Starting phenix.real_space_refine on Fri Mar 22 06:24:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abe_15318/03_2024/8abe_15318_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abe_15318/03_2024/8abe_15318.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abe_15318/03_2024/8abe_15318_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abe_15318/03_2024/8abe_15318_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abe_15318/03_2024/8abe_15318_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abe_15318/03_2024/8abe_15318.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abe_15318/03_2024/8abe_15318.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abe_15318/03_2024/8abe_15318_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abe_15318/03_2024/8abe_15318_updated.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 8 7.16 5 P 30 5.49 5 S 102 5.16 5 C 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 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 272": "OE1" <-> "OE2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P GLU 137": "OE1" <-> "OE2" Residue "P GLU 178": "OE1" <-> "OE2" Residue "P GLU 213": "OE1" <-> "OE2" Residue "P 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 ARG 188": "NH1" <-> "NH2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "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 TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "N ARG 4": "NH1" <-> "NH2" Residue "N ARG 70": "NH1" <-> "NH2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 110": "NH1" <-> "NH2" Residue "N GLU 272": "OE1" <-> "OE2" Residue "N ARG 283": "NH1" <-> "NH2" Residue "N ARG 310": "NH1" <-> "NH2" Residue "N ARG 314": "NH1" <-> "NH2" Residue "N TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "R GLU 12": "OE1" <-> "OE2" Residue "R GLU 50": "OE1" <-> "OE2" Residue "R GLU 51": "OE1" <-> "OE2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R ARG 61": "NH1" <-> "NH2" Residue "R GLU 66": "OE1" <-> "OE2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R ARG 73": "NH1" <-> "NH2" Residue "R ARG 76": "NH1" <-> "NH2" Residue "R GLU 96": "OE1" <-> "OE2" Residue "R GLU 110": "OE1" <-> "OE2" Residue "R GLU 123": "OE1" <-> "OE2" Residue "Q GLU 88": "OE1" <-> "OE2" Residue "Q GLU 118": "OE1" <-> "OE2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "Q GLU 126": "OE1" <-> "OE2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "L GLU 141": "OE1" <-> "OE2" Residue "L ARG 188": "NH1" <-> "NH2" Residue "L GLU 354": "OE1" <-> "OE2" Residue "L ARG 384": "NH1" <-> "NH2" Residue "L GLU 424": "OE1" <-> "OE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M GLU 78": "OE1" <-> "OE2" Residue "M GLU 117": "OE1" <-> "OE2" Residue "M ARG 140": "NH1" <-> "NH2" Residue "M GLU 150": "OE1" <-> "OE2" Residue "M ARG 234": "NH1" <-> "NH2" Residue "M GLU 313": "OE1" <-> "OE2" Residue "M GLU 350": "OE1" <-> "OE2" Residue "M GLU 376": "OE1" <-> "OE2" Residue "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 TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 34": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32540 Number of models: 1 Model: "" Number of chains: 32 Chain: "C" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "P" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1445 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 11, 'TRANS': 174} Chain: "G" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "A" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "B" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "D" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "I" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "J" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "N" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "E" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "R" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "Q" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "L" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "M" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "O" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "S" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "T" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "U" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "C" Number of atoms: 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: "N" 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: "E" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'LMT': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 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: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 30.092 49.960 34.487 1.00 85.40 S ATOM 4207 SG CYS P 187 32.630 47.255 33.484 1.00 99.81 S Time building chain proxies: 16.28, per 1000 atoms: 0.50 Number of scatterers: 32540 At special positions: 0 Unit cell: (119.691, 129.735, 164.889, 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=2.06 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.06 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.07 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.06 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.68 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 301 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 170 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 190 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 187 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 168 " Number of angles added : 3 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7486 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 188 helices and 15 sheets defined 54.6% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.06 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: 3.933A pdb=" N PHE C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY C 33 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR C 46 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.620A 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: 3.781A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 135 removed outlier: 3.538A pdb=" N LEU C 134 " --> pdb=" O MET C 130 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 153 removed outlier: 3.555A pdb=" N LEU C 150 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL C 151 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER C 152 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 4.335A 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: 4.074A pdb=" N THR C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 246 removed outlier: 6.896A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.863A 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: 3.806A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LEU C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.979A 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: 4.122A pdb=" N PHE C 363 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 382 Processing helix chain 'P' and resid 59 through 91 removed outlier: 3.610A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN P 90 " --> pdb=" O ASP P 86 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N MET P 91 " --> pdb=" O PHE P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 98 No H-bonds generated for 'chain 'P' and resid 95 through 98' Processing helix chain 'P' and resid 132 through 138 Processing helix chain 'P' and resid 152 through 155 No H-bonds generated for 'chain 'P' and resid 152 through 155' Processing helix chain 'G' and resid 4 through 16 Processing helix chain 'G' and resid 18 through 35 Proline residue: G 26 - end of helix Processing helix chain 'G' and resid 37 through 40 Processing helix chain 'G' and resid 44 through 47 Processing helix chain 'G' and resid 53 through 60 Processing helix chain 'G' and resid 64 through 83 Processing helix chain 'G' and resid 89 through 91 No H-bonds generated for 'chain 'G' and resid 89 through 91' Processing helix chain 'G' and resid 95 through 97 No H-bonds generated for 'chain 'G' and resid 95 through 97' Processing helix chain 'G' and resid 103 through 121 removed outlier: 3.713A 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 136 Processing helix chain 'F' and resid 139 through 145 removed outlier: 3.595A pdb=" N VAL F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.527A pdb=" N HIS A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 4.178A 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: 3.843A pdb=" N VAL A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Proline residue: A 124 - end of helix removed outlier: 3.825A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 156 removed outlier: 4.032A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU A 156 " --> pdb=" O THR A 152 " (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: 3.532A 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: 4.011A 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: 3.607A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 395 removed outlier: 3.554A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.263A 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: 3.659A pdb=" N ASP A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.986A 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: 3.646A pdb=" N LYS B 116 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 4.277A 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: 3.718A pdb=" N LEU B 263 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 removed outlier: 3.906A pdb=" N THR B 282 " --> pdb=" O LEU B 278 " (cutoff:3.500A) 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: 3.679A 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 203 through 206 No H-bonds generated for 'chain 'D' and resid 203 through 206' Processing helix chain 'D' and resid 210 through 218 removed outlier: 3.587A 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 80 removed outlier: 4.390A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.759A 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: 5.159A pdb=" N HIS I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 49 removed outlier: 3.547A 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: 3.939A pdb=" N PHE N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY N 33 " --> pdb=" O TRP N 30 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR N 46 " --> pdb=" O GLN N 43 " (cutoff:3.500A) removed outlier: 3.597A 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: 3.790A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 135 removed outlier: 3.558A pdb=" N LEU N 134 " --> pdb=" O MET N 130 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 138 through 153 removed outlier: 3.569A pdb=" N LEU N 150 " --> pdb=" O VAL N 146 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL N 151 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER N 152 " --> pdb=" O CYS N 148 " (cutoff:3.500A) removed outlier: 4.330A 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: 4.087A pdb=" N THR N 203 " --> pdb=" O ILE N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 246 removed outlier: 6.902A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.858A 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: 3.802A 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: 4.589A pdb=" N LEU N 303 " --> pdb=" O ILE N 299 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE N 304 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 3.972A 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: 4.133A 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: 3.628A pdb=" N SER E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 4.901A 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: 3.708A 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 136 Processing helix chain 'Q' and resid 139 through 145 removed outlier: 3.598A pdb=" N VAL Q 145 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 72 through 79 removed outlier: 3.504A pdb=" N HIS L 78 " --> pdb=" O HIS L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 99 Processing helix chain 'L' and resid 120 through 135 removed outlier: 3.843A pdb=" N VAL L 123 " --> pdb=" O LYS L 120 " (cutoff:3.500A) Proline residue: L 124 - end of helix removed outlier: 3.827A pdb=" N VAL L 127 " --> pdb=" O PRO L 124 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU L 134 " --> pdb=" O ALA L 131 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN L 135 " --> pdb=" O ASP L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 156 removed outlier: 4.033A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) removed outlier: 4.035A 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: 3.997A 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: 3.624A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 395 removed outlier: 3.683A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.268A 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: 3.665A pdb=" N ASP L 468 " --> pdb=" O ARG L 464 " (cutoff:3.500A) removed outlier: 3.981A 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: 3.637A pdb=" N VAL M 108 " --> pdb=" O PRO M 105 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS M 116 " --> pdb=" O ASN M 113 " (cutoff:3.500A) removed outlier: 4.257A 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: 3.701A 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: 3.923A 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: 3.580A 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 80 removed outlier: 4.390A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.761A 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: 5.160A pdb=" N HIS T 55 " --> pdb=" O LYS T 51 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS T 56 " --> pdb=" O ASP T 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 49 removed outlier: 3.556A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.545A 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: 3.890A 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: 4.184A pdb=" N LYS B 24 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 231 through 235 removed outlier: 3.600A pdb=" N ASN B 241 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 156 through 158 Processing sheet with id= J, first strand: chain 'N' and resid 21 through 23 Processing sheet with id= K, first strand: chain 'L' and resid 31 through 34 Processing sheet with id= L, first strand: chain 'L' and resid 266 through 271 Processing sheet with id= M, first strand: chain 'M' and resid 16 through 20 removed outlier: 4.206A 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: 3.576A 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 1581 hydrogen bonds defined for protein. 4323 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: 10.75 Time building geometry restraints manager: 13.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.40: 13564 1.40 - 1.61: 19597 1.61 - 1.82: 167 1.82 - 2.03: 19 2.03 - 2.24: 20 Bond restraints: 33367 Sorted by residual: bond pdb=" C2C HEC O 401 " pdb=" C3C HEC O 401 " ideal model delta sigma weight residual 1.334 1.461 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C2C HEC D 401 " pdb=" C3C HEC D 401 " ideal model delta sigma weight residual 1.334 1.458 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" C2B HEC O 401 " pdb=" C3B HEC O 401 " ideal model delta sigma weight residual 1.334 1.455 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" C2A HEC D 401 " pdb=" C3A HEC D 401 " ideal model delta sigma weight residual 1.334 1.452 -0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" C3B HEC D 401 " pdb=" CAB HEC D 401 " ideal model delta sigma weight residual 1.544 1.432 0.112 2.00e-02 2.50e+03 3.15e+01 ... (remaining 33362 not shown) Histogram of bond angle deviations from ideal: 84.72 - 103.63: 613 103.63 - 122.54: 39602 122.54 - 141.44: 5125 141.44 - 160.35: 0 160.35 - 179.26: 12 Bond angle restraints: 45352 Sorted by residual: angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.27 95.28 15.99 1.47e+00 4.63e-01 1.18e+02 angle pdb=" C GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta sigma weight residual 111.27 95.77 15.50 1.47e+00 4.63e-01 1.11e+02 angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 93.19 11.14 1.14e+00 7.69e-01 9.55e+01 angle pdb=" C GLN B 215 " pdb=" CA GLN B 215 " pdb=" CB GLN B 215 " ideal model delta sigma weight residual 109.64 92.54 17.10 1.77e+00 3.19e-01 9.33e+01 angle pdb=" C GLN M 215 " pdb=" CA GLN M 215 " pdb=" CB GLN M 215 " ideal model delta sigma weight residual 109.64 92.58 17.06 1.77e+00 3.19e-01 9.29e+01 ... (remaining 45347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.66: 18852 31.66 - 63.31: 1010 63.31 - 94.97: 96 94.97 - 126.63: 2 126.63 - 158.29: 3 Dihedral angle restraints: 19963 sinusoidal: 8344 harmonic: 11619 Sorted by residual: dihedral pdb=" C GLN M 215 " pdb=" N GLN M 215 " pdb=" CA GLN M 215 " pdb=" CB GLN M 215 " ideal model delta harmonic sigma weight residual -122.60 -101.65 -20.95 0 2.50e+00 1.60e-01 7.02e+01 dihedral pdb=" C GLN B 215 " pdb=" N GLN B 215 " pdb=" CA GLN B 215 " pdb=" CB GLN B 215 " ideal model delta harmonic sigma weight residual -122.60 -101.67 -20.93 0 2.50e+00 1.60e-01 7.01e+01 dihedral pdb=" C GLU O 283 " pdb=" N GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta harmonic sigma weight residual -122.60 -103.30 -19.30 0 2.50e+00 1.60e-01 5.96e+01 ... (remaining 19960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.167: 4340 0.167 - 0.334: 577 0.334 - 0.501: 38 0.501 - 0.669: 3 0.669 - 0.836: 4 Chirality restraints: 4962 Sorted by residual: chirality pdb=" CB4 CDL N 505 " pdb=" CB3 CDL N 505 " pdb=" CB6 CDL N 505 " pdb=" OB6 CDL N 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.74 -0.84 2.00e-01 2.50e+01 1.75e+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 -1.77 -0.81 2.00e-01 2.50e+01 1.63e+01 chirality pdb=" CB4 CDL S 702 " pdb=" CB3 CDL S 702 " pdb=" CB6 CDL S 702 " pdb=" OB6 CDL S 702 " both_signs ideal model delta sigma weight residual False -2.57 -1.80 -0.77 2.00e-01 2.50e+01 1.49e+01 ... (remaining 4959 not shown) Planarity restraints: 5700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS L 78 " 0.025 2.00e-02 2.50e+03 5.22e-02 2.73e+01 pdb=" C HIS L 78 " -0.090 2.00e-02 2.50e+03 pdb=" O HIS L 78 " 0.034 2.00e-02 2.50e+03 pdb=" N LEU L 79 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS N 96 " -0.052 2.00e-02 2.50e+03 3.99e-02 2.38e+01 pdb=" CG HIS N 96 " 0.069 2.00e-02 2.50e+03 pdb=" ND1 HIS N 96 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS N 96 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 HIS N 96 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 HIS N 96 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEM N 502 " 0.009 2.00e-02 2.50e+03 2.99e-02 2.02e+01 pdb=" C2C HEM N 502 " 0.029 2.00e-02 2.50e+03 pdb=" C3C HEM N 502 " 0.006 2.00e-02 2.50e+03 pdb=" C4C HEM N 502 " 0.038 2.00e-02 2.50e+03 pdb=" CAC HEM N 502 " -0.035 2.00e-02 2.50e+03 pdb=" CHC HEM N 502 " -0.054 2.00e-02 2.50e+03 pdb=" CHD HEM N 502 " -0.029 2.00e-02 2.50e+03 pdb=" CMC HEM N 502 " 0.011 2.00e-02 2.50e+03 pdb=" NC HEM N 502 " 0.025 2.00e-02 2.50e+03 ... (remaining 5697 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 228 2.62 - 3.19: 28570 3.19 - 3.76: 53720 3.76 - 4.33: 79564 4.33 - 4.90: 122142 Nonbonded interactions: 284224 Sorted by model distance: nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.050 2.520 nonbonded pdb=" NE2 HIS C 183 " pdb="FE HEM C 501 " model vdw 2.061 3.080 nonbonded pdb=" NE2 HIS N 82 " pdb="FE HEM N 501 " model vdw 2.066 3.080 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.155 3.080 nonbonded pdb=" SD MET O 248 " pdb="FE HEC O 401 " model vdw 2.231 3.360 ... (remaining 284219 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' selection = chain 'N' } 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' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.650 Check model and map are aligned: 0.500 Set scattering table: 0.320 Process input model: 88.130 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9255 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 : 0.010 0.183 33367 Z= 0.668 Angle : 1.724 20.096 45352 Z= 1.066 Chirality : 0.113 0.836 4962 Planarity : 0.008 0.146 5700 Dihedral : 18.058 158.287 12462 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.37 % Allowed : 6.77 % Favored : 89.86 % Cbeta Deviations : 0.99 % 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: -1.16 (0.12), residues: 3955 helix: -0.82 (0.09), residues: 2142 sheet: 0.17 (0.25), residues: 351 loop : -0.65 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.009 TRP O 280 HIS 0.019 0.005 HIS L 279 PHE 0.059 0.007 PHE B 107 TYR 0.055 0.008 TYR O 259 ARG 0.046 0.003 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 573 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 461 time to evaluate : 4.151 Fit side-chains REVERT: P 102 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7424 (mppt) REVERT: P 104 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8514 (mp0) REVERT: P 112 LEU cc_start: 0.9236 (mt) cc_final: 0.8996 (tp) REVERT: P 134 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7611 (mt-10) REVERT: P 158 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7273 (tppt) REVERT: P 182 PHE cc_start: 0.8571 (m-80) cc_final: 0.8193 (m-80) REVERT: P 197 SER cc_start: 0.8274 (OUTLIER) cc_final: 0.7815 (t) REVERT: G 9 LYS cc_start: 0.9048 (mttp) cc_final: 0.8731 (tttt) REVERT: F 84 GLU cc_start: 0.8691 (tt0) cc_final: 0.8259 (mt-10) REVERT: F 88 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8225 (mm-30) REVERT: A 97 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8203 (mp0) REVERT: B 170 TYR cc_start: 0.8294 (p90) cc_final: 0.7668 (p90) REVERT: B 205 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8560 (tm-30) REVERT: B 364 MET cc_start: 0.8899 (tpp) cc_final: 0.8692 (tpp) REVERT: D 90 HIS cc_start: 0.9138 (m-70) cc_final: 0.8875 (m-70) REVERT: I 30 ASP cc_start: 0.9152 (t70) cc_final: 0.8880 (t70) REVERT: I 43 ARG cc_start: 0.8721 (mtm110) cc_final: 0.8409 (ttp-110) REVERT: J 73 ARG cc_start: 0.9020 (ptt-90) cc_final: 0.8743 (ptt180) REVERT: N 69 MET cc_start: 0.9450 (mmm) cc_final: 0.9142 (mmm) REVERT: R 33 LYS cc_start: 0.9335 (tttt) cc_final: 0.9120 (ttpp) REVERT: Q 103 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7869 (mt-10) REVERT: L 87 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8538 (mtt90) REVERT: L 390 LYS cc_start: 0.9044 (tptt) cc_final: 0.8828 (mtmt) REVERT: M 16 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8728 (p) REVERT: M 205 GLN cc_start: 0.9048 (tm-30) cc_final: 0.8666 (tm130) REVERT: M 331 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8183 (pm20) REVERT: U 73 ARG cc_start: 0.8774 (ptt-90) cc_final: 0.8416 (ptt180) outliers start: 112 outliers final: 12 residues processed: 526 average time/residue: 1.7411 time to fit residues: 1055.1542 Evaluate side-chains 334 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 315 time to evaluate : 3.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 136 PHE Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 102 LYS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 117 ILE Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain P residue 197 SER Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain N residue 178 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 331 GLU 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: 10.0000 chunk 297 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 200 optimal weight: 0.5980 chunk 158 optimal weight: 0.8980 chunk 307 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 chunk 228 optimal weight: 6.9990 chunk 355 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN C 22 GLN C 173 ASN C 202 HIS C 332 ASN P 85 GLN P 90 ASN P 115 ASN G 84 HIS F 97 HIS F 109 GLN A 74 HIS A 222 HIS A 332 ASN A 371 ASN A 379 ASN B 87 HIS B 197 ASN B 295 ASN B 354 ASN B 377 ASN J 80 ASN N 14 ASN N 202 HIS N 332 ASN E 90 ASN R 84 HIS L 332 ASN L 371 ASN M 87 HIS M 377 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9181 moved from start: 0.1889 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= 0.195 Angle : 0.602 15.406 45352 Z= 0.297 Chirality : 0.041 0.160 4962 Planarity : 0.004 0.033 5700 Dihedral : 13.979 153.541 5312 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 1.53 % Allowed : 10.53 % 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: 0.86 (0.13), residues: 3955 helix: 0.97 (0.11), residues: 2144 sheet: 0.66 (0.26), residues: 366 loop : 0.13 (0.17), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 156 HIS 0.008 0.001 HIS F 97 PHE 0.020 0.002 PHE L 334 TYR 0.020 0.002 TYR D 237 ARG 0.006 0.001 ARG E 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 345 time to evaluate : 3.479 Fit side-chains REVERT: G 9 LYS cc_start: 0.9007 (mttp) cc_final: 0.8688 (tttt) REVERT: F 84 GLU cc_start: 0.8648 (tt0) cc_final: 0.8232 (mt-10) REVERT: F 88 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8218 (mm-30) REVERT: F 120 LYS cc_start: 0.9343 (mttp) cc_final: 0.9138 (mmtm) REVERT: A 397 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8153 (mt) REVERT: B 139 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.9073 (ttmm) REVERT: B 170 TYR cc_start: 0.8191 (p90) cc_final: 0.7892 (p90) REVERT: B 251 GLU cc_start: 0.8381 (pm20) cc_final: 0.8128 (pm20) REVERT: B 364 MET cc_start: 0.8935 (tpp) cc_final: 0.8696 (tpp) REVERT: I 30 ASP cc_start: 0.9042 (t70) cc_final: 0.8829 (t70) REVERT: J 15 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8481 (ptmm) REVERT: Q 96 HIS cc_start: 0.8634 (t-170) cc_final: 0.8376 (t70) REVERT: M 364 MET cc_start: 0.8730 (tpp) cc_final: 0.8352 (tpt) REVERT: U 73 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8398 (ptt180) outliers start: 51 outliers final: 11 residues processed: 381 average time/residue: 1.6747 time to fit residues: 738.2639 Evaluate side-chains 305 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 291 time to evaluate : 3.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 139 ASN Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 296 optimal weight: 8.9990 chunk 242 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 356 optimal weight: 0.9990 chunk 385 optimal weight: 8.9990 chunk 317 optimal weight: 3.9990 chunk 353 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 286 optimal weight: 0.0470 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN P 150 GLN F 109 GLN B 377 ASN D 90 HIS I 39 ASN J 58 GLN J 80 ASN M 197 ASN M 316 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9229 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 33367 Z= 0.338 Angle : 0.611 14.759 45352 Z= 0.297 Chirality : 0.044 0.160 4962 Planarity : 0.004 0.045 5700 Dihedral : 13.202 150.149 5268 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.44 % Allowed : 11.13 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.13), residues: 3955 helix: 1.39 (0.11), residues: 2136 sheet: 0.87 (0.26), residues: 360 loop : 0.42 (0.17), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 142 HIS 0.016 0.001 HIS C 197 PHE 0.021 0.002 PHE L 334 TYR 0.019 0.002 TYR D 117 ARG 0.004 0.000 ARG D 289 *********************** 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 345 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 297 time to evaluate : 3.831 Fit side-chains REVERT: P 201 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.8238 (mmm160) REVERT: G 9 LYS cc_start: 0.9039 (mttp) cc_final: 0.8720 (tttt) REVERT: G 112 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8380 (tt0) REVERT: F 84 GLU cc_start: 0.8625 (tt0) cc_final: 0.8226 (mt-10) REVERT: F 120 LYS cc_start: 0.9336 (mttp) cc_final: 0.9118 (mmtm) REVERT: A 99 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8771 (ttm) REVERT: A 397 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8223 (mt) REVERT: B 139 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.9070 (ttmm) REVERT: B 168 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8534 (mt0) REVERT: B 170 TYR cc_start: 0.8150 (p90) cc_final: 0.7841 (p90) REVERT: B 251 GLU cc_start: 0.8521 (pm20) cc_final: 0.8315 (pm20) REVERT: B 353 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: B 364 MET cc_start: 0.8982 (tpp) cc_final: 0.8703 (tpp) REVERT: I 30 ASP cc_start: 0.9057 (t70) cc_final: 0.8856 (t70) REVERT: J 15 LYS cc_start: 0.8786 (mtmm) cc_final: 0.8535 (ptpt) REVERT: M 364 MET cc_start: 0.8699 (tpp) cc_final: 0.8350 (tpt) REVERT: U 73 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8309 (ptt180) outliers start: 48 outliers final: 17 residues processed: 321 average time/residue: 1.7552 time to fit residues: 653.8023 Evaluate side-chains 309 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 285 time to evaluate : 4.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 168 GLN Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 170 optimal weight: 0.8980 chunk 239 optimal weight: 1.9990 chunk 357 optimal weight: 1.9990 chunk 378 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 339 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN B 316 GLN B 377 ASN D 90 HIS J 58 GLN J 80 ASN N 22 GLN Q 92 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9205 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 33367 Z= 0.227 Angle : 0.536 13.741 45352 Z= 0.259 Chirality : 0.041 0.150 4962 Planarity : 0.004 0.048 5700 Dihedral : 12.605 149.399 5266 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.14 % Allowed : 11.67 % 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: 1.69 (0.13), residues: 3955 helix: 1.63 (0.11), residues: 2133 sheet: 0.95 (0.26), residues: 360 loop : 0.56 (0.17), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 142 HIS 0.009 0.001 HIS C 197 PHE 0.020 0.001 PHE L 334 TYR 0.016 0.001 TYR D 117 ARG 0.003 0.000 ARG B 372 *********************** 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 328 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 290 time to evaluate : 3.959 Fit side-chains revert: symmetry clash REVERT: G 9 LYS cc_start: 0.9033 (mttp) cc_final: 0.8726 (tttt) REVERT: F 84 GLU cc_start: 0.8562 (tt0) cc_final: 0.8237 (mt-10) REVERT: F 120 LYS cc_start: 0.9336 (mttp) cc_final: 0.9101 (mmtp) REVERT: A 397 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8295 (mt) REVERT: B 170 TYR cc_start: 0.8201 (p90) cc_final: 0.7744 (p90) REVERT: B 353 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7387 (mt-10) REVERT: B 364 MET cc_start: 0.8995 (tpp) cc_final: 0.8723 (tpp) REVERT: J 74 GLU cc_start: 0.8342 (pm20) cc_final: 0.8089 (pp20) REVERT: M 101 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8848 (tttp) REVERT: M 364 MET cc_start: 0.8638 (tpp) cc_final: 0.8235 (tpt) REVERT: U 73 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8406 (ptt180) outliers start: 38 outliers final: 13 residues processed: 316 average time/residue: 1.7049 time to fit residues: 623.8503 Evaluate side-chains 294 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 277 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 139 ASN Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 282 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 323 optimal weight: 0.3980 chunk 261 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 340 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN F 116 HIS B 316 GLN B 377 ASN J 58 GLN J 80 ASN L 332 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9222 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33367 Z= 0.286 Angle : 0.561 14.155 45352 Z= 0.271 Chirality : 0.042 0.150 4962 Planarity : 0.004 0.049 5700 Dihedral : 12.426 149.397 5265 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.38 % Allowed : 11.76 % Favored : 86.86 % 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: 1.76 (0.13), residues: 3955 helix: 1.69 (0.11), residues: 2127 sheet: 0.97 (0.27), residues: 360 loop : 0.60 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 142 HIS 0.014 0.001 HIS C 197 PHE 0.021 0.002 PHE L 334 TYR 0.018 0.002 TYR D 117 ARG 0.003 0.000 ARG S 51 *********************** 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 330 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 284 time to evaluate : 3.707 Fit side-chains revert: symmetry clash REVERT: G 9 LYS cc_start: 0.9043 (mttp) cc_final: 0.8741 (tttt) REVERT: G 112 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8340 (tt0) REVERT: F 84 GLU cc_start: 0.8577 (tt0) cc_final: 0.8240 (mt-10) REVERT: F 120 LYS cc_start: 0.9332 (mttp) cc_final: 0.9113 (mmtm) REVERT: A 99 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8741 (ttm) REVERT: B 170 TYR cc_start: 0.8229 (p90) cc_final: 0.7721 (p90) REVERT: B 353 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7358 (mt-10) REVERT: B 364 MET cc_start: 0.9001 (tpp) cc_final: 0.8769 (tpp) REVERT: M 364 MET cc_start: 0.8608 (tpp) cc_final: 0.8219 (tpt) REVERT: U 73 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8382 (ptt180) outliers start: 46 outliers final: 24 residues processed: 312 average time/residue: 1.7136 time to fit residues: 620.6406 Evaluate side-chains 304 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 276 time to evaluate : 3.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 139 ASN Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 115 ASP Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 103 GLU Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 0.9990 chunk 341 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 222 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 379 optimal weight: 7.9990 chunk 314 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 199 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN B 377 ASN D 90 HIS J 58 GLN J 80 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9221 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33367 Z= 0.277 Angle : 0.552 13.985 45352 Z= 0.268 Chirality : 0.042 0.148 4962 Planarity : 0.004 0.049 5700 Dihedral : 12.276 149.282 5265 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.35 % Allowed : 12.09 % Favored : 86.56 % 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: 1.81 (0.13), residues: 3955 helix: 1.72 (0.11), residues: 2127 sheet: 0.99 (0.27), residues: 360 loop : 0.65 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 142 HIS 0.013 0.001 HIS C 197 PHE 0.021 0.002 PHE A 334 TYR 0.017 0.002 TYR D 117 ARG 0.003 0.000 ARG S 51 *********************** 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 331 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 286 time to evaluate : 3.559 Fit side-chains revert: symmetry clash REVERT: P 119 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8861 (ttpt) REVERT: G 9 LYS cc_start: 0.9041 (mttp) cc_final: 0.8746 (tttt) REVERT: G 112 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: F 84 GLU cc_start: 0.8582 (tt0) cc_final: 0.8218 (mt-10) REVERT: F 120 LYS cc_start: 0.9284 (mttp) cc_final: 0.9018 (mmtm) REVERT: A 87 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.8420 (ptp90) REVERT: A 99 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8750 (ttm) REVERT: B 170 TYR cc_start: 0.8236 (p90) cc_final: 0.7712 (p90) REVERT: B 353 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7362 (mt-10) REVERT: B 364 MET cc_start: 0.9000 (tpp) cc_final: 0.8766 (tpp) REVERT: J 74 GLU cc_start: 0.8381 (pm20) cc_final: 0.8095 (pp20) REVERT: N 202 HIS cc_start: 0.9406 (OUTLIER) cc_final: 0.8915 (t-90) REVERT: M 364 MET cc_start: 0.8593 (tpp) cc_final: 0.8197 (tpt) REVERT: U 73 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8355 (ptt180) outliers start: 45 outliers final: 24 residues processed: 313 average time/residue: 1.7959 time to fit residues: 659.6941 Evaluate side-chains 309 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 278 time to evaluate : 3.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 139 ASN Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 95 LYS Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain N residue 202 HIS Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 103 GLU Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 0.0070 chunk 42 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 276 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 319 optimal weight: 0.9980 chunk 211 optimal weight: 0.9990 chunk 377 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 chunk 230 optimal weight: 0.3980 chunk 174 optimal weight: 4.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN B 377 ASN J 58 GLN J 80 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9188 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 33367 Z= 0.166 Angle : 0.497 13.183 45352 Z= 0.240 Chirality : 0.039 0.147 4962 Planarity : 0.004 0.049 5700 Dihedral : 11.787 148.959 5265 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.11 % Allowed : 12.57 % Favored : 86.32 % 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: 1.98 (0.14), residues: 3955 helix: 1.87 (0.11), residues: 2128 sheet: 1.04 (0.27), residues: 360 loop : 0.70 (0.17), residues: 1467 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 0.019 0.001 PHE A 334 TYR 0.013 0.001 TYR D 117 ARG 0.002 0.000 ARG R 61 *********************** 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 329 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 292 time to evaluate : 3.662 Fit side-chains REVERT: P 112 LEU cc_start: 0.9241 (tp) cc_final: 0.8985 (tp) REVERT: G 9 LYS cc_start: 0.9035 (mttp) cc_final: 0.8730 (tttt) REVERT: G 112 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8329 (tt0) REVERT: F 84 GLU cc_start: 0.8586 (tt0) cc_final: 0.8240 (mt-10) REVERT: F 100 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8366 (mm-30) REVERT: F 120 LYS cc_start: 0.9305 (mttp) cc_final: 0.9024 (mmtp) REVERT: A 87 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8213 (ptp90) REVERT: B 170 TYR cc_start: 0.8231 (p90) cc_final: 0.7723 (p90) REVERT: B 353 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7273 (mt-10) REVERT: B 364 MET cc_start: 0.9016 (tpp) cc_final: 0.8763 (tpp) REVERT: J 74 GLU cc_start: 0.8349 (pm20) cc_final: 0.8129 (pp20) REVERT: M 101 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8840 (tttp) REVERT: M 364 MET cc_start: 0.8550 (tpp) cc_final: 0.8143 (tpt) outliers start: 37 outliers final: 16 residues processed: 313 average time/residue: 1.7287 time to fit residues: 626.4170 Evaluate side-chains 308 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 288 time to evaluate : 3.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain P residue 139 ASN Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 101 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 225 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 240 optimal weight: 3.9990 chunk 257 optimal weight: 7.9990 chunk 186 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 296 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN B 377 ASN J 58 GLN J 80 ASN L 91 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9203 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33367 Z= 0.224 Angle : 0.523 13.668 45352 Z= 0.251 Chirality : 0.041 0.146 4962 Planarity : 0.004 0.049 5700 Dihedral : 11.760 148.864 5265 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.90 % Allowed : 12.90 % Favored : 86.20 % 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: 1.99 (0.14), residues: 3955 helix: 1.85 (0.11), residues: 2134 sheet: 1.08 (0.27), residues: 360 loop : 0.75 (0.17), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 142 HIS 0.012 0.001 HIS C 197 PHE 0.020 0.001 PHE A 334 TYR 0.016 0.001 TYR D 117 ARG 0.002 0.000 ARG G 61 *********************** 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 323 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 293 time to evaluate : 3.459 Fit side-chains revert: symmetry clash REVERT: P 112 LEU cc_start: 0.9244 (tp) cc_final: 0.8993 (tp) REVERT: G 9 LYS cc_start: 0.9041 (mttp) cc_final: 0.8736 (tttt) REVERT: G 112 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8359 (tt0) REVERT: F 84 GLU cc_start: 0.8585 (tt0) cc_final: 0.8215 (mt-10) REVERT: F 120 LYS cc_start: 0.9305 (mttp) cc_final: 0.9034 (mmtp) REVERT: A 87 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8357 (ptp90) REVERT: A 99 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8750 (ttm) REVERT: B 170 TYR cc_start: 0.8233 (p90) cc_final: 0.7711 (p90) REVERT: B 353 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7282 (mt-10) REVERT: B 364 MET cc_start: 0.8999 (tpp) cc_final: 0.8771 (tpp) REVERT: M 101 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8844 (tttp) REVERT: M 364 MET cc_start: 0.8549 (tpp) cc_final: 0.8135 (tpt) outliers start: 30 outliers final: 21 residues processed: 309 average time/residue: 1.7133 time to fit residues: 613.0081 Evaluate side-chains 311 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 285 time to evaluate : 3.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain P residue 139 ASN Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 103 GLU Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain S residue 71 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 2.9990 chunk 361 optimal weight: 3.9990 chunk 330 optimal weight: 3.9990 chunk 352 optimal weight: 6.9990 chunk 211 optimal weight: 0.9990 chunk 153 optimal weight: 7.9990 chunk 276 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 318 optimal weight: 0.9990 chunk 332 optimal weight: 0.9980 chunk 350 optimal weight: 7.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 115 ASN P 193 HIS F 109 GLN B 377 ASN J 58 GLN J 80 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9193 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33367 Z= 0.187 Angle : 0.514 13.577 45352 Z= 0.246 Chirality : 0.040 0.145 4962 Planarity : 0.004 0.049 5700 Dihedral : 11.595 148.802 5265 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.05 % Allowed : 12.87 % Favored : 86.08 % 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: 1.88 (0.11), residues: 2134 sheet: 1.11 (0.27), residues: 360 loop : 0.76 (0.17), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 142 HIS 0.009 0.001 HIS C 197 PHE 0.019 0.001 PHE A 334 TYR 0.015 0.001 TYR D 117 ARG 0.002 0.000 ARG G 61 *********************** 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 324 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 289 time to evaluate : 3.526 Fit side-chains revert: symmetry clash REVERT: P 112 LEU cc_start: 0.9240 (tp) cc_final: 0.9018 (tp) REVERT: G 9 LYS cc_start: 0.9038 (mttp) cc_final: 0.8733 (tttt) REVERT: G 112 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8344 (tt0) REVERT: F 84 GLU cc_start: 0.8591 (tt0) cc_final: 0.8230 (mt-10) REVERT: A 87 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8306 (ptp90) REVERT: A 99 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8748 (ttm) REVERT: B 170 TYR cc_start: 0.8229 (p90) cc_final: 0.7733 (p90) REVERT: B 353 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7266 (mt-10) REVERT: B 364 MET cc_start: 0.8994 (tpp) cc_final: 0.8765 (tpp) REVERT: Q 110 GLU cc_start: 0.8528 (pt0) cc_final: 0.8224 (pp20) REVERT: M 101 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8851 (tttp) REVERT: M 364 MET cc_start: 0.8518 (tpp) cc_final: 0.8093 (tpt) outliers start: 35 outliers final: 21 residues processed: 308 average time/residue: 1.6985 time to fit residues: 606.3747 Evaluate side-chains 308 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 282 time to evaluate : 3.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 139 ASN Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 16 LYS Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 103 GLU Chi-restraints excluded: chain Q residue 107 LYS Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain S residue 71 THR 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: 9.9990 chunk 227 optimal weight: 0.7980 chunk 176 optimal weight: 6.9990 chunk 258 optimal weight: 0.7980 chunk 390 optimal weight: 3.9990 chunk 359 optimal weight: 3.9990 chunk 310 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 240 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 B 377 ASN D 90 HIS J 58 GLN J 80 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9210 moved from start: 0.2440 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= 0.258 Angle : 0.551 16.118 45352 Z= 0.263 Chirality : 0.041 0.147 4962 Planarity : 0.004 0.049 5700 Dihedral : 11.672 148.765 5265 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.84 % Allowed : 12.99 % Favored : 86.17 % 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: 2.00 (0.14), residues: 3955 helix: 1.85 (0.11), residues: 2134 sheet: 1.10 (0.27), residues: 360 loop : 0.76 (0.17), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 142 HIS 0.013 0.001 HIS C 197 PHE 0.021 0.001 PHE A 334 TYR 0.017 0.001 TYR D 117 ARG 0.007 0.000 ARG M 183 ********************** 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 314 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 286 time to evaluate : 3.474 Fit side-chains revert: symmetry clash REVERT: P 112 LEU cc_start: 0.9252 (tp) cc_final: 0.9011 (tp) REVERT: G 9 LYS cc_start: 0.9044 (mttp) cc_final: 0.8739 (tttt) REVERT: G 112 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8375 (tt0) REVERT: F 84 GLU cc_start: 0.8597 (tt0) cc_final: 0.8219 (mt-10) REVERT: F 120 LYS cc_start: 0.9258 (mttp) cc_final: 0.9011 (mmtm) REVERT: A 87 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8382 (ptp90) REVERT: A 99 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8761 (ttm) REVERT: B 170 TYR cc_start: 0.8256 (p90) cc_final: 0.7718 (p90) REVERT: B 353 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7296 (mt-10) REVERT: B 364 MET cc_start: 0.8991 (tpp) cc_final: 0.8788 (tpp) REVERT: D 85 MET cc_start: 0.8538 (mtm) cc_final: 0.8298 (ptp) REVERT: Q 110 GLU cc_start: 0.8543 (pt0) cc_final: 0.8228 (pp20) REVERT: M 364 MET cc_start: 0.8530 (tpp) cc_final: 0.8100 (tpt) outliers start: 28 outliers final: 20 residues processed: 302 average time/residue: 1.7366 time to fit residues: 607.9518 Evaluate side-chains 306 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 282 time to evaluate : 4.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 139 ASN Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 136 ASP Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 103 GLU Chi-restraints excluded: chain Q residue 107 LYS Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 71 THR 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: 0.0270 chunk 95 optimal weight: 3.9990 chunk 286 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 311 optimal weight: 0.3980 chunk 130 optimal weight: 10.0000 chunk 319 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 57 optimal weight: 0.2980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN A 192 GLN A 364 HIS B 316 GLN B 377 ASN J 58 GLN J 80 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.075922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.057986 restraints weight = 56099.685| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 1.63 r_work: 0.2632 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9153 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 33367 Z= 0.144 Angle : 0.488 12.322 45352 Z= 0.233 Chirality : 0.039 0.154 4962 Planarity : 0.004 0.049 5700 Dihedral : 11.176 148.367 5265 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.60 % Allowed : 13.29 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.14), residues: 3955 helix: 1.99 (0.11), residues: 2126 sheet: 1.15 (0.27), residues: 363 loop : 0.78 (0.17), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 142 HIS 0.006 0.001 HIS C 197 PHE 0.017 0.001 PHE A 334 TYR 0.013 0.001 TYR O 221 ARG 0.006 0.000 ARG M 183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11552.60 seconds wall clock time: 205 minutes 43.32 seconds (12343.32 seconds total)