Starting phenix.real_space_refine on Thu Feb 22 01:13:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab9_15315/02_2024/8ab9_15315_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab9_15315/02_2024/8ab9_15315.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab9_15315/02_2024/8ab9_15315_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab9_15315/02_2024/8ab9_15315_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab9_15315/02_2024/8ab9_15315_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab9_15315/02_2024/8ab9_15315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab9_15315/02_2024/8ab9_15315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab9_15315/02_2024/8ab9_15315_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab9_15315/02_2024/8ab9_15315_updated.pdb" } resolution = 3.3 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 8 7.16 5 P 30 5.49 5 S 102 5.16 5 C 21031 2.51 5 N 5296 2.21 5 O 6073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 4": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "P GLU 134": "OE1" <-> "OE2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P GLU 137": "OE1" <-> "OE2" Residue "P GLU 178": "OE1" <-> "OE2" Residue "P GLU 213": "OE1" <-> "OE2" Residue "P GLU 220": "OE1" <-> "OE2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G ARG 61": "NH1" <-> "NH2" Residue "G GLU 66": "OE1" <-> "OE2" Residue "G ARG 70": "NH1" <-> "NH2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G GLU 96": "OE1" <-> "OE2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F GLU 121": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B GLU 350": "OE1" <-> "OE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "D ARG 189": "NH1" <-> "NH2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "D TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D ARG 321": "NH1" <-> "NH2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "N ARG 4": "NH1" <-> "NH2" Residue "N ARG 70": "NH1" <-> "NH2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "N TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 110": "NH1" <-> "NH2" Residue "N PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 283": "NH1" <-> "NH2" Residue "N ARG 310": "NH1" <-> "NH2" Residue "N ARG 314": "NH1" <-> "NH2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "R GLU 12": "OE1" <-> "OE2" Residue "R GLU 50": "OE1" <-> "OE2" Residue "R GLU 51": "OE1" <-> "OE2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R ARG 61": "NH1" <-> "NH2" Residue "R GLU 66": "OE1" <-> "OE2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R ARG 73": "NH1" <-> "NH2" Residue "R ARG 76": "NH1" <-> "NH2" Residue "R GLU 96": "OE1" <-> "OE2" Residue "R GLU 110": "OE1" <-> "OE2" Residue "R GLU 123": "OE1" <-> "OE2" Residue "Q GLU 88": "OE1" <-> "OE2" Residue "Q GLU 118": "OE1" <-> "OE2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "Q GLU 126": "OE1" <-> "OE2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "L GLU 141": "OE1" <-> "OE2" Residue "L ARG 188": "NH1" <-> "NH2" Residue "L PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 354": "OE1" <-> "OE2" Residue "L ARG 384": "NH1" <-> "NH2" Residue "L GLU 424": "OE1" <-> "OE2" Residue "L GLU 457": "OE1" <-> "OE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M GLU 78": "OE1" <-> "OE2" Residue "M TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 117": "OE1" <-> "OE2" Residue "M ARG 140": "NH1" <-> "NH2" Residue "M GLU 150": "OE1" <-> "OE2" Residue "M ARG 234": "NH1" <-> "NH2" Residue "M GLU 313": "OE1" <-> "OE2" Residue "M GLU 350": "OE1" <-> "OE2" Residue "M GLU 376": "OE1" <-> "OE2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "O ARG 132": "NH1" <-> "NH2" Residue "O ARG 136": "NH1" <-> "NH2" Residue "O GLU 164": "OE1" <-> "OE2" Residue "O ARG 170": "NH1" <-> "NH2" Residue "O ARG 189": "NH1" <-> "NH2" Residue "O ARG 207": "NH1" <-> "NH2" Residue "O TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 250": "NH1" <-> "NH2" Residue "O GLU 260": "OE1" <-> "OE2" Residue "O ARG 289": "NH1" <-> "NH2" Residue "O ARG 321": "NH1" <-> "NH2" Residue "S PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 34": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32540 Number of models: 1 Model: "" Number of chains: 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: "J" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 298 Unusual residues: {'CDL': 2, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 127 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 29.983 52.027 37.153 1.00138.40 S ATOM 4207 SG CYS P 187 32.583 49.171 36.973 1.00126.56 S Time building chain proxies: 17.20, per 1000 atoms: 0.53 Number of scatterers: 32540 At special positions: 0 Unit cell: (118.833, 129.636, 163.707, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 8 26.01 S 102 16.00 P 30 15.00 O 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=2.02 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.05 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=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.46 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 301 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 170 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 190 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 168 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 187 " Number of angles added : 3 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7486 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 185 helices and 15 sheets defined 54.3% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.26 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: 3.934A pdb=" N PHE C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY C 33 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR C 46 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.583A 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: 3.729A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 135 removed outlier: 4.139A pdb=" N VAL C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 153 removed outlier: 3.532A pdb=" N LEU C 150 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL C 151 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER C 152 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 4.316A 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: 4.042A pdb=" N THR C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 246 removed outlier: 6.806A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.781A 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: 3.832A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.962A 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: 4.052A pdb=" N PHE C 363 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 381 Processing helix chain 'P' and resid 59 through 91 removed outlier: 3.590A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN P 90 " --> pdb=" O ASP P 86 " (cutoff:3.500A) removed outlier: 4.891A 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: 3.650A pdb=" N ASN G 121 " --> pdb=" O ASP G 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 88 Processing helix chain 'F' and resid 92 through 110 Processing helix chain 'F' and resid 124 through 137 Processing helix chain 'F' and resid 139 through 145 removed outlier: 3.565A 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: 3.507A pdb=" N HIS A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 4.204A 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: 3.816A pdb=" N VAL A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Proline residue: A 124 - end of helix removed outlier: 3.876A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.704A 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 154 removed outlier: 4.000A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.566A 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: 4.001A 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: 3.593A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 395 removed outlier: 3.577A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.400A 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: 3.688A pdb=" N ASP A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET A 469 " --> pdb=" O ILE A 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 70 through 79 Processing helix chain 'B' and resid 101 through 117 Proline residue: B 105 - end of helix removed outlier: 3.582A pdb=" N LYS B 116 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU B 117 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 129 through 141 Processing helix chain 'B' and resid 144 through 157 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 200 through 210 removed outlier: 3.526A pdb=" N THR B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.705A pdb=" N LEU B 263 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 311 through 330 Processing helix chain 'B' and resid 334 through 353 Processing helix chain 'B' and resid 355 through 367 removed outlier: 3.663A 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: 3.522A 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 320 Proline residue: D 317 - end of helix Processing helix chain 'H' and resid 40 through 80 removed outlier: 4.381A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.699A 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: 5.005A pdb=" N HIS I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LYS I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 49 removed outlier: 3.566A 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: 3.932A pdb=" N PHE N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLY N 33 " --> pdb=" O TRP N 30 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR N 46 " --> pdb=" O GLN N 43 " (cutoff:3.500A) removed outlier: 3.589A 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: 3.716A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 135 removed outlier: 4.169A pdb=" N VAL N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 138 through 153 removed outlier: 3.551A pdb=" N LEU N 150 " --> pdb=" O VAL N 146 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL N 151 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER N 152 " --> pdb=" O CYS N 148 " (cutoff:3.500A) removed outlier: 4.278A 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: 4.041A pdb=" N THR N 203 " --> pdb=" O ILE N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 246 removed outlier: 6.791A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.789A 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: 3.826A pdb=" N ILE N 299 " --> pdb=" O MET N 295 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU N 302 " --> pdb=" O ALA N 298 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU N 303 " --> pdb=" O ILE N 299 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE N 304 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU N 305 " --> pdb=" O ILE N 301 " (cutoff:3.500A) Proline residue: N 306 - end of helix Processing helix chain 'N' and resid 320 through 340 Processing helix chain 'N' and resid 348 through 364 removed outlier: 4.045A pdb=" N PHE N 363 " --> pdb=" O TYR N 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 366 through 381 Processing helix chain 'E' and resid 59 through 91 removed outlier: 3.634A pdb=" N SER E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 4.882A 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: 3.654A pdb=" N ASN R 121 " --> pdb=" O ASP R 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 88 Processing helix chain 'Q' and resid 92 through 110 Processing helix chain 'Q' and resid 124 through 137 Processing helix chain 'Q' and resid 139 through 145 removed outlier: 3.567A pdb=" N VAL Q 145 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 72 through 79 Processing helix chain 'L' and resid 89 through 99 Processing helix chain 'L' and resid 120 through 135 removed outlier: 3.816A pdb=" N VAL L 123 " --> pdb=" O LYS L 120 " (cutoff:3.500A) Proline residue: L 124 - end of helix removed outlier: 3.863A pdb=" N VAL L 127 " --> pdb=" O PRO L 124 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU L 134 " --> pdb=" O ALA L 131 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN L 135 " --> pdb=" O ASP L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 154 removed outlier: 3.997A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 160 No H-bonds generated for 'chain 'L' and resid 158 through 160' Processing helix chain 'L' and resid 162 through 174 Processing helix chain 'L' and resid 179 through 181 No H-bonds generated for 'chain 'L' and resid 179 through 181' Processing helix chain 'L' and resid 188 through 193 removed outlier: 3.563A pdb=" N THR L 193 " --> pdb=" O GLU L 189 " (cutoff:3.500A) 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: 3.998A 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: 3.607A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 395 removed outlier: 3.631A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.417A 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: 3.688A pdb=" N ASP L 468 " --> pdb=" O ARG L 464 " (cutoff:3.500A) removed outlier: 3.988A 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: 3.592A pdb=" N VAL M 108 " --> pdb=" O PRO M 105 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS M 116 " --> pdb=" O ASN M 113 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU M 117 " --> pdb=" O VAL M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 127 Processing helix chain 'M' and resid 129 through 141 Processing helix chain 'M' and resid 144 through 157 Processing helix chain 'M' and resid 160 through 162 No H-bonds generated for 'chain 'M' and resid 160 through 162' Processing helix chain 'M' and resid 175 through 185 Processing helix chain 'M' and resid 188 through 190 No H-bonds generated for 'chain 'M' and resid 188 through 190' Processing helix chain 'M' and resid 200 through 210 removed outlier: 3.519A pdb=" N THR M 209 " --> pdb=" O GLN M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 263 removed outlier: 3.704A 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: 3.880A 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 No H-bonds generated for 'chain 'O' and resid 135 through 138' Processing helix chain 'O' and resid 145 through 153 Processing helix chain 'O' and resid 185 through 192 Processing helix chain 'O' and resid 210 through 218 removed outlier: 3.520A 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 320 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 40 through 80 removed outlier: 4.361A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.685A 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: 4.977A pdb=" N HIS T 55 " --> pdb=" O LYS T 51 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LYS T 56 " --> pdb=" O ASP T 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 49 removed outlier: 3.564A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.569A 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: 3.921A 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 removed outlier: 3.536A pdb=" N SER P 192 " --> pdb=" O CYS P 187 " (cutoff:3.500A) 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: 4.062A 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: 3.585A 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: 4.067A 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: 3.566A 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 1582 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: 10.32 Time building geometry restraints manager: 14.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.40: 13591 1.40 - 1.61: 19566 1.61 - 1.82: 166 1.82 - 2.03: 25 2.03 - 2.23: 19 Bond restraints: 33367 Sorted by residual: bond pdb=" N TYR H 9 " pdb=" CA TYR H 9 " ideal model delta sigma weight residual 1.458 1.632 -0.174 1.90e-02 2.77e+03 8.43e+01 bond pdb=" N TYR S 9 " pdb=" CA TYR S 9 " ideal model delta sigma weight residual 1.458 1.616 -0.158 1.90e-02 2.77e+03 6.91e+01 bond pdb=" N ALA T 4 " pdb=" CA ALA T 4 " ideal model delta sigma weight residual 1.458 1.613 -0.155 1.90e-02 2.77e+03 6.66e+01 bond pdb=" N ALA I 4 " pdb=" CA ALA I 4 " ideal model delta sigma weight residual 1.458 1.604 -0.146 1.90e-02 2.77e+03 5.92e+01 bond pdb=" C3B HEC O 401 " pdb=" CAB HEC O 401 " ideal model delta sigma weight residual 1.544 1.420 0.124 2.00e-02 2.50e+03 3.86e+01 ... (remaining 33362 not shown) Histogram of bond angle deviations from ideal: 84.09 - 103.09: 481 103.09 - 122.10: 38341 122.10 - 141.11: 6518 141.11 - 160.11: 0 160.11 - 179.12: 12 Bond angle restraints: 45352 Sorted by residual: angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 91.56 12.77 1.14e+00 7.69e-01 1.25e+02 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 92.13 12.20 1.20e+00 6.94e-01 1.03e+02 angle pdb=" C GLN M 215 " pdb=" CA GLN M 215 " pdb=" CB GLN M 215 " ideal model delta sigma weight residual 109.64 94.44 15.20 1.77e+00 3.19e-01 7.38e+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 94.62 15.02 1.77e+00 3.19e-01 7.20e+01 angle pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " pdb="FE2 FES P 301 " ideal model delta sigma weight residual 75.66 85.13 -9.47 1.14e+00 7.69e-01 6.90e+01 ... (remaining 45347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.97: 18796 31.97 - 63.93: 1058 63.93 - 95.90: 105 95.90 - 127.86: 1 127.86 - 159.83: 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 -103.89 -18.71 0 2.50e+00 1.60e-01 5.60e+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 -104.26 -18.34 0 2.50e+00 1.60e-01 5.38e+01 dihedral pdb=" C2B HEC D 401 " pdb=" C3B HEC D 401 " pdb=" CAB HEC D 401 " pdb=" CBB HEC D 401 " ideal model delta sinusoidal sigma weight residual 60.00 -4.73 64.73 2 1.00e+01 1.00e-02 3.93e+01 ... (remaining 19960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.194: 4554 0.194 - 0.387: 390 0.387 - 0.581: 14 0.581 - 0.774: 0 0.774 - 0.968: 4 Chirality restraints: 4962 Sorted by residual: chirality pdb=" CB4 CDL N 506 " pdb=" CB3 CDL N 506 " pdb=" CB6 CDL N 506 " pdb=" OB6 CDL N 506 " both_signs ideal model delta sigma weight residual False -2.57 -1.61 -0.97 2.00e-01 2.50e+01 2.34e+01 chirality pdb=" CB4 CDL O 402 " pdb=" CB3 CDL O 402 " pdb=" CB6 CDL O 402 " pdb=" OB6 CDL O 402 " both_signs ideal model delta sigma weight residual False -2.57 -1.68 -0.89 2.00e-01 2.50e+01 1.99e+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 -1.74 -0.83 2.00e-01 2.50e+01 1.74e+01 ... (remaining 4959 not shown) Planarity restraints: 5700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC O 401 " -0.019 2.00e-02 2.50e+03 2.99e-02 2.01e+01 pdb=" C2C HEC O 401 " -0.014 2.00e-02 2.50e+03 pdb=" C3C HEC O 401 " 0.025 2.00e-02 2.50e+03 pdb=" C4C HEC O 401 " -0.010 2.00e-02 2.50e+03 pdb=" CAC HEC O 401 " 0.042 2.00e-02 2.50e+03 pdb=" CHC HEC O 401 " 0.050 2.00e-02 2.50e+03 pdb=" CHD HEC O 401 " -0.025 2.00e-02 2.50e+03 pdb=" CMC HEC O 401 " -0.042 2.00e-02 2.50e+03 pdb=" NC HEC O 401 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEC O 401 " 0.003 2.00e-02 2.50e+03 2.84e-02 1.81e+01 pdb=" C1B HEC O 401 " 0.006 2.00e-02 2.50e+03 pdb=" C2B HEC O 401 " -0.025 2.00e-02 2.50e+03 pdb=" C3B HEC O 401 " -0.027 2.00e-02 2.50e+03 pdb=" C4B HEC O 401 " 0.003 2.00e-02 2.50e+03 pdb=" CAB HEC O 401 " 0.059 2.00e-02 2.50e+03 pdb=" CHB HEC O 401 " 0.032 2.00e-02 2.50e+03 pdb=" CHC HEC O 401 " -0.027 2.00e-02 2.50e+03 pdb=" CMB HEC O 401 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS N 96 " -0.041 2.00e-02 2.50e+03 3.38e-02 1.72e+01 pdb=" CG HIS N 96 " 0.060 2.00e-02 2.50e+03 pdb=" ND1 HIS N 96 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS N 96 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 HIS N 96 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS N 96 " -0.035 2.00e-02 2.50e+03 ... (remaining 5697 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 216 2.62 - 3.19: 28792 3.19 - 3.76: 53758 3.76 - 4.33: 80497 4.33 - 4.90: 122724 Nonbonded interactions: 285987 Sorted by model distance: nonbonded pdb=" NE2 HIS N 82 " pdb="FE HEM N 501 " model vdw 2.046 3.080 nonbonded pdb=" NE2 HIS C 82 " pdb="FE HEM C 501 " model vdw 2.047 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.120 2.520 nonbonded pdb=" ND2 ASN C 149 " pdb=" O LEU P 171 " model vdw 2.126 2.520 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.149 3.080 ... (remaining 285982 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = (chain 'C' and (resid 1 through 383 or resid 501 through 503)) selection = (chain 'N' and (resid 1 through 383 or resid 501 through 503)) } ncs_group { reference = chain 'D' selection = (chain 'O' and (resid 85 through 328 or resid 401)) } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = (chain 'H' and resid 9 through 93) selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = (chain 'J' and resid 8 through 82) selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 12.160 Check model and map are aligned: 0.520 Set scattering table: 0.330 Process input model: 90.220 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.280 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9196 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.230 33367 Z= 0.712 Angle : 1.787 16.340 45352 Z= 1.122 Chirality : 0.114 0.968 4962 Planarity : 0.007 0.044 5700 Dihedral : 18.507 159.827 12462 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.50 % Favored : 97.45 % Rotamer: Outliers : 3.82 % Allowed : 8.24 % Favored : 87.94 % Cbeta Deviations : 1.36 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.12), residues: 3955 helix: -1.26 (0.09), residues: 2158 sheet: -0.08 (0.26), residues: 353 loop : -0.74 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.008 TRP A 474 HIS 0.026 0.005 HIS C 253 PHE 0.045 0.007 PHE C 234 TYR 0.049 0.007 TYR H 9 ARG 0.021 0.002 ARG L 269 *********************** 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 614 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 487 time to evaluate : 3.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 LYS cc_start: 0.9452 (tttt) cc_final: 0.8949 (tptt) REVERT: C 229 ASP cc_start: 0.9275 (m-30) cc_final: 0.8993 (m-30) REVERT: C 239 MET cc_start: 0.9118 (ttp) cc_final: 0.8668 (mmt) REVERT: C 309 ASP cc_start: 0.9348 (t0) cc_final: 0.9107 (t0) REVERT: P 74 MET cc_start: 0.9154 (ttp) cc_final: 0.8913 (tmm) REVERT: P 123 LYS cc_start: 0.9096 (mttt) cc_final: 0.8817 (mttp) REVERT: P 150 GLN cc_start: 0.6698 (tt0) cc_final: 0.6176 (tt0) REVERT: P 154 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8238 (tp30) REVERT: P 222 LEU cc_start: 0.9527 (pp) cc_final: 0.9172 (tt) REVERT: G 9 LYS cc_start: 0.9409 (mttp) cc_final: 0.9095 (tttt) REVERT: F 80 ILE cc_start: 0.9263 (mt) cc_final: 0.9018 (tt) REVERT: F 109 GLN cc_start: 0.9413 (mt0) cc_final: 0.9118 (mt0) REVERT: F 114 TYR cc_start: 0.8543 (t80) cc_final: 0.7891 (t80) REVERT: F 126 GLU cc_start: 0.9166 (mp0) cc_final: 0.8899 (mp0) REVERT: A 87 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8118 (mtp85) REVERT: A 97 GLU cc_start: 0.9411 (OUTLIER) cc_final: 0.8953 (mp0) REVERT: I 30 ASP cc_start: 0.9532 (t70) cc_final: 0.9234 (t0) REVERT: I 43 ARG cc_start: 0.9302 (mtm110) cc_final: 0.9017 (ttp80) REVERT: J 11 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8779 (ptpp) REVERT: J 55 ARG cc_start: 0.8926 (ttm-80) cc_final: 0.8316 (ttm-80) REVERT: N 288 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8523 (ttpt) REVERT: E 55 ASP cc_start: 0.9248 (OUTLIER) cc_final: 0.8704 (p0) REVERT: R 85 LYS cc_start: 0.9398 (mttm) cc_final: 0.9147 (mmtm) REVERT: Q 80 ILE cc_start: 0.9454 (mt) cc_final: 0.9177 (mt) REVERT: Q 113 ASP cc_start: 0.9250 (m-30) cc_final: 0.8961 (t0) REVERT: Q 122 ASP cc_start: 0.8745 (p0) cc_final: 0.8499 (p0) REVERT: Q 126 GLU cc_start: 0.9480 (mp0) cc_final: 0.9112 (mp0) REVERT: L 36 LYS cc_start: 0.9549 (mmtt) cc_final: 0.9345 (mmtt) REVERT: L 97 GLU cc_start: 0.9530 (OUTLIER) cc_final: 0.9323 (mt-10) REVERT: M 16 SER cc_start: 0.9166 (OUTLIER) cc_final: 0.8872 (p) REVERT: M 58 GLU cc_start: 0.9459 (OUTLIER) cc_final: 0.9241 (tm-30) REVERT: M 124 GLU cc_start: 0.9407 (mt-10) cc_final: 0.9164 (mt-10) REVERT: T 30 ASP cc_start: 0.9541 (t70) cc_final: 0.9187 (t0) REVERT: T 38 ASP cc_start: 0.9164 (m-30) cc_final: 0.8841 (t0) REVERT: U 13 SER cc_start: 0.9324 (t) cc_final: 0.8965 (p) REVERT: U 55 ARG cc_start: 0.8883 (ttm-80) cc_final: 0.8658 (ttm-80) REVERT: U 58 GLN cc_start: 0.9145 (tp40) cc_final: 0.8657 (mt0) REVERT: U 59 ASP cc_start: 0.9288 (m-30) cc_final: 0.9064 (m-30) REVERT: U 74 GLU cc_start: 0.8907 (mp0) cc_final: 0.8583 (pm20) REVERT: U 80 ASN cc_start: 0.9169 (t0) cc_final: 0.8439 (p0) outliers start: 127 outliers final: 21 residues processed: 570 average time/residue: 0.4950 time to fit residues: 431.8618 Evaluate side-chains 357 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 328 time to evaluate : 3.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 197 SER Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 109 PRO Chi-restraints excluded: chain N residue 178 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 288 LYS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 378 SER Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 261 SER Chi-restraints excluded: chain M residue 386 LEU 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: 7.9990 chunk 297 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 307 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 228 optimal weight: 0.0030 chunk 355 optimal weight: 0.7980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN C 14 ASN C 173 ASN C 202 HIS C 332 ASN P 85 GLN G 54 ASN G 84 HIS F 135 ASN A 196 ASN A 222 HIS A 371 ASN B 87 HIS N 11 ASN N 14 ASN N 177 GLN N 202 HIS N 332 ASN R 84 HIS ** L 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 371 ASN M 87 HIS ** M 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 ASN M 377 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33367 Z= 0.180 Angle : 0.599 15.819 45352 Z= 0.296 Chirality : 0.041 0.223 4962 Planarity : 0.004 0.037 5700 Dihedral : 14.080 154.531 5331 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.38 % Allowed : 11.13 % Favored : 87.49 % 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: 0.58 (0.13), residues: 3955 helix: 0.75 (0.11), residues: 2135 sheet: 0.59 (0.27), residues: 359 loop : -0.03 (0.17), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 156 HIS 0.006 0.001 HIS C 197 PHE 0.020 0.002 PHE L 334 TYR 0.017 0.002 TYR D 237 ARG 0.004 0.001 ARG P 121 *********************** 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 401 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 355 time to evaluate : 4.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 16 TYR cc_start: 0.8978 (m-80) cc_final: 0.8714 (m-80) REVERT: C 217 ASP cc_start: 0.8573 (t70) cc_final: 0.8323 (t0) REVERT: C 239 MET cc_start: 0.9070 (ttp) cc_final: 0.8662 (mmt) REVERT: C 309 ASP cc_start: 0.9307 (t0) cc_final: 0.9096 (t0) REVERT: P 154 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8281 (tp30) REVERT: P 155 ARG cc_start: 0.6199 (mtp85) cc_final: 0.5934 (mtp85) REVERT: P 222 LEU cc_start: 0.9392 (pp) cc_final: 0.9107 (tt) REVERT: G 9 LYS cc_start: 0.9328 (mttp) cc_final: 0.9066 (tttp) REVERT: G 31 TYR cc_start: 0.9318 (t80) cc_final: 0.8833 (t80) REVERT: G 120 ASP cc_start: 0.9448 (m-30) cc_final: 0.9141 (m-30) REVERT: F 109 GLN cc_start: 0.9402 (mt0) cc_final: 0.9121 (mt0) REVERT: A 97 GLU cc_start: 0.9420 (OUTLIER) cc_final: 0.8909 (mp0) REVERT: B 60 PHE cc_start: 0.9446 (OUTLIER) cc_final: 0.9138 (t80) REVERT: I 30 ASP cc_start: 0.9407 (t70) cc_final: 0.9146 (t0) REVERT: J 11 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8719 (ptpp) REVERT: J 51 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8695 (tm-30) REVERT: N 369 MET cc_start: 0.8658 (mmp) cc_final: 0.8413 (mtt) REVERT: E 55 ASP cc_start: 0.9262 (OUTLIER) cc_final: 0.8560 (p0) REVERT: R 85 LYS cc_start: 0.9329 (mttm) cc_final: 0.9094 (mmtm) REVERT: Q 122 ASP cc_start: 0.8592 (p0) cc_final: 0.8067 (p0) REVERT: Q 126 GLU cc_start: 0.9517 (mp0) cc_final: 0.9081 (mp0) REVERT: L 36 LYS cc_start: 0.9573 (mmtt) cc_final: 0.9361 (mmtt) REVERT: L 97 GLU cc_start: 0.9517 (OUTLIER) cc_final: 0.9256 (mt-10) REVERT: M 58 GLU cc_start: 0.9413 (OUTLIER) cc_final: 0.9149 (tm-30) REVERT: M 124 GLU cc_start: 0.9329 (mt-10) cc_final: 0.9096 (mt-10) REVERT: M 356 ASP cc_start: 0.9197 (OUTLIER) cc_final: 0.8979 (m-30) REVERT: S 51 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8469 (ptm160) REVERT: T 38 ASP cc_start: 0.9029 (m-30) cc_final: 0.8816 (t0) REVERT: U 13 SER cc_start: 0.9321 (t) cc_final: 0.8983 (p) REVERT: U 58 GLN cc_start: 0.9107 (tp40) cc_final: 0.8867 (tp40) REVERT: U 59 ASP cc_start: 0.9317 (m-30) cc_final: 0.9089 (m-30) REVERT: U 74 GLU cc_start: 0.8958 (mp0) cc_final: 0.8718 (pm20) REVERT: U 80 ASN cc_start: 0.9184 (t0) cc_final: 0.8399 (p0) outliers start: 46 outliers final: 12 residues processed: 388 average time/residue: 0.4735 time to fit residues: 291.1924 Evaluate side-chains 324 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 304 time to evaluate : 4.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 378 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 356 ASP Chi-restraints excluded: chain S residue 51 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 296 optimal weight: 7.9990 chunk 242 optimal weight: 7.9990 chunk 98 optimal weight: 0.0070 chunk 356 optimal weight: 0.4980 chunk 385 optimal weight: 9.9990 chunk 317 optimal weight: 0.9990 chunk 353 optimal weight: 7.9990 chunk 121 optimal weight: 0.0770 chunk 286 optimal weight: 8.9990 overall best weight: 1.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 GLN B 316 GLN B 354 ASN D 166 ASN Q 137 ASN ** L 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 92 HIS M 316 GLN O 90 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9129 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33367 Z= 0.199 Angle : 0.528 14.294 45352 Z= 0.255 Chirality : 0.040 0.190 4962 Planarity : 0.004 0.041 5700 Dihedral : 12.947 149.846 5292 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.41 % Allowed : 11.43 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.13), residues: 3955 helix: 1.43 (0.11), residues: 2132 sheet: 0.63 (0.27), residues: 371 loop : 0.28 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 142 HIS 0.006 0.001 HIS C 197 PHE 0.016 0.001 PHE L 334 TYR 0.019 0.001 TYR M 170 ARG 0.009 0.000 ARG P 128 *********************** 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 369 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 322 time to evaluate : 3.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.9091 (ttp) cc_final: 0.8648 (mmt) REVERT: C 287 ASP cc_start: 0.8292 (t0) cc_final: 0.8060 (t0) REVERT: P 154 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8370 (tp30) REVERT: P 164 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.7120 (ptt) REVERT: P 222 LEU cc_start: 0.9330 (pp) cc_final: 0.9030 (tt) REVERT: G 9 LYS cc_start: 0.9466 (mttp) cc_final: 0.9107 (tttp) REVERT: G 120 ASP cc_start: 0.9485 (m-30) cc_final: 0.9227 (m-30) REVERT: A 97 GLU cc_start: 0.9385 (OUTLIER) cc_final: 0.8863 (mp0) REVERT: B 60 PHE cc_start: 0.9451 (OUTLIER) cc_final: 0.9037 (t80) REVERT: I 30 ASP cc_start: 0.9411 (t70) cc_final: 0.9130 (t0) REVERT: J 11 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8689 (ptpp) REVERT: J 51 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8759 (tm-30) REVERT: E 55 ASP cc_start: 0.9233 (OUTLIER) cc_final: 0.8429 (p0) REVERT: R 85 LYS cc_start: 0.9337 (mttm) cc_final: 0.9087 (mmtm) REVERT: Q 100 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8859 (mm-30) REVERT: Q 113 ASP cc_start: 0.9245 (t0) cc_final: 0.9029 (t0) REVERT: Q 114 TYR cc_start: 0.8599 (t80) cc_final: 0.8233 (t80) REVERT: Q 126 GLU cc_start: 0.9441 (mp0) cc_final: 0.9083 (mp0) REVERT: L 36 LYS cc_start: 0.9583 (mmtt) cc_final: 0.9374 (mmtt) REVERT: L 97 GLU cc_start: 0.9500 (OUTLIER) cc_final: 0.9231 (mt-10) REVERT: M 58 GLU cc_start: 0.9357 (OUTLIER) cc_final: 0.9142 (tm-30) REVERT: O 201 SER cc_start: 0.9293 (m) cc_final: 0.9080 (p) REVERT: T 30 ASP cc_start: 0.9395 (t0) cc_final: 0.9009 (t0) REVERT: T 38 ASP cc_start: 0.9024 (m-30) cc_final: 0.8819 (t0) REVERT: T 39 ASN cc_start: 0.9004 (m-40) cc_final: 0.8756 (m-40) REVERT: U 13 SER cc_start: 0.9273 (t) cc_final: 0.8933 (p) REVERT: U 80 ASN cc_start: 0.9190 (t0) cc_final: 0.8371 (p0) outliers start: 47 outliers final: 20 residues processed: 353 average time/residue: 0.4610 time to fit residues: 260.1184 Evaluate side-chains 329 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 302 time to evaluate : 3.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain P residue 164 MET Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 14 ILE Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 183 THR Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain L residue 378 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain O residue 90 HIS Chi-restraints excluded: chain S residue 28 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 1.9990 chunk 268 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 239 optimal weight: 5.9990 chunk 357 optimal weight: 0.9980 chunk 378 optimal weight: 8.9990 chunk 186 optimal weight: 2.9990 chunk 339 optimal weight: 9.9990 chunk 102 optimal weight: 0.0970 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 GLN N 11 ASN E 85 GLN R 45 ASN Q 135 ASN ** L 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9147 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33367 Z= 0.251 Angle : 0.535 16.715 45352 Z= 0.252 Chirality : 0.041 0.178 4962 Planarity : 0.004 0.044 5700 Dihedral : 12.464 150.375 5288 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.41 % Allowed : 11.82 % Favored : 86.77 % 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: 1.57 (0.14), residues: 3955 helix: 1.63 (0.11), residues: 2132 sheet: 0.62 (0.27), residues: 371 loop : 0.40 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 142 HIS 0.020 0.001 HIS O 90 PHE 0.014 0.001 PHE L 334 TYR 0.020 0.001 TYR M 170 ARG 0.009 0.000 ARG F 144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 309 time to evaluate : 3.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.9110 (ttp) cc_final: 0.8643 (mmt) REVERT: C 287 ASP cc_start: 0.8356 (t0) cc_final: 0.8085 (t0) REVERT: P 130 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.6028 (tpp80) REVERT: P 154 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8449 (tp30) REVERT: P 201 ARG cc_start: 0.8587 (mtp85) cc_final: 0.7842 (ttm110) REVERT: P 222 LEU cc_start: 0.9304 (pp) cc_final: 0.9024 (tt) REVERT: G 9 LYS cc_start: 0.9478 (mttp) cc_final: 0.9130 (tttp) REVERT: G 120 ASP cc_start: 0.9483 (m-30) cc_final: 0.9206 (m-30) REVERT: A 97 GLU cc_start: 0.9399 (OUTLIER) cc_final: 0.8863 (mp0) REVERT: D 131 ASP cc_start: 0.9259 (t0) cc_final: 0.9045 (p0) REVERT: I 30 ASP cc_start: 0.9425 (t70) cc_final: 0.9148 (t0) REVERT: J 11 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8729 (ptpp) REVERT: J 51 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8789 (tm-30) REVERT: E 55 ASP cc_start: 0.9186 (OUTLIER) cc_final: 0.8740 (p0) REVERT: R 85 LYS cc_start: 0.9364 (mttm) cc_final: 0.9114 (mmtm) REVERT: R 110 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8793 (mm-30) REVERT: Q 113 ASP cc_start: 0.9239 (t0) cc_final: 0.9009 (t0) REVERT: Q 114 TYR cc_start: 0.8555 (t80) cc_final: 0.8168 (t80) REVERT: Q 126 GLU cc_start: 0.9468 (mp0) cc_final: 0.9031 (mp0) REVERT: Q 131 GLN cc_start: 0.9404 (tp40) cc_final: 0.8871 (mp10) REVERT: L 36 LYS cc_start: 0.9587 (mmtt) cc_final: 0.9373 (mmtt) REVERT: L 97 GLU cc_start: 0.9491 (OUTLIER) cc_final: 0.9270 (mt-10) REVERT: M 58 GLU cc_start: 0.9358 (OUTLIER) cc_final: 0.9151 (tm-30) REVERT: O 201 SER cc_start: 0.9331 (m) cc_final: 0.9111 (p) REVERT: S 51 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8859 (ptm160) REVERT: T 30 ASP cc_start: 0.9389 (t0) cc_final: 0.9002 (t0) REVERT: T 39 ASN cc_start: 0.8982 (m-40) cc_final: 0.8774 (m-40) REVERT: U 13 SER cc_start: 0.9268 (t) cc_final: 0.8918 (p) REVERT: U 80 ASN cc_start: 0.9202 (t0) cc_final: 0.8374 (p0) outliers start: 47 outliers final: 27 residues processed: 343 average time/residue: 0.4415 time to fit residues: 242.6775 Evaluate side-chains 335 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 301 time to evaluate : 3.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 14 ILE Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain O residue 90 HIS Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain U residue 56 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 9.9990 chunk 215 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 282 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 323 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 0.9980 chunk 340 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 192 GLN ** L 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9147 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33367 Z= 0.233 Angle : 0.518 15.670 45352 Z= 0.244 Chirality : 0.040 0.165 4962 Planarity : 0.004 0.043 5700 Dihedral : 11.994 149.497 5285 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.32 % Allowed : 12.21 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.14), residues: 3955 helix: 1.80 (0.11), residues: 2122 sheet: 0.64 (0.26), residues: 371 loop : 0.48 (0.17), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 142 HIS 0.006 0.001 HIS C 197 PHE 0.013 0.001 PHE L 334 TYR 0.023 0.001 TYR G 31 ARG 0.006 0.000 ARG F 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 316 time to evaluate : 3.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.9124 (ttp) cc_final: 0.8649 (mmt) REVERT: C 287 ASP cc_start: 0.8386 (t0) cc_final: 0.8130 (t0) REVERT: C 341 GLN cc_start: 0.9326 (pp30) cc_final: 0.8954 (pp30) REVERT: P 128 ARG cc_start: 0.6938 (mmm-85) cc_final: 0.6514 (mmm160) REVERT: P 130 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.5971 (tpp80) REVERT: P 154 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8506 (tp30) REVERT: P 201 ARG cc_start: 0.8602 (mtp85) cc_final: 0.7851 (ttm110) REVERT: P 222 LEU cc_start: 0.9250 (pp) cc_final: 0.8973 (tt) REVERT: G 9 LYS cc_start: 0.9484 (mttp) cc_final: 0.9128 (tttp) REVERT: G 120 ASP cc_start: 0.9488 (m-30) cc_final: 0.9206 (m-30) REVERT: I 30 ASP cc_start: 0.9417 (t70) cc_final: 0.9155 (t0) REVERT: J 11 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8776 (ptpp) REVERT: J 51 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8788 (tm-30) REVERT: N 159 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8806 (mm-30) REVERT: E 55 ASP cc_start: 0.9152 (OUTLIER) cc_final: 0.8694 (p0) REVERT: R 85 LYS cc_start: 0.9374 (mttm) cc_final: 0.9126 (mmtm) REVERT: R 110 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8826 (mm-30) REVERT: Q 113 ASP cc_start: 0.9275 (t0) cc_final: 0.9067 (t0) REVERT: Q 114 TYR cc_start: 0.8576 (t80) cc_final: 0.8219 (t80) REVERT: Q 126 GLU cc_start: 0.9380 (mp0) cc_final: 0.9063 (mp0) REVERT: Q 131 GLN cc_start: 0.9420 (tp40) cc_final: 0.8861 (mp10) REVERT: L 36 LYS cc_start: 0.9595 (mmtt) cc_final: 0.9390 (mmtt) REVERT: L 97 GLU cc_start: 0.9482 (OUTLIER) cc_final: 0.9241 (mt-10) REVERT: O 201 SER cc_start: 0.9343 (m) cc_final: 0.9102 (p) REVERT: S 51 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8796 (ptm160) REVERT: T 30 ASP cc_start: 0.9381 (t0) cc_final: 0.9010 (t0) REVERT: U 13 SER cc_start: 0.9278 (t) cc_final: 0.8907 (p) REVERT: U 80 ASN cc_start: 0.9184 (t0) cc_final: 0.8345 (p0) outliers start: 44 outliers final: 27 residues processed: 349 average time/residue: 0.4595 time to fit residues: 256.6666 Evaluate side-chains 334 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 302 time to evaluate : 3.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain O residue 90 HIS Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain U residue 69 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 0.4980 chunk 341 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 222 optimal weight: 0.2980 chunk 93 optimal weight: 9.9990 chunk 379 optimal weight: 6.9990 chunk 314 optimal weight: 1.9990 chunk 175 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 199 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 332 ASN D 236 ASN ** L 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9156 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33367 Z= 0.262 Angle : 0.523 16.877 45352 Z= 0.247 Chirality : 0.041 0.157 4962 Planarity : 0.004 0.044 5700 Dihedral : 11.714 149.543 5277 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.44 % Allowed : 12.45 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.14), residues: 3955 helix: 1.84 (0.11), residues: 2124 sheet: 0.61 (0.26), residues: 371 loop : 0.52 (0.18), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 142 HIS 0.007 0.001 HIS C 197 PHE 0.013 0.001 PHE N 90 TYR 0.024 0.001 TYR M 170 ARG 0.006 0.000 ARG F 144 *********************** 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 361 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 313 time to evaluate : 3.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 239 MET cc_start: 0.9138 (ttp) cc_final: 0.8629 (mmt) REVERT: C 287 ASP cc_start: 0.8481 (t0) cc_final: 0.8223 (t0) REVERT: C 341 GLN cc_start: 0.9315 (pp30) cc_final: 0.8920 (pp30) REVERT: P 128 ARG cc_start: 0.7021 (mmm-85) cc_final: 0.6567 (mmm160) REVERT: P 130 ARG cc_start: 0.6824 (OUTLIER) cc_final: 0.6339 (tpp80) REVERT: P 150 GLN cc_start: 0.7108 (tt0) cc_final: 0.6587 (tt0) REVERT: P 154 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8552 (tp30) REVERT: P 222 LEU cc_start: 0.9193 (pp) cc_final: 0.8982 (tt) REVERT: G 9 LYS cc_start: 0.9489 (mttp) cc_final: 0.9135 (tttp) REVERT: G 120 ASP cc_start: 0.9481 (m-30) cc_final: 0.9173 (m-30) REVERT: F 140 ASP cc_start: 0.9336 (m-30) cc_final: 0.9071 (t0) REVERT: I 30 ASP cc_start: 0.9424 (t70) cc_final: 0.9157 (t0) REVERT: J 11 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8800 (ptpp) REVERT: J 51 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8796 (tm-30) REVERT: N 159 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8844 (mm-30) REVERT: E 55 ASP cc_start: 0.9162 (OUTLIER) cc_final: 0.8680 (p0) REVERT: R 85 LYS cc_start: 0.9396 (mttm) cc_final: 0.9151 (mmtm) REVERT: Q 114 TYR cc_start: 0.8592 (t80) cc_final: 0.8201 (t80) REVERT: Q 126 GLU cc_start: 0.9406 (mp0) cc_final: 0.8984 (mp0) REVERT: Q 131 GLN cc_start: 0.9445 (tp40) cc_final: 0.8865 (mp10) REVERT: L 36 LYS cc_start: 0.9599 (mmtt) cc_final: 0.9395 (mmtt) REVERT: L 97 GLU cc_start: 0.9484 (OUTLIER) cc_final: 0.9240 (mt-10) REVERT: M 197 ASN cc_start: 0.8756 (t0) cc_final: 0.7979 (t0) REVERT: O 201 SER cc_start: 0.9367 (m) cc_final: 0.9117 (p) REVERT: S 51 ARG cc_start: 0.9232 (OUTLIER) cc_final: 0.8788 (ptm160) REVERT: T 30 ASP cc_start: 0.9384 (t0) cc_final: 0.9019 (t0) REVERT: U 13 SER cc_start: 0.9316 (t) cc_final: 0.8944 (p) REVERT: U 80 ASN cc_start: 0.9193 (t0) cc_final: 0.8306 (p0) outliers start: 48 outliers final: 31 residues processed: 345 average time/residue: 0.4669 time to fit residues: 257.2852 Evaluate side-chains 337 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 301 time to evaluate : 3.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain U residue 59 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 0.2980 chunk 42 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 276 optimal weight: 0.7980 chunk 214 optimal weight: 4.9990 chunk 319 optimal weight: 0.0470 chunk 211 optimal weight: 0.7980 chunk 377 optimal weight: 7.9990 chunk 236 optimal weight: 0.0670 chunk 230 optimal weight: 0.0020 chunk 174 optimal weight: 0.9990 overall best weight: 0.2424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 343 HIS A 192 GLN D 93 HIS ** L 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 33367 Z= 0.126 Angle : 0.465 9.905 45352 Z= 0.227 Chirality : 0.038 0.146 4962 Planarity : 0.003 0.042 5700 Dihedral : 11.170 147.995 5277 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.93 % Allowed : 13.38 % Favored : 85.68 % 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: 1.99 (0.11), residues: 2120 sheet: 0.77 (0.26), residues: 369 loop : 0.62 (0.18), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 280 HIS 0.004 0.001 HIS M 87 PHE 0.014 0.001 PHE A 334 TYR 0.022 0.001 TYR G 31 ARG 0.005 0.000 ARG G 60 *********************** 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 364 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 333 time to evaluate : 3.824 Fit side-chains REVERT: C 239 MET cc_start: 0.9111 (ttp) cc_final: 0.8626 (mmt) REVERT: C 249 ASP cc_start: 0.9220 (OUTLIER) cc_final: 0.9012 (m-30) REVERT: C 287 ASP cc_start: 0.8424 (t0) cc_final: 0.8137 (t0) REVERT: C 341 GLN cc_start: 0.9189 (pp30) cc_final: 0.8835 (pp30) REVERT: P 128 ARG cc_start: 0.6982 (mmm-85) cc_final: 0.6585 (mmm160) REVERT: P 130 ARG cc_start: 0.6780 (OUTLIER) cc_final: 0.6264 (tpp80) REVERT: P 150 GLN cc_start: 0.7163 (tt0) cc_final: 0.6622 (tt0) REVERT: P 154 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8572 (tp30) REVERT: G 9 LYS cc_start: 0.9467 (mttp) cc_final: 0.9107 (tttp) REVERT: G 120 ASP cc_start: 0.9471 (m-30) cc_final: 0.9155 (m-30) REVERT: F 140 ASP cc_start: 0.9301 (m-30) cc_final: 0.9100 (t0) REVERT: B 213 ASP cc_start: 0.9557 (m-30) cc_final: 0.9233 (t0) REVERT: I 30 ASP cc_start: 0.9399 (t70) cc_final: 0.9139 (t0) REVERT: J 11 LYS cc_start: 0.9134 (mmmt) cc_final: 0.8803 (ptpp) REVERT: N 159 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8814 (mm-30) REVERT: E 55 ASP cc_start: 0.9090 (OUTLIER) cc_final: 0.8569 (p0) REVERT: R 85 LYS cc_start: 0.9356 (mttm) cc_final: 0.9044 (mtmm) REVERT: R 110 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8812 (mm-30) REVERT: Q 114 TYR cc_start: 0.8537 (t80) cc_final: 0.8131 (t80) REVERT: Q 126 GLU cc_start: 0.9259 (mp0) cc_final: 0.8962 (mp0) REVERT: Q 131 GLN cc_start: 0.9394 (tp40) cc_final: 0.8866 (mp10) REVERT: L 97 GLU cc_start: 0.9435 (OUTLIER) cc_final: 0.9176 (mt-10) REVERT: M 197 ASN cc_start: 0.8705 (t0) cc_final: 0.7910 (t0) REVERT: O 193 GLN cc_start: 0.9405 (mp10) cc_final: 0.9152 (mp10) REVERT: O 201 SER cc_start: 0.9322 (m) cc_final: 0.9072 (p) REVERT: T 30 ASP cc_start: 0.9346 (t0) cc_final: 0.8993 (t0) REVERT: U 13 SER cc_start: 0.9266 (t) cc_final: 0.8890 (p) REVERT: U 80 ASN cc_start: 0.9136 (t0) cc_final: 0.8186 (p0) outliers start: 31 outliers final: 20 residues processed: 356 average time/residue: 0.4578 time to fit residues: 262.0325 Evaluate side-chains 332 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 308 time to evaluate : 3.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 249 ASP Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain L residue 65 GLU Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain O residue 90 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 74 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 240 optimal weight: 4.9990 chunk 257 optimal weight: 10.0000 chunk 186 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 296 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 137 ASN D 93 HIS Q 96 HIS ** L 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 377 ASN O 90 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33367 Z= 0.167 Angle : 0.474 11.232 45352 Z= 0.229 Chirality : 0.039 0.143 4962 Planarity : 0.003 0.045 5700 Dihedral : 11.070 149.080 5273 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.87 % Allowed : 13.89 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.14), residues: 3955 helix: 2.00 (0.11), residues: 2132 sheet: 0.76 (0.26), residues: 371 loop : 0.66 (0.18), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 142 HIS 0.005 0.001 HIS C 197 PHE 0.023 0.001 PHE P 64 TYR 0.021 0.001 TYR M 170 ARG 0.008 0.000 ARG P 201 *********************** 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 338 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 309 time to evaluate : 4.184 Fit side-chains revert: symmetry clash REVERT: C 239 MET cc_start: 0.9111 (ttp) cc_final: 0.8626 (mmt) REVERT: C 287 ASP cc_start: 0.8499 (t0) cc_final: 0.8215 (t0) REVERT: C 341 GLN cc_start: 0.9208 (pp30) cc_final: 0.8856 (pp30) REVERT: P 128 ARG cc_start: 0.6988 (mmm-85) cc_final: 0.6604 (mmm160) REVERT: P 130 ARG cc_start: 0.6901 (OUTLIER) cc_final: 0.6349 (tpp80) REVERT: P 150 GLN cc_start: 0.7182 (tt0) cc_final: 0.6685 (tt0) REVERT: P 154 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8581 (tp30) REVERT: P 222 LEU cc_start: 0.8647 (tt) cc_final: 0.8309 (tt) REVERT: G 9 LYS cc_start: 0.9473 (mttp) cc_final: 0.9123 (tttt) REVERT: G 120 ASP cc_start: 0.9473 (m-30) cc_final: 0.9174 (m-30) REVERT: F 140 ASP cc_start: 0.9302 (m-30) cc_final: 0.9084 (t0) REVERT: B 213 ASP cc_start: 0.9567 (m-30) cc_final: 0.9249 (t0) REVERT: I 30 ASP cc_start: 0.9409 (t70) cc_final: 0.9168 (t0) REVERT: J 11 LYS cc_start: 0.9121 (mmmt) cc_final: 0.8790 (ptpp) REVERT: N 159 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8848 (mm-30) REVERT: E 55 ASP cc_start: 0.9083 (OUTLIER) cc_final: 0.8559 (p0) REVERT: R 85 LYS cc_start: 0.9351 (mttm) cc_final: 0.9149 (mmtm) REVERT: Q 84 GLU cc_start: 0.9371 (mt-10) cc_final: 0.9076 (mp0) REVERT: Q 114 TYR cc_start: 0.8541 (t80) cc_final: 0.8116 (t80) REVERT: Q 126 GLU cc_start: 0.9343 (mp0) cc_final: 0.8984 (mp0) REVERT: Q 131 GLN cc_start: 0.9409 (tp40) cc_final: 0.8870 (mp10) REVERT: L 97 GLU cc_start: 0.9448 (OUTLIER) cc_final: 0.9186 (mt-10) REVERT: M 197 ASN cc_start: 0.8753 (t0) cc_final: 0.7923 (t0) REVERT: O 193 GLN cc_start: 0.9395 (mp10) cc_final: 0.9141 (mp10) REVERT: O 201 SER cc_start: 0.9380 (m) cc_final: 0.9134 (p) REVERT: T 30 ASP cc_start: 0.9354 (t0) cc_final: 0.9012 (t0) REVERT: U 13 SER cc_start: 0.9279 (t) cc_final: 0.8918 (p) REVERT: U 80 ASN cc_start: 0.9105 (t0) cc_final: 0.8135 (p0) outliers start: 29 outliers final: 24 residues processed: 327 average time/residue: 0.4670 time to fit residues: 247.1681 Evaluate side-chains 330 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 303 time to evaluate : 4.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain L residue 65 GLU Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain O residue 90 HIS Chi-restraints excluded: chain S residue 28 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 9.9990 chunk 361 optimal weight: 3.9990 chunk 330 optimal weight: 10.0000 chunk 352 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 276 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 318 optimal weight: 0.9990 chunk 332 optimal weight: 6.9990 chunk 350 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 70 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33367 Z= 0.189 Angle : 0.482 11.610 45352 Z= 0.232 Chirality : 0.039 0.143 4962 Planarity : 0.003 0.045 5700 Dihedral : 11.025 149.171 5273 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.87 % Allowed : 13.77 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.14), residues: 3955 helix: 2.01 (0.11), residues: 2128 sheet: 0.69 (0.26), residues: 376 loop : 0.72 (0.18), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 142 HIS 0.012 0.001 HIS O 90 PHE 0.012 0.001 PHE A 334 TYR 0.024 0.001 TYR G 31 ARG 0.007 0.000 ARG P 201 *********************** 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 335 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 306 time to evaluate : 4.173 Fit side-chains revert: symmetry clash REVERT: C 239 MET cc_start: 0.9119 (ttp) cc_final: 0.8625 (mmt) REVERT: C 287 ASP cc_start: 0.8575 (t0) cc_final: 0.8316 (t0) REVERT: C 341 GLN cc_start: 0.9218 (pp30) cc_final: 0.8858 (pp30) REVERT: P 128 ARG cc_start: 0.6975 (mmm-85) cc_final: 0.6585 (mmm160) REVERT: P 130 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.6088 (mmm-85) REVERT: P 150 GLN cc_start: 0.7212 (tt0) cc_final: 0.6747 (tt0) REVERT: P 154 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8583 (tp30) REVERT: P 222 LEU cc_start: 0.8621 (tt) cc_final: 0.8411 (tt) REVERT: G 9 LYS cc_start: 0.9474 (mttp) cc_final: 0.9116 (tttt) REVERT: G 120 ASP cc_start: 0.9474 (m-30) cc_final: 0.9168 (m-30) REVERT: F 140 ASP cc_start: 0.9307 (m-30) cc_final: 0.9093 (t0) REVERT: B 213 ASP cc_start: 0.9569 (m-30) cc_final: 0.9254 (t0) REVERT: I 30 ASP cc_start: 0.9404 (t70) cc_final: 0.9158 (t0) REVERT: J 11 LYS cc_start: 0.9121 (mmmt) cc_final: 0.8798 (ptpp) REVERT: N 159 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8860 (mm-30) REVERT: E 55 ASP cc_start: 0.9071 (OUTLIER) cc_final: 0.8555 (p0) REVERT: R 85 LYS cc_start: 0.9371 (mttm) cc_final: 0.9080 (mtmm) REVERT: R 110 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8886 (mm-30) REVERT: Q 84 GLU cc_start: 0.9360 (mt-10) cc_final: 0.9038 (mp0) REVERT: Q 114 TYR cc_start: 0.8552 (t80) cc_final: 0.8156 (t80) REVERT: Q 126 GLU cc_start: 0.9346 (mp0) cc_final: 0.8985 (mp0) REVERT: Q 131 GLN cc_start: 0.9409 (tp40) cc_final: 0.8895 (mp10) REVERT: L 97 GLU cc_start: 0.9415 (OUTLIER) cc_final: 0.9035 (mt-10) REVERT: M 197 ASN cc_start: 0.8741 (t0) cc_final: 0.7871 (t0) REVERT: M 339 ARG cc_start: 0.9301 (OUTLIER) cc_final: 0.9076 (ttm-80) REVERT: O 193 GLN cc_start: 0.9404 (mp10) cc_final: 0.9164 (mp10) REVERT: O 201 SER cc_start: 0.9398 (m) cc_final: 0.9146 (p) REVERT: T 30 ASP cc_start: 0.9355 (t0) cc_final: 0.9016 (t0) REVERT: U 13 SER cc_start: 0.9280 (t) cc_final: 0.8915 (p) REVERT: U 80 ASN cc_start: 0.9118 (t0) cc_final: 0.8874 (t0) outliers start: 29 outliers final: 22 residues processed: 326 average time/residue: 0.4540 time to fit residues: 239.5285 Evaluate side-chains 331 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 305 time to evaluate : 3.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain L residue 65 GLU Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 339 ARG Chi-restraints excluded: chain O residue 90 HIS Chi-restraints excluded: chain S residue 28 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 9.9990 chunk 372 optimal weight: 7.9990 chunk 227 optimal weight: 0.5980 chunk 176 optimal weight: 10.0000 chunk 258 optimal weight: 8.9990 chunk 390 optimal weight: 1.9990 chunk 359 optimal weight: 3.9990 chunk 310 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 240 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 HIS ** L 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9160 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 33367 Z= 0.295 Angle : 0.545 16.329 45352 Z= 0.255 Chirality : 0.041 0.145 4962 Planarity : 0.004 0.046 5700 Dihedral : 11.188 149.998 5273 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.11 % Allowed : 13.65 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.14), residues: 3955 helix: 1.96 (0.11), residues: 2126 sheet: 0.68 (0.26), residues: 371 loop : 0.71 (0.18), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 142 HIS 0.008 0.001 HIS C 197 PHE 0.016 0.001 PHE N 240 TYR 0.027 0.001 TYR M 170 ARG 0.007 0.000 ARG P 201 ********************** 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 340 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 303 time to evaluate : 3.902 Fit side-chains revert: symmetry clash REVERT: C 239 MET cc_start: 0.9147 (ttp) cc_final: 0.8635 (mmt) REVERT: C 272 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8745 (mm-30) REVERT: C 287 ASP cc_start: 0.8649 (t0) cc_final: 0.8388 (t0) REVERT: C 341 GLN cc_start: 0.9269 (pp30) cc_final: 0.8869 (pp30) REVERT: P 128 ARG cc_start: 0.7026 (mmm-85) cc_final: 0.6679 (mmm160) REVERT: P 130 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6395 (tpp80) REVERT: P 150 GLN cc_start: 0.7214 (tt0) cc_final: 0.6647 (tt0) REVERT: P 154 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8528 (tm-30) REVERT: P 222 LEU cc_start: 0.8619 (tt) cc_final: 0.8403 (tt) REVERT: G 9 LYS cc_start: 0.9474 (mttp) cc_final: 0.9125 (tttt) REVERT: G 120 ASP cc_start: 0.9476 (m-30) cc_final: 0.9173 (m-30) REVERT: I 30 ASP cc_start: 0.9430 (t70) cc_final: 0.9181 (t0) REVERT: J 11 LYS cc_start: 0.9141 (mmmt) cc_final: 0.8825 (ptpp) REVERT: N 159 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8926 (mm-30) REVERT: E 55 ASP cc_start: 0.9092 (OUTLIER) cc_final: 0.8644 (p0) REVERT: R 85 LYS cc_start: 0.9424 (mttm) cc_final: 0.9147 (mtmm) REVERT: Q 84 GLU cc_start: 0.9357 (mt-10) cc_final: 0.9036 (mp0) REVERT: Q 114 TYR cc_start: 0.8576 (t80) cc_final: 0.8224 (t80) REVERT: Q 126 GLU cc_start: 0.9366 (mp0) cc_final: 0.9001 (mp0) REVERT: Q 131 GLN cc_start: 0.9430 (tp40) cc_final: 0.8884 (mp10) REVERT: L 97 GLU cc_start: 0.9437 (OUTLIER) cc_final: 0.9024 (mt-10) REVERT: M 197 ASN cc_start: 0.8765 (t0) cc_final: 0.7844 (t0) REVERT: M 339 ARG cc_start: 0.9318 (OUTLIER) cc_final: 0.9067 (ttm-80) REVERT: O 193 GLN cc_start: 0.9438 (mp10) cc_final: 0.9175 (mp10) REVERT: O 201 SER cc_start: 0.9411 (m) cc_final: 0.9166 (p) REVERT: T 30 ASP cc_start: 0.9379 (t0) cc_final: 0.9038 (t0) REVERT: U 13 SER cc_start: 0.9319 (t) cc_final: 0.9106 (t) REVERT: U 80 ASN cc_start: 0.9152 (t0) cc_final: 0.8902 (t0) outliers start: 37 outliers final: 30 residues processed: 328 average time/residue: 0.4580 time to fit residues: 243.2074 Evaluate side-chains 332 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 298 time to evaluate : 3.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 90 ASN Chi-restraints excluded: chain L residue 65 GLU Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 339 ARG Chi-restraints excluded: chain S residue 28 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 8.9990 chunk 331 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 286 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 311 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 319 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 HIS ** L 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 408 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.067235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.053299 restraints weight = 80365.243| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.04 r_work: 0.2605 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33367 Z= 0.163 Angle : 0.490 12.890 45352 Z= 0.235 Chirality : 0.039 0.142 4962 Planarity : 0.003 0.046 5700 Dihedral : 11.021 149.006 5273 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.99 % Allowed : 13.65 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.14), residues: 3955 helix: 2.00 (0.11), residues: 2110 sheet: 0.62 (0.26), residues: 376 loop : 0.73 (0.18), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 142 HIS 0.007 0.001 HIS Q 96 PHE 0.013 0.001 PHE A 334 TYR 0.022 0.001 TYR M 170 ARG 0.009 0.000 ARG F 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6980.84 seconds wall clock time: 129 minutes 23.01 seconds (7763.01 seconds total)