERT: J 55 ARG cc_start: 0.8814 (ttm-80) cc_final: 0.8364 (tpp80) REVERT: J 59 ASP cc_start: 0.9454 (m-30) cc_final: 0.9198 (m-30) REVERT: J 73 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8558 (mtt90) REVERT: J 80 ASN cc_start: 0.9208 (t0) cc_final: 0.8914 (t0) REVERT: N 217 ASP cc_start: 0.9001 (t0) cc_final: 0.8710 (t0) REVERT: N 369 MET cc_start: 0.8782 (mmm) cc_final: 0.8531 (ptt) REVERT: E 55 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8302 (p0) REVERT: R 50 GLU cc_start: 0.8999 (pt0) cc_final: 0.8704 (pm20) REVERT: R 117 ASP cc_start: 0.8976 (m-30) cc_final: 0.8730 (t0) REVERT: Q 100 GLU cc_start: 0.9447 (mm-30) cc_final: 0.9212 (mt-10) REVERT: Q 114 TYR cc_start: 0.8460 (t80) cc_final: 0.8162 (t80) REVERT: Q 115 ASP cc_start: 0.9029 (p0) cc_final: 0.8525 (p0) REVERT: Q 116 HIS cc_start: 0.8852 (m-70) cc_final: 0.8396 (m-70) REVERT: Q 126 GLU cc_start: 0.9443 (mp0) cc_final: 0.9179 (mp0) REVERT: Q 140 ASP cc_start: 0.9235 (m-30) cc_final: 0.8705 (t0) REVERT: M 60 PHE cc_start: 0.9504 (OUTLIER) cc_final: 0.9218 (t80) REVERT: M 205 GLN cc_start: 0.9049 (tm-30) cc_final: 0.8746 (tm-30) REVERT: M 309 ASP cc_start: 0.9334 (m-30) cc_final: 0.8909 (t0) REVERT: M 373 ILE cc_start: 0.9347 (mm) cc_final: 0.9119 (tt) REVERT: S 78 GLU cc_start: 0.9318 (tt0) cc_final: 0.9052 (pp20) REVERT: T 30 ASP cc_start: 0.9310 (t70) cc_final: 0.9011 (t0) REVERT: T 43 ARG cc_start: 0.9184 (mtm110) cc_final: 0.8729 (ttp80) REVERT: U 51 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8719 (tm-30) REVERT: U 58 GLN cc_start: 0.9345 (tp40) cc_final: 0.9083 (mt0) REVERT: U 59 ASP cc_start: 0.9517 (m-30) cc_final: 0.9304 (m-30) REVERT: U 73 ARG cc_start: 0.9022 (ptt-90) cc_final: 0.8818 (ptt-90) REVERT: U 80 ASN cc_start: 0.9207 (t0) cc_final: 0.8955 (t0) outliers start: 44 outliers final: 21 residues processed: 373 average time/residue: 0.4742 time to fit residues: 279.9673 Evaluate side-chains 340 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 313 time to evaluate : 3.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 136 ASP Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 213 ASP 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: 1.9990 chunk 110 optimal weight: 0.8980 chunk 296 optimal weight: 7.9990 chunk 242 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 356 optimal weight: 5.9990 chunk 385 optimal weight: 9.9990 chunk 317 optimal weight: 2.9990 chunk 353 optimal weight: 0.6980 chunk 121 optimal weight: 10.0000 chunk 286 optimal weight: 7.9990 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 177 GLN P 115 ASN F 109 GLN A 192 GLN B 316 GLN D 93 HIS N 11 ASN N 177 GLN Q 131 GLN L 177 ASN M 92 HIS M 316 GLN M 377 ASN O 93 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9178 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 33367 Z= 0.280 Angle : 0.560 16.416 45352 Z= 0.268 Chirality : 0.041 0.150 4962 Planarity : 0.004 0.050 5700 Dihedral : 12.750 151.378 5291 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.35 % Allowed : 10.71 % Favored : 87.94 % 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: 1.29 (0.13), residues: 3955 helix: 1.38 (0.11), residues: 2114 sheet: 0.49 (0.27), residues: 369 loop : 0.36 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 142 HIS 0.007 0.001 HIS C 197 PHE 0.018 0.001 PHE L 334 TYR 0.019 0.001 TYR A 106 ARG 0.004 0.000 ARG P 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 374 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 329 time to evaluate : 3.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 309 ASP cc_start: 0.9299 (t0) cc_final: 0.9028 (t0) REVERT: P 116 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8162 (m) REVERT: G 9 LYS cc_start: 0.9011 (mttp) cc_final: 0.8637 (tttm) REVERT: F 110 GLU cc_start: 0.9391 (pt0) cc_final: 0.9041 (pp20) REVERT: A 397 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8126 (mt) REVERT: A 433 HIS cc_start: 0.8854 (t70) cc_final: 0.8564 (m-70) REVERT: B 251 GLU cc_start: 0.9445 (mt-10) cc_final: 0.9240 (pm20) REVERT: D 89 GLU cc_start: 0.9504 (mt-10) cc_final: 0.9154 (mt-10) REVERT: D 163 ASP cc_start: 0.9396 (m-30) cc_final: 0.8913 (p0) REVERT: I 7 PHE cc_start: 0.8881 (t80) cc_final: 0.8576 (m-80) REVERT: I 54 ARG cc_start: 0.9195 (ttp80) cc_final: 0.8986 (ttp80) REVERT: J 11 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8819 (pttm) REVERT: J 13 SER cc_start: 0.9449 (t) cc_final: 0.9141 (p) REVERT: J 55 ARG cc_start: 0.8853 (ttm-80) cc_final: 0.8450 (tpp80) REVERT: J 59 ASP cc_start: 0.9411 (m-30) cc_final: 0.9182 (m-30) REVERT: J 73 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8630 (mtt90) REVERT: J 80 ASN cc_start: 0.9220 (t0) cc_final: 0.8874 (t0) REVERT: N 217 ASP cc_start: 0.8970 (t0) cc_final: 0.8671 (t0) REVERT: E 55 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8282 (p0) REVERT: R 50 GLU cc_start: 0.8998 (pt0) cc_final: 0.8708 (pm20) REVERT: R 117 ASP cc_start: 0.8997 (m-30) cc_final: 0.8768 (t0) REVERT: Q 100 GLU cc_start: 0.9466 (mm-30) cc_final: 0.9193 (mt-10) REVERT: Q 113 ASP cc_start: 0.9167 (t0) cc_final: 0.8929 (t0) REVERT: Q 114 TYR cc_start: 0.8473 (t80) cc_final: 0.8166 (t80) REVERT: Q 115 ASP cc_start: 0.9011 (p0) cc_final: 0.8585 (p0) REVERT: Q 116 HIS cc_start: 0.8873 (m-70) cc_final: 0.8471 (m-70) REVERT: Q 126 GLU cc_start: 0.9442 (mp0) cc_final: 0.9178 (mp0) REVERT: Q 140 ASP cc_start: 0.9246 (m-30) cc_final: 0.8703 (t0) REVERT: M 31 GLN cc_start: 0.9053 (mt0) cc_final: 0.8763 (tt0) REVERT: M 60 PHE cc_start: 0.9514 (OUTLIER) cc_final: 0.9160 (t80) REVERT: M 309 ASP cc_start: 0.9335 (m-30) cc_final: 0.8921 (t0) REVERT: S 51 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.7098 (ptm-80) REVERT: S 78 GLU cc_start: 0.9309 (tt0) cc_final: 0.9040 (pp20) REVERT: T 30 ASP cc_start: 0.9337 (t70) cc_final: 0.9069 (t0) REVERT: T 43 ARG cc_start: 0.9057 (mtm110) cc_final: 0.8695 (ttp80) REVERT: U 11 LYS cc_start: 0.9039 (tmtt) cc_final: 0.8698 (ptmm) REVERT: U 51 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8640 (tm-30) REVERT: U 58 GLN cc_start: 0.9321 (tp40) cc_final: 0.9053 (mt0) REVERT: U 73 ARG cc_start: 0.9064 (ptt-90) cc_final: 0.8843 (ptt180) outliers start: 45 outliers final: 21 residues processed: 363 average time/residue: 0.4567 time to fit residues: 264.7872 Evaluate side-chains 328 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 300 time to evaluate : 3.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 5.9990 chunk 268 optimal weight: 7.9990 chunk 185 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 170 optimal weight: 0.9980 chunk 239 optimal weight: 0.6980 chunk 357 optimal weight: 0.9980 chunk 378 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 339 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 115 ASN F 109 GLN Q 131 GLN M 377 ASN O 236 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9167 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33367 Z= 0.223 Angle : 0.515 14.327 45352 Z= 0.246 Chirality : 0.040 0.192 4962 Planarity : 0.004 0.053 5700 Dihedral : 12.119 150.124 5286 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.20 % Allowed : 11.61 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.14), residues: 3955 helix: 1.63 (0.11), residues: 2122 sheet: 0.55 (0.27), residues: 369 loop : 0.48 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 142 HIS 0.007 0.001 HIS C 197 PHE 0.017 0.001 PHE L 334 TYR 0.016 0.001 TYR A 106 ARG 0.007 0.000 ARG Q 144 *********************** 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 354 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 314 time to evaluate : 3.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 195 ASP cc_start: 0.8895 (t0) cc_final: 0.8650 (t70) REVERT: G 9 LYS cc_start: 0.9017 (mttp) cc_final: 0.8640 (tttm) REVERT: F 93 ASP cc_start: 0.9400 (p0) cc_final: 0.9097 (p0) REVERT: F 110 GLU cc_start: 0.9436 (pt0) cc_final: 0.9134 (pp20) REVERT: A 433 HIS cc_start: 0.8835 (t70) cc_final: 0.8566 (m-70) REVERT: B 251 GLU cc_start: 0.9449 (mt-10) cc_final: 0.9248 (pm20) REVERT: I 7 PHE cc_start: 0.8892 (t80) cc_final: 0.8582 (m-80) REVERT: I 54 ARG cc_start: 0.9192 (ttp80) cc_final: 0.8975 (ttp80) REVERT: J 13 SER cc_start: 0.9476 (t) cc_final: 0.9153 (p) REVERT: J 55 ARG cc_start: 0.8854 (ttm-80) cc_final: 0.8615 (tpp80) REVERT: J 73 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8537 (mtt90) REVERT: J 80 ASN cc_start: 0.9238 (t0) cc_final: 0.8872 (t0) REVERT: E 55 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8282 (p0) REVERT: R 50 GLU cc_start: 0.8959 (pt0) cc_final: 0.8707 (pm20) REVERT: R 117 ASP cc_start: 0.8968 (m-30) cc_final: 0.8754 (t0) REVERT: Q 100 GLU cc_start: 0.9471 (mm-30) cc_final: 0.9232 (mt-10) REVERT: Q 113 ASP cc_start: 0.9176 (t0) cc_final: 0.8953 (t0) REVERT: Q 114 TYR cc_start: 0.8451 (t80) cc_final: 0.8152 (t80) REVERT: Q 115 ASP cc_start: 0.9027 (p0) cc_final: 0.8620 (p0) REVERT: Q 116 HIS cc_start: 0.8878 (m-70) cc_final: 0.8498 (m-70) REVERT: Q 126 GLU cc_start: 0.9384 (mp0) cc_final: 0.9114 (mp0) REVERT: Q 140 ASP cc_start: 0.9252 (m-30) cc_final: 0.8699 (t0) REVERT: L 390 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8944 (mtmm) REVERT: M 31 GLN cc_start: 0.9055 (mt0) cc_final: 0.8752 (tt0) REVERT: M 60 PHE cc_start: 0.9511 (OUTLIER) cc_final: 0.9179 (t80) REVERT: M 292 THR cc_start: 0.9282 (OUTLIER) cc_final: 0.9054 (p) REVERT: M 309 ASP cc_start: 0.9314 (m-30) cc_final: 0.8883 (t0) REVERT: S 51 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.7893 (ptm-80) REVERT: S 78 GLU cc_start: 0.9308 (tt0) cc_final: 0.9040 (pp20) REVERT: T 30 ASP cc_start: 0.9276 (t70) cc_final: 0.9007 (t0) REVERT: T 43 ARG cc_start: 0.9021 (mtm110) cc_final: 0.8637 (ttp80) REVERT: U 11 LYS cc_start: 0.8995 (tmtt) cc_final: 0.8631 (ptmm) REVERT: U 51 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8652 (tm-30) REVERT: U 58 GLN cc_start: 0.9296 (tp40) cc_final: 0.9039 (mt0) REVERT: U 73 ARG cc_start: 0.9100 (ptt-90) cc_final: 0.8879 (ptt180) outliers start: 40 outliers final: 21 residues processed: 345 average time/residue: 0.4482 time to fit residues: 248.7680 Evaluate side-chains 329 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 302 time to evaluate : 3.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain L residue 396 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 0.2980 chunk 215 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 282 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 323 optimal weight: 0.1980 chunk 261 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 2.9990 chunk 340 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 115 ASN F 109 GLN A 323 ASN N 14 ASN Q 131 GLN M 377 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9187 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33367 Z= 0.287 Angle : 0.542 16.151 45352 Z= 0.255 Chirality : 0.041 0.177 4962 Planarity : 0.004 0.054 5700 Dihedral : 11.708 149.831 5277 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.29 % Allowed : 11.70 % Favored : 87.01 % 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: 1.66 (0.14), residues: 3955 helix: 1.72 (0.11), residues: 2110 sheet: 0.53 (0.27), residues: 369 loop : 0.49 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 142 HIS 0.008 0.001 HIS C 197 PHE 0.016 0.001 PHE L 334 TYR 0.017 0.001 TYR N 225 ARG 0.006 0.000 ARG Q 144 *********************** 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 350 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 307 time to evaluate : 3.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 309 ASP cc_start: 0.9287 (t0) cc_final: 0.8990 (t0) REVERT: G 9 LYS cc_start: 0.9023 (mttp) cc_final: 0.8653 (tttm) REVERT: G 12 GLU cc_start: 0.9430 (OUTLIER) cc_final: 0.9168 (mp0) REVERT: A 433 HIS cc_start: 0.8863 (t70) cc_final: 0.8587 (m-70) REVERT: B 251 GLU cc_start: 0.9450 (mt-10) cc_final: 0.9232 (pm20) REVERT: I 7 PHE cc_start: 0.8900 (t80) cc_final: 0.8575 (m-80) REVERT: I 54 ARG cc_start: 0.9206 (ttp80) cc_final: 0.8988 (ttp80) REVERT: J 13 SER cc_start: 0.9504 (t) cc_final: 0.9218 (p) REVERT: J 55 ARG cc_start: 0.8862 (ttm-80) cc_final: 0.8609 (tpp80) REVERT: J 73 ARG cc_start: 0.8988 (OUTLIER) cc_final: 0.8633 (mtt90) REVERT: J 80 ASN cc_start: 0.9269 (t0) cc_final: 0.8890 (t0) REVERT: E 55 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8296 (p0) REVERT: R 50 GLU cc_start: 0.8955 (pt0) cc_final: 0.8724 (pm20) REVERT: R 117 ASP cc_start: 0.8972 (m-30) cc_final: 0.8756 (t0) REVERT: Q 100 GLU cc_start: 0.9464 (mm-30) cc_final: 0.9209 (mt-10) REVERT: Q 113 ASP cc_start: 0.9185 (t0) cc_final: 0.8984 (t0) REVERT: Q 114 TYR cc_start: 0.8426 (t80) cc_final: 0.8131 (t80) REVERT: Q 115 ASP cc_start: 0.9013 (p0) cc_final: 0.8641 (p0) REVERT: Q 116 HIS cc_start: 0.8842 (m-70) cc_final: 0.8490 (m-70) REVERT: Q 126 GLU cc_start: 0.9337 (mp0) cc_final: 0.9014 (mp0) REVERT: Q 140 ASP cc_start: 0.9271 (m-30) cc_final: 0.8761 (t0) REVERT: L 390 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8942 (mtmm) REVERT: M 60 PHE cc_start: 0.9538 (OUTLIER) cc_final: 0.9147 (t80) REVERT: M 292 THR cc_start: 0.9291 (OUTLIER) cc_final: 0.9048 (p) REVERT: M 309 ASP cc_start: 0.9328 (m-30) cc_final: 0.8912 (t0) REVERT: M 339 ARG cc_start: 0.9483 (OUTLIER) cc_final: 0.9161 (ttp-110) REVERT: S 78 GLU cc_start: 0.9302 (tt0) cc_final: 0.9042 (pp20) REVERT: T 30 ASP cc_start: 0.9296 (t70) cc_final: 0.9046 (t0) REVERT: T 43 ARG cc_start: 0.8989 (mtm110) cc_final: 0.8645 (ttp80) REVERT: U 11 LYS cc_start: 0.8976 (tmtt) cc_final: 0.8596 (ptmm) REVERT: U 51 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8811 (tm-30) REVERT: U 58 GLN cc_start: 0.9296 (tp40) cc_final: 0.9038 (mt0) outliers start: 43 outliers final: 26 residues processed: 341 average time/residue: 0.4519 time to fit residues: 248.0497 Evaluate side-chains 331 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 298 time to evaluate : 3.303 ------------------------------------------------------------------------------- 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 143 VAL Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain L residue 396 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 339 ARG Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 3.9990 chunk 341 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 222 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 379 optimal weight: 6.9990 chunk 314 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN A 332 ASN Q 131 GLN ** M 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 377 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9207 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 33367 Z= 0.415 Angle : 0.591 17.937 45352 Z= 0.277 Chirality : 0.043 0.145 4962 Planarity : 0.004 0.054 5700 Dihedral : 11.712 149.947 5273 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.29 % Allowed : 12.09 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.14), residues: 3955 helix: 1.69 (0.11), residues: 2110 sheet: 0.41 (0.26), residues: 369 loop : 0.54 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 142 HIS 0.009 0.001 HIS C 197 PHE 0.019 0.001 PHE N 240 TYR 0.018 0.001 TYR N 225 ARG 0.003 0.000 ARG P 201 *********************** 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 346 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 303 time to evaluate : 3.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 309 ASP cc_start: 0.9345 (t0) cc_final: 0.9047 (t0) REVERT: G 9 LYS cc_start: 0.9058 (mttp) cc_final: 0.8689 (tttm) REVERT: G 12 GLU cc_start: 0.9442 (OUTLIER) cc_final: 0.9180 (mp0) REVERT: G 96 GLU cc_start: 0.9428 (mp0) cc_final: 0.9069 (mp0) REVERT: F 103 GLU cc_start: 0.9392 (mm-30) cc_final: 0.9027 (tp30) REVERT: F 110 GLU cc_start: 0.9359 (pt0) cc_final: 0.9044 (pp20) REVERT: B 251 GLU cc_start: 0.9451 (mt-10) cc_final: 0.9215 (pm20) REVERT: I 7 PHE cc_start: 0.8900 (t80) cc_final: 0.8583 (m-80) REVERT: J 13 SER cc_start: 0.9509 (t) cc_final: 0.9289 (p) REVERT: J 55 ARG cc_start: 0.8870 (ttm-80) cc_final: 0.8604 (tpp80) REVERT: J 73 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8731 (mtm-85) REVERT: J 80 ASN cc_start: 0.9284 (t0) cc_final: 0.8944 (t0) REVERT: E 55 ASP cc_start: 0.8972 (OUTLIER) cc_final: 0.8371 (p0) REVERT: R 50 GLU cc_start: 0.8972 (pt0) cc_final: 0.8720 (pm20) REVERT: R 117 ASP cc_start: 0.8971 (m-30) cc_final: 0.8744 (t0) REVERT: Q 100 GLU cc_start: 0.9466 (mm-30) cc_final: 0.9173 (mt-10) REVERT: Q 114 TYR cc_start: 0.8416 (t80) cc_final: 0.8134 (t80) REVERT: Q 115 ASP cc_start: 0.9016 (p0) cc_final: 0.8668 (p0) REVERT: Q 116 HIS cc_start: 0.8839 (m-70) cc_final: 0.8514 (m-70) REVERT: Q 126 GLU cc_start: 0.9335 (mp0) cc_final: 0.9037 (mp0) REVERT: Q 140 ASP cc_start: 0.9297 (m-30) cc_final: 0.8763 (t0) REVERT: L 390 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8946 (mtmm) REVERT: M 60 PHE cc_start: 0.9560 (OUTLIER) cc_final: 0.9137 (t80) REVERT: M 292 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.9024 (p) REVERT: M 309 ASP cc_start: 0.9330 (m-30) cc_final: 0.8932 (t0) REVERT: S 78 GLU cc_start: 0.9305 (tt0) cc_final: 0.9040 (pp20) REVERT: T 30 ASP cc_start: 0.9319 (t70) cc_final: 0.9094 (t0) REVERT: T 43 ARG cc_start: 0.8989 (mtm110) cc_final: 0.8630 (ttp80) REVERT: U 11 LYS cc_start: 0.8976 (tmtt) cc_final: 0.8590 (ptmm) REVERT: U 51 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8836 (tm-30) REVERT: U 58 GLN cc_start: 0.9290 (tp40) cc_final: 0.9034 (mt0) outliers start: 43 outliers final: 31 residues processed: 337 average time/residue: 0.4396 time to fit residues: 238.8201 Evaluate side-chains 334 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 297 time to evaluate : 3.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain L residue 396 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 216 optimal weight: 0.7980 chunk 276 optimal weight: 10.0000 chunk 214 optimal weight: 0.7980 chunk 319 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 377 optimal weight: 0.6980 chunk 236 optimal weight: 1.9990 chunk 230 optimal weight: 7.9990 chunk 174 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 157 GLN ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 GLN F 135 ASN Q 131 GLN Q 135 ASN ** M 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 377 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9160 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 33367 Z= 0.151 Angle : 0.494 13.576 45352 Z= 0.236 Chirality : 0.039 0.141 4962 Planarity : 0.004 0.052 5700 Dihedral : 11.230 149.154 5270 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.14 % Allowed : 12.45 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.14), residues: 3955 helix: 1.86 (0.11), residues: 2114 sheet: 0.49 (0.27), residues: 369 loop : 0.55 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 142 HIS 0.007 0.001 HIS F 96 PHE 0.014 0.001 PHE L 334 TYR 0.021 0.001 TYR F 114 ARG 0.006 0.000 ARG I 54 *********************** 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 347 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 309 time to evaluate : 4.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 309 ASP cc_start: 0.9326 (t0) cc_final: 0.9003 (t0) REVERT: G 9 LYS cc_start: 0.9019 (mttp) cc_final: 0.8629 (tttm) REVERT: G 12 GLU cc_start: 0.9446 (OUTLIER) cc_final: 0.9162 (mp0) REVERT: G 96 GLU cc_start: 0.9395 (mp0) cc_final: 0.9023 (mp0) REVERT: F 103 GLU cc_start: 0.9378 (mm-30) cc_final: 0.9016 (tp30) REVERT: F 107 LYS cc_start: 0.9255 (ttpp) cc_final: 0.9044 (ttpp) REVERT: F 110 GLU cc_start: 0.9369 (pt0) cc_final: 0.9023 (pp20) REVERT: F 133 CYS cc_start: 0.8449 (t) cc_final: 0.8195 (t) REVERT: A 433 HIS cc_start: 0.8848 (t70) cc_final: 0.8587 (m-70) REVERT: D 235 MET cc_start: 0.8309 (mmt) cc_final: 0.8107 (mmm) REVERT: I 7 PHE cc_start: 0.8880 (t80) cc_final: 0.8558 (m-80) REVERT: I 54 ARG cc_start: 0.9234 (ttp80) cc_final: 0.8922 (ttp-110) REVERT: J 13 SER cc_start: 0.9478 (t) cc_final: 0.9233 (p) REVERT: J 55 ARG cc_start: 0.8859 (ttm-80) cc_final: 0.8618 (tpp80) REVERT: J 73 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8746 (mtm-85) REVERT: J 80 ASN cc_start: 0.9267 (t0) cc_final: 0.9039 (t0) REVERT: E 55 ASP cc_start: 0.8930 (OUTLIER) cc_final: 0.8311 (p0) REVERT: R 50 GLU cc_start: 0.8926 (pt0) cc_final: 0.8672 (pm20) REVERT: Q 100 GLU cc_start: 0.9457 (mm-30) cc_final: 0.9205 (mt-10) REVERT: Q 114 TYR cc_start: 0.8370 (t80) cc_final: 0.7949 (t80) REVERT: Q 115 ASP cc_start: 0.9037 (p0) cc_final: 0.8721 (p0) REVERT: Q 116 HIS cc_start: 0.8861 (m-70) cc_final: 0.8521 (m-70) REVERT: Q 140 ASP cc_start: 0.9264 (m-30) cc_final: 0.8702 (t0) REVERT: M 60 PHE cc_start: 0.9513 (OUTLIER) cc_final: 0.9152 (t80) REVERT: M 309 ASP cc_start: 0.9301 (m-30) cc_final: 0.8868 (t0) REVERT: S 78 GLU cc_start: 0.9313 (tt0) cc_final: 0.9050 (pp20) REVERT: T 30 ASP cc_start: 0.9246 (t70) cc_final: 0.9008 (t0) REVERT: T 43 ARG cc_start: 0.8992 (mtm110) cc_final: 0.8602 (ttt180) REVERT: U 11 LYS cc_start: 0.8976 (tmtt) cc_final: 0.8591 (ptmm) REVERT: U 51 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8738 (tm-30) REVERT: U 58 GLN cc_start: 0.9286 (tp40) cc_final: 0.9032 (mt0) outliers start: 38 outliers final: 27 residues processed: 338 average time/residue: 0.4495 time to fit residues: 245.3759 Evaluate side-chains 331 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 300 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 396 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 chunk 225 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 240 optimal weight: 0.4980 chunk 257 optimal weight: 6.9990 chunk 186 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 296 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 GLN A 364 HIS Q 131 GLN ** M 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 377 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9141 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 33367 Z= 0.146 Angle : 0.470 11.983 45352 Z= 0.227 Chirality : 0.039 0.141 4962 Planarity : 0.004 0.053 5700 Dihedral : 10.782 148.756 5270 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.84 % Allowed : 12.81 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.14), residues: 3955 helix: 1.96 (0.11), residues: 2114 sheet: 0.63 (0.27), residues: 369 loop : 0.64 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 142 HIS 0.009 0.001 HIS F 96 PHE 0.014 0.001 PHE A 334 TYR 0.021 0.001 TYR F 114 ARG 0.005 0.000 ARG I 54 *********************** 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 341 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 313 time to evaluate : 4.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 9 LYS cc_start: 0.9017 (mttp) cc_final: 0.8621 (tttm) REVERT: G 12 GLU cc_start: 0.9450 (OUTLIER) cc_final: 0.9173 (mp0) REVERT: F 103 GLU cc_start: 0.9360 (mm-30) cc_final: 0.8912 (tp30) REVERT: F 107 LYS cc_start: 0.9249 (ttpp) cc_final: 0.8947 (tppt) REVERT: I 7 PHE cc_start: 0.8829 (t80) cc_final: 0.8533 (m-80) REVERT: I 54 ARG cc_start: 0.9237 (ttp80) cc_final: 0.9030 (ttp-110) REVERT: J 13 SER cc_start: 0.9447 (t) cc_final: 0.9230 (p) REVERT: J 55 ARG cc_start: 0.8871 (ttm-80) cc_final: 0.8634 (tpp80) REVERT: J 69 GLU cc_start: 0.8587 (pp20) cc_final: 0.8328 (tt0) REVERT: J 73 ARG cc_start: 0.9029 (ptt-90) cc_final: 0.8700 (mtm-85) REVERT: J 80 ASN cc_start: 0.9270 (t0) cc_final: 0.9050 (t0) REVERT: E 55 ASP cc_start: 0.8927 (m-30) cc_final: 0.8261 (p0) REVERT: R 50 GLU cc_start: 0.8905 (pt0) cc_final: 0.8617 (pm20) REVERT: R 123 GLU cc_start: 0.9539 (tt0) cc_final: 0.9219 (pt0) REVERT: Q 100 GLU cc_start: 0.9456 (mm-30) cc_final: 0.9146 (mt-10) REVERT: Q 114 TYR cc_start: 0.8325 (t80) cc_final: 0.8069 (t80) REVERT: Q 115 ASP cc_start: 0.9048 (p0) cc_final: 0.8700 (p0) REVERT: Q 116 HIS cc_start: 0.8877 (m-70) cc_final: 0.8550 (m-70) REVERT: Q 140 ASP cc_start: 0.9253 (m-30) cc_final: 0.8718 (t0) REVERT: M 60 PHE cc_start: 0.9498 (OUTLIER) cc_final: 0.9123 (t80) REVERT: M 309 ASP cc_start: 0.9320 (m-30) cc_final: 0.8860 (t0) REVERT: S 78 GLU cc_start: 0.9287 (tt0) cc_final: 0.9012 (pp20) REVERT: T 30 ASP cc_start: 0.9218 (t70) cc_final: 0.8980 (t0) REVERT: T 43 ARG cc_start: 0.8981 (mtm110) cc_final: 0.8589 (ttt180) REVERT: U 11 LYS cc_start: 0.8947 (tmtt) cc_final: 0.8568 (ptmm) REVERT: U 51 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8715 (tm-30) REVERT: U 58 GLN cc_start: 0.9277 (tp40) cc_final: 0.9029 (mt0) outliers start: 28 outliers final: 20 residues processed: 334 average time/residue: 0.4586 time to fit residues: 247.1706 Evaluate side-chains 323 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 301 time to evaluate : 3.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain U residue 13 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 10.0000 chunk 361 optimal weight: 0.7980 chunk 330 optimal weight: 9.9990 chunk 352 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 276 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 318 optimal weight: 6.9990 chunk 332 optimal weight: 0.9980 chunk 350 optimal weight: 8.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 HIS R 45 ASN ** M 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9163 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33367 Z= 0.222 Angle : 0.503 13.888 45352 Z= 0.240 Chirality : 0.040 0.143 4962 Planarity : 0.004 0.052 5700 Dihedral : 10.751 148.729 5268 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.93 % Allowed : 13.05 % Favored : 86.02 % 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: 1.96 (0.11), residues: 2115 sheet: 0.62 (0.27), residues: 369 loop : 0.66 (0.17), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 142 HIS 0.009 0.001 HIS F 96 PHE 0.015 0.001 PHE A 334 TYR 0.021 0.001 TYR F 114 ARG 0.004 0.000 ARG I 54 *********************** 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 327 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 296 time to evaluate : 4.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 309 ASP cc_start: 0.9287 (t0) cc_final: 0.8998 (t0) REVERT: P 68 MET cc_start: 0.8809 (ttm) cc_final: 0.8315 (ttp) REVERT: G 9 LYS cc_start: 0.9029 (mttp) cc_final: 0.8642 (tttm) REVERT: G 12 GLU cc_start: 0.9455 (OUTLIER) cc_final: 0.9183 (mp0) REVERT: F 103 GLU cc_start: 0.9356 (mm-30) cc_final: 0.8922 (tp30) REVERT: D 248 MET cc_start: 0.8746 (ttp) cc_final: 0.8490 (ttp) REVERT: I 7 PHE cc_start: 0.8850 (t80) cc_final: 0.8552 (m-80) REVERT: I 54 ARG cc_start: 0.9250 (ttp80) cc_final: 0.9043 (ttp-110) REVERT: J 55 ARG cc_start: 0.8878 (ttm-80) cc_final: 0.8666 (ttm-80) REVERT: J 69 GLU cc_start: 0.8568 (pp20) cc_final: 0.8305 (tt0) REVERT: J 73 ARG cc_start: 0.9025 (ptt-90) cc_final: 0.8696 (mtm-85) REVERT: J 80 ASN cc_start: 0.9285 (t0) cc_final: 0.9056 (t0) REVERT: E 55 ASP cc_start: 0.8988 (m-30) cc_final: 0.8350 (p0) REVERT: R 50 GLU cc_start: 0.8924 (pt0) cc_final: 0.8637 (pm20) REVERT: Q 100 GLU cc_start: 0.9446 (mm-30) cc_final: 0.9163 (mt-10) REVERT: Q 114 TYR cc_start: 0.8341 (t80) cc_final: 0.7978 (t80) REVERT: Q 115 ASP cc_start: 0.9001 (p0) cc_final: 0.8708 (p0) REVERT: Q 116 HIS cc_start: 0.8878 (m-70) cc_final: 0.8546 (m-70) REVERT: Q 140 ASP cc_start: 0.9275 (m-30) cc_final: 0.8745 (t0) REVERT: L 390 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8894 (mttp) REVERT: M 60 PHE cc_start: 0.9514 (OUTLIER) cc_final: 0.9136 (t80) REVERT: M 309 ASP cc_start: 0.9341 (m-30) cc_final: 0.8869 (t0) REVERT: S 78 GLU cc_start: 0.9301 (tt0) cc_final: 0.9019 (pp20) REVERT: T 30 ASP cc_start: 0.9240 (t70) cc_final: 0.9006 (t0) REVERT: T 43 ARG cc_start: 0.8974 (mtm110) cc_final: 0.8574 (ttt180) REVERT: U 51 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8760 (tm-30) REVERT: U 58 GLN cc_start: 0.9276 (tp40) cc_final: 0.9030 (mt0) outliers start: 31 outliers final: 23 residues processed: 319 average time/residue: 0.4662 time to fit residues: 241.6309 Evaluate side-chains 319 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 293 time to evaluate : 3.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 261 SER Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain U residue 13 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 4.9990 chunk 372 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 176 optimal weight: 0.7980 chunk 258 optimal weight: 2.9990 chunk 390 optimal weight: 0.7980 chunk 359 optimal weight: 0.9980 chunk 310 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 240 optimal weight: 0.5980 chunk 190 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 139 ASN ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 131 GLN ** M 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9140 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 33367 Z= 0.147 Angle : 0.475 11.981 45352 Z= 0.229 Chirality : 0.039 0.142 4962 Planarity : 0.004 0.052 5700 Dihedral : 10.552 148.496 5268 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.78 % Allowed : 13.17 % Favored : 86.05 % 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: 2.03 (0.14), residues: 3955 helix: 2.02 (0.11), residues: 2113 sheet: 0.66 (0.27), residues: 369 loop : 0.67 (0.17), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 142 HIS 0.009 0.001 HIS F 96 PHE 0.013 0.001 PHE A 334 TYR 0.022 0.001 TYR F 114 ARG 0.005 0.000 ARG I 54 ********************** 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 326 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 300 time to evaluate : 4.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 309 ASP cc_start: 0.9282 (t0) cc_final: 0.9001 (t0) REVERT: P 68 MET cc_start: 0.8769 (ttm) cc_final: 0.8355 (ttp) REVERT: G 9 LYS cc_start: 0.9025 (mttp) cc_final: 0.8634 (tttm) REVERT: G 12 GLU cc_start: 0.9455 (OUTLIER) cc_final: 0.9186 (mp0) REVERT: I 7 PHE cc_start: 0.8830 (t80) cc_final: 0.8550 (m-80) REVERT: I 54 ARG cc_start: 0.9246 (ttp80) cc_final: 0.9044 (ttp-110) REVERT: J 69 GLU cc_start: 0.8566 (pp20) cc_final: 0.8314 (tt0) REVERT: J 73 ARG cc_start: 0.9023 (ptt-90) cc_final: 0.8697 (mtm-85) REVERT: J 80 ASN cc_start: 0.9282 (t0) cc_final: 0.9048 (t0) REVERT: E 54 LYS cc_start: 0.9164 (tppt) cc_final: 0.8860 (tmtm) REVERT: E 55 ASP cc_start: 0.8989 (m-30) cc_final: 0.8415 (p0) REVERT: R 50 GLU cc_start: 0.8917 (pt0) cc_final: 0.8611 (pm20) REVERT: Q 100 GLU cc_start: 0.9442 (mm-30) cc_final: 0.9159 (mt-10) REVERT: Q 114 TYR cc_start: 0.8361 (t80) cc_final: 0.7995 (t80) REVERT: Q 115 ASP cc_start: 0.9063 (p0) cc_final: 0.8755 (p0) REVERT: Q 116 HIS cc_start: 0.8879 (m-70) cc_final: 0.8545 (m-70) REVERT: Q 131 GLN cc_start: 0.9069 (mm-40) cc_final: 0.8604 (mp10) REVERT: Q 140 ASP cc_start: 0.9272 (m-30) cc_final: 0.8748 (t0) REVERT: M 60 PHE cc_start: 0.9499 (OUTLIER) cc_final: 0.9116 (t80) REVERT: M 309 ASP cc_start: 0.9334 (m-30) cc_final: 0.8854 (t0) REVERT: S 78 GLU cc_start: 0.9291 (tt0) cc_final: 0.9023 (pp20) REVERT: T 30 ASP cc_start: 0.9218 (t70) cc_final: 0.8983 (t0) REVERT: T 43 ARG cc_start: 0.8957 (mtm110) cc_final: 0.8570 (ttt180) REVERT: U 11 LYS cc_start: 0.8893 (tmtt) cc_final: 0.8463 (ptmm) REVERT: U 51 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8697 (tm-30) REVERT: U 58 GLN cc_start: 0.9276 (tp40) cc_final: 0.9028 (mt0) outliers start: 26 outliers final: 21 residues processed: 322 average time/residue: 0.4569 time to fit residues: 240.7809 Evaluate side-chains 317 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 294 time to evaluate : 4.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 12 GLU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 108 ASP Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain D residue 236 ASN Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 60 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 2.9990 chunk 331 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 286 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 311 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 319 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 ASN ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.066580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.051363 restraints weight = 75052.864| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 2.40 r_work: 0.2509 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2366 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33367 Z= 0.219 Angle : 0.506 13.639 45352 Z= 0.240 Chirality : 0.040 0.151 4962 Planarity : 0.004 0.052 5700 Dihedral : 10.545 148.814 5267 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.87 % Allowed : 13.29 % Favored : 85.83 % 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: 2.01 (0.14), residues: 3955 helix: 1.99 (0.11), residues: 2119 sheet: 0.64 (0.27), residues: 369 loop : 0.68 (0.18), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 142 HIS 0.009 0.001 HIS F 96 PHE 0.014 0.001 PHE A 334 TYR 0.021 0.001 TYR F 114 ARG 0.007 0.000 ARG J 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6982.41 seconds wall clock time: 129 minutes 11.41 seconds (7751.41 seconds total)