Starting phenix.real_space_refine on Thu Feb 22 02:13:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abi_15322/02_2024/8abi_15322_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abi_15322/02_2024/8abi_15322.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abi_15322/02_2024/8abi_15322_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abi_15322/02_2024/8abi_15322_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abi_15322/02_2024/8abi_15322_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abi_15322/02_2024/8abi_15322.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abi_15322/02_2024/8abi_15322.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abi_15322/02_2024/8abi_15322_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abi_15322/02_2024/8abi_15322_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 8 7.16 5 P 30 5.49 5 S 102 5.16 5 C 21039 2.51 5 N 5300 2.21 5 O 6069 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 4": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P GLU 137": "OE1" <-> "OE2" Residue "P GLU 178": "OE1" <-> "OE2" Residue "P GLU 213": "OE1" <-> "OE2" Residue "P PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 220": "OE1" <-> "OE2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G ARG 61": "NH1" <-> "NH2" Residue "G GLU 66": "OE1" <-> "OE2" Residue "G ARG 70": "NH1" <-> "NH2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G GLU 96": "OE1" <-> "OE2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F GLU 121": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B GLU 350": "OE1" <-> "OE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "D ARG 189": "NH1" <-> "NH2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "D TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D ARG 321": "NH1" <-> "NH2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "J TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 4": "NH1" <-> "NH2" Residue "N ARG 70": "NH1" <-> "NH2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "N ARG 110": "NH1" <-> "NH2" Residue "N PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 283": "NH1" <-> "NH2" Residue "N ARG 310": "NH1" <-> "NH2" Residue "N ARG 314": "NH1" <-> "NH2" Residue "N TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "R GLU 12": "OE1" <-> "OE2" Residue "R GLU 50": "OE1" <-> "OE2" Residue "R GLU 51": "OE1" <-> "OE2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R ARG 61": "NH1" <-> "NH2" Residue "R GLU 66": "OE1" <-> "OE2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R ARG 73": "NH1" <-> "NH2" Residue "R ARG 76": "NH1" <-> "NH2" Residue "R GLU 96": "OE1" <-> "OE2" Residue "R GLU 110": "OE1" <-> "OE2" Residue "R GLU 123": "OE1" <-> "OE2" Residue "Q GLU 88": "OE1" <-> "OE2" Residue "Q GLU 118": "OE1" <-> "OE2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "Q GLU 126": "OE1" <-> "OE2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "L GLU 141": "OE1" <-> "OE2" Residue "L ARG 188": "NH1" <-> "NH2" Residue "L GLU 354": "OE1" <-> "OE2" Residue "L ARG 384": "NH1" <-> "NH2" Residue "L GLU 424": "OE1" <-> "OE2" Residue "L GLU 457": "OE1" <-> "OE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M GLU 78": "OE1" <-> "OE2" Residue "M GLU 117": "OE1" <-> "OE2" Residue "M ARG 140": "NH1" <-> "NH2" Residue "M GLU 150": "OE1" <-> "OE2" Residue "M ARG 234": "NH1" <-> "NH2" Residue "M GLU 313": "OE1" <-> "OE2" Residue "M GLU 350": "OE1" <-> "OE2" Residue "M GLU 376": "OE1" <-> "OE2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "O ARG 132": "NH1" <-> "NH2" Residue "O ARG 136": "NH1" <-> "NH2" Residue "O GLU 164": "OE1" <-> "OE2" Residue "O ARG 170": "NH1" <-> "NH2" Residue "O ARG 189": "NH1" <-> "NH2" Residue "O ARG 207": "NH1" <-> "NH2" Residue "O TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 250": "NH1" <-> "NH2" Residue "O GLU 260": "OE1" <-> "OE2" Residue "O ARG 289": "NH1" <-> "NH2" Residue "O ARG 321": "NH1" <-> "NH2" Residue "S PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 34": "OE1" <-> "OE2" Residue "U TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32548 Number of models: 1 Model: "" Number of chains: 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: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 339 Unusual residues: {'AWB': 1, 'CDL': 3, 'HEM': 2, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 190 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 50 Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "J" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 293 Unusual residues: {'AWB': 1, 'CDL': 2, 'HEM': 2, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 136 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "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 31.387 47.893 26.800 1.00345.56 S ATOM 4207 SG CYS P 187 33.675 46.143 24.220 1.00298.67 S Time building chain proxies: 17.10, per 1000 atoms: 0.53 Number of scatterers: 32548 At special positions: 0 Unit cell: (118.833, 129.636, 165.369, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 8 26.01 S 102 16.00 P 30 15.00 O 6069 8.00 N 5300 7.00 C 21039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS P 173 " - pdb=" SG CYS P 189 " distance=2.04 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.06 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.06 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.39 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 301 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 170 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 190 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 187 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 168 " Number of angles added : 3 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7486 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 184 helices and 15 sheets defined 54.2% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.37 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: 3.920A pdb=" N PHE C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY C 33 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR C 46 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.636A 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: 3.734A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 135 removed outlier: 4.154A pdb=" N VAL C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 153 removed outlier: 4.037A pdb=" N VAL C 151 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER C 152 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 4.291A 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: 4.171A pdb=" N THR C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 246 removed outlier: 6.800A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.768A 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: 3.813A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Proline residue: C 306 - end of helix Processing helix chain 'C' and resid 320 through 340 Processing helix chain 'C' and resid 348 through 364 removed outlier: 4.092A pdb=" N PHE C 363 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 382 Processing helix chain 'P' and resid 59 through 91 removed outlier: 3.630A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN P 90 " --> pdb=" O ASP P 86 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N MET P 91 " --> pdb=" O PHE P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 100 Processing helix chain 'P' and resid 132 through 138 Processing helix chain 'P' and resid 152 through 155 No H-bonds generated for 'chain 'P' and resid 152 through 155' Processing helix chain 'G' and resid 4 through 16 Processing helix chain 'G' and resid 18 through 35 Proline residue: G 26 - end of helix Processing helix chain 'G' and resid 37 through 40 Processing helix chain 'G' and resid 44 through 47 Processing helix chain 'G' and resid 53 through 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: 3.667A pdb=" N ASN G 121 " --> pdb=" O ASP G 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 88 Processing helix chain 'F' and resid 92 through 110 Processing helix chain 'F' and resid 124 through 137 Processing helix chain 'F' and resid 139 through 145 removed outlier: 3.586A pdb=" N VAL F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.552A pdb=" N HIS A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 4.161A 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: 3.835A pdb=" N VAL A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Proline residue: A 124 - end of helix removed outlier: 3.875A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 154 removed outlier: 3.998A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.572A pdb=" N THR A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 206 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.521A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.963A 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: 3.659A 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: 3.594A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.447A 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: 3.622A pdb=" N ASP A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.947A 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: 3.597A pdb=" N LYS B 116 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 4.218A 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: 3.517A pdb=" N THR B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.736A 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: 3.703A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 383 through 394 Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'D' and resid 87 through 90 No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 124 through 126 No H-bonds generated for 'chain 'D' and resid 124 through 126' Processing helix chain 'D' and resid 135 through 138 Processing helix chain 'D' and resid 145 through 153 Processing helix chain 'D' and resid 185 through 192 Processing helix chain 'D' and resid 210 through 218 removed outlier: 3.554A pdb=" N PHE D 215 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 282 Processing helix chain 'D' and resid 286 through 319 Proline residue: D 317 - end of helix Processing helix chain 'H' and resid 40 through 80 removed outlier: 4.344A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.745A 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: 5.032A pdb=" N HIS I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 49 removed outlier: 3.502A pdb=" N LYS J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 3.563A 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: 3.923A pdb=" N PHE N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY N 33 " --> pdb=" O TRP N 30 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR N 46 " --> pdb=" O GLN N 43 " (cutoff:3.500A) removed outlier: 3.639A 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: 3.742A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 135 removed outlier: 4.180A pdb=" N VAL N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 138 through 153 removed outlier: 4.148A pdb=" N VAL N 151 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER N 152 " --> pdb=" O CYS N 148 " (cutoff:3.500A) removed outlier: 4.264A 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: 4.156A pdb=" N THR N 203 " --> pdb=" O ILE N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 246 removed outlier: 6.806A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR N 232 " --> pdb=" O LYS N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 254 through 257 Processing helix chain 'N' and resid 273 through 284 Proline residue: N 277 - end of helix Processing helix chain 'N' and resid 288 through 308 removed outlier: 3.805A pdb=" N ILE N 299 " --> pdb=" O MET N 295 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU N 302 " --> pdb=" O ALA N 298 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU N 303 " --> pdb=" O ILE N 299 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE N 304 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 4.007A 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: 4.099A pdb=" N PHE N 363 " --> pdb=" O TYR N 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 366 through 382 Processing helix chain 'E' and resid 59 through 91 removed outlier: 3.633A pdb=" N SER E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 4.871A 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: 3.675A 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: 3.595A pdb=" N VAL Q 145 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 72 through 79 removed outlier: 3.522A pdb=" N HIS L 78 " --> pdb=" O HIS L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 99 Processing helix chain 'L' and resid 120 through 135 removed outlier: 3.830A pdb=" N VAL L 123 " --> pdb=" O LYS L 120 " (cutoff:3.500A) Proline residue: L 124 - end of helix removed outlier: 3.874A pdb=" N VAL L 127 " --> pdb=" O PRO L 124 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU L 134 " --> pdb=" O ALA L 131 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN L 135 " --> pdb=" O ASP L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 154 removed outlier: 3.994A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.768A 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 191 No H-bonds generated for 'chain 'L' and resid 188 through 191' Processing helix chain 'L' and resid 196 through 206 Processing helix chain 'L' and resid 209 through 211 No H-bonds generated for 'chain 'L' and resid 209 through 211' Processing helix chain 'L' and resid 222 through 232 Processing helix chain 'L' and resid 294 through 304 removed outlier: 3.525A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 312 through 316 removed outlier: 3.984A 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: 3.658A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 395 removed outlier: 3.650A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.448A 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: 3.615A pdb=" N ASP L 468 " --> pdb=" O ARG L 464 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET L 469 " --> pdb=" O ILE L 465 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 47 No H-bonds generated for 'chain 'M' and resid 45 through 47' Processing helix chain 'M' and resid 53 through 59 Processing helix chain 'M' and resid 70 through 79 Processing helix chain 'M' and resid 101 through 117 Proline residue: M 105 - end of helix removed outlier: 3.632A pdb=" N VAL M 108 " --> pdb=" O PRO M 105 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS M 116 " --> pdb=" O ASN M 113 " (cutoff:3.500A) removed outlier: 4.221A 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: 3.522A pdb=" N THR M 209 " --> pdb=" O GLN M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 263 removed outlier: 3.735A 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: 3.879A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 375 through 377 No H-bonds generated for 'chain 'M' and resid 375 through 377' Processing helix chain 'M' and resid 383 through 394 Processing helix chain 'M' and resid 407 through 409 No H-bonds generated for 'chain 'M' and resid 407 through 409' Processing helix chain 'M' and resid 413 through 415 No H-bonds generated for 'chain 'M' and resid 413 through 415' Processing helix chain 'O' and resid 87 through 90 No H-bonds generated for 'chain 'O' and resid 87 through 90' Processing helix chain 'O' and resid 110 through 122 Processing helix chain 'O' and resid 124 through 126 No H-bonds generated for 'chain 'O' and resid 124 through 126' Processing helix chain 'O' and resid 135 through 138 Processing helix chain 'O' and resid 145 through 153 Processing helix chain 'O' and resid 185 through 192 Processing helix chain 'O' and resid 210 through 218 removed outlier: 3.556A pdb=" N PHE O 215 " --> pdb=" O ASP O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 267 through 282 Processing helix chain 'O' and resid 286 through 319 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 40 through 80 removed outlier: 4.331A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL S 59 " --> pdb=" O GLN S 55 " (cutoff:3.500A) Proline residue: S 62 - end of helix Processing helix chain 'S' and resid 86 through 92 Processing helix chain 'T' and resid 5 through 11 Processing helix chain 'T' and resid 15 through 44 Processing helix chain 'T' and resid 50 through 56 removed outlier: 5.014A pdb=" N HIS T 55 " --> pdb=" O LYS T 51 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LYS T 56 " --> pdb=" O ASP T 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 49 removed outlier: 3.552A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.551A 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: 3.894A pdb=" N LYS P 114 " --> pdb=" O HIS P 129 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'P' and resid 185 through 187 Processing sheet with id= E, first strand: chain 'A' and resid 31 through 34 Processing sheet with id= F, first strand: chain 'A' and resid 266 through 271 Processing sheet with id= G, first strand: chain 'B' and resid 16 through 20 removed outlier: 4.110A 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: 3.601A 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: 4.096A 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: 3.581A pdb=" N ASN M 241 " --> pdb=" O GLY M 308 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'O' and resid 156 through 158 1580 hydrogen bonds defined for protein. 4317 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.89 Time building geometry restraints manager: 14.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.40: 13579 1.40 - 1.61: 19582 1.61 - 1.82: 170 1.82 - 2.03: 26 2.03 - 2.24: 18 Bond restraints: 33375 Sorted by residual: bond pdb=" N ALA T 4 " pdb=" CA ALA T 4 " ideal model delta sigma weight residual 1.458 1.607 -0.149 1.90e-02 2.77e+03 6.13e+01 bond pdb=" N ALA I 4 " pdb=" CA ALA I 4 " ideal model delta sigma weight residual 1.458 1.601 -0.143 1.90e-02 2.77e+03 5.64e+01 bond pdb=" C2C HEC O 401 " pdb=" C3C HEC O 401 " ideal model delta sigma weight residual 1.334 1.454 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" N TYR H 9 " pdb=" CA TYR H 9 " ideal model delta sigma weight residual 1.458 1.571 -0.113 1.90e-02 2.77e+03 3.54e+01 bond pdb=" C3B HEC O 401 " pdb=" CAB HEC O 401 " ideal model delta sigma weight residual 1.544 1.429 0.115 2.00e-02 2.50e+03 3.29e+01 ... (remaining 33370 not shown) Histogram of bond angle deviations from ideal: 85.03 - 103.83: 690 103.83 - 122.63: 39281 122.63 - 141.44: 5383 141.44 - 160.24: 0 160.24 - 179.04: 12 Bond angle restraints: 45366 Sorted by residual: angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 91.84 12.49 1.14e+00 7.69e-01 1.20e+02 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 91.92 12.41 1.20e+00 6.94e-01 1.07e+02 angle pdb=" CG ARG M 90 " pdb=" CD ARG M 90 " pdb=" NE ARG M 90 " ideal model delta sigma weight residual 112.00 93.81 18.19 2.20e+00 2.07e-01 6.84e+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 85.06 -9.40 1.14e+00 7.69e-01 6.80e+01 angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.14 98.38 12.76 1.56e+00 4.11e-01 6.69e+01 ... (remaining 45361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.04: 18804 32.04 - 64.07: 1031 64.07 - 96.11: 98 96.11 - 128.14: 1 128.14 - 160.18: 3 Dihedral angle restraints: 19937 sinusoidal: 8318 harmonic: 11619 Sorted by residual: dihedral pdb=" C GLN B 215 " pdb=" N GLN B 215 " pdb=" CA GLN B 215 " pdb=" CB GLN B 215 " ideal model delta harmonic sigma weight residual -122.60 -105.29 -17.31 0 2.50e+00 1.60e-01 4.80e+01 dihedral pdb=" C GLN M 215 " pdb=" N GLN M 215 " pdb=" CA GLN M 215 " pdb=" CB GLN M 215 " ideal model delta harmonic sigma weight residual -122.60 -105.41 -17.19 0 2.50e+00 1.60e-01 4.73e+01 dihedral pdb=" C GLU O 283 " pdb=" N GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta harmonic sigma weight residual -122.60 -106.34 -16.26 0 2.50e+00 1.60e-01 4.23e+01 ... (remaining 19934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.235: 4726 0.235 - 0.469: 217 0.469 - 0.704: 5 0.704 - 0.938: 2 0.938 - 1.173: 2 Chirality restraints: 4952 Sorted by residual: chirality pdb=" CB4 CDL C 505 " pdb=" CB3 CDL C 505 " pdb=" CB6 CDL C 505 " pdb=" OB6 CDL C 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.40 -1.17 2.00e-01 2.50e+01 3.44e+01 chirality pdb=" CB4 CDL C 508 " pdb=" CB3 CDL C 508 " pdb=" CB6 CDL C 508 " pdb=" OB6 CDL C 508 " both_signs ideal model delta sigma weight residual False -2.57 -1.53 -1.05 2.00e-01 2.50e+01 2.75e+01 chirality pdb=" CB4 CDL N 507 " pdb=" CB3 CDL N 507 " pdb=" CB6 CDL N 507 " pdb=" OB6 CDL N 507 " both_signs ideal model delta sigma weight residual False -2.57 -1.66 -0.92 2.00e-01 2.50e+01 2.11e+01 ... (remaining 4949 not shown) Planarity restraints: 5712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 AWB N 506 " -0.007 2.00e-02 2.50e+03 2.44e-01 5.95e+02 pdb=" C21 AWB N 506 " 0.400 2.00e-02 2.50e+03 pdb=" N1 AWB N 506 " -0.176 2.00e-02 2.50e+03 pdb=" O5 AWB N 506 " -0.217 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 AWB C 506 " 0.023 2.00e-02 2.50e+03 2.43e-01 5.92e+02 pdb=" C21 AWB C 506 " -0.402 2.00e-02 2.50e+03 pdb=" N1 AWB C 506 " 0.153 2.00e-02 2.50e+03 pdb=" O5 AWB C 506 " 0.227 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEC D 401 " -0.001 2.00e-02 2.50e+03 3.03e-02 2.07e+01 pdb=" C1B HEC D 401 " 0.020 2.00e-02 2.50e+03 pdb=" C2B HEC D 401 " 0.030 2.00e-02 2.50e+03 pdb=" C3B HEC D 401 " 0.004 2.00e-02 2.50e+03 pdb=" C4B HEC D 401 " 0.005 2.00e-02 2.50e+03 pdb=" CAB HEC D 401 " -0.056 2.00e-02 2.50e+03 pdb=" CHB HEC D 401 " -0.051 2.00e-02 2.50e+03 pdb=" CHC HEC D 401 " 0.023 2.00e-02 2.50e+03 pdb=" CMB HEC D 401 " 0.027 2.00e-02 2.50e+03 ... (remaining 5709 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 288 2.63 - 3.19: 29082 3.19 - 3.76: 54244 3.76 - 4.33: 80259 4.33 - 4.90: 122452 Nonbonded interactions: 286325 Sorted by model distance: nonbonded pdb=" NE2 HIS C 183 " pdb="FE HEM C 501 " model vdw 2.058 3.080 nonbonded pdb=" NE2 HIS N 183 " pdb="FE HEM N 501 " model vdw 2.067 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.100 2.520 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.165 3.080 nonbonded pdb=" NE2 HIS C 197 " pdb="FE HEM C 502 " model vdw 2.207 3.080 ... (remaining 286320 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 or resid 506 throug \ h 507)) selection = (chain 'N' and (resid 1 through 383 or resid 501 through 503 or resid 506 throug \ h 507)) } ncs_group { reference = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = (chain 'H' and resid 9 through 93) selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = (chain 'J' and resid 8 through 82) selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.260 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: 0.000 Extract box with map and model: 10.650 Check model and map are aligned: 0.480 Set scattering table: 0.330 Process input model: 90.570 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 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 0.203 33375 Z= 0.735 Angle : 1.826 18.191 45366 Z= 1.139 Chirality : 0.120 1.173 4952 Planarity : 0.009 0.244 5712 Dihedral : 18.406 160.181 12436 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.65 % Favored : 97.32 % Rotamer: Outliers : 3.82 % Allowed : 8.45 % Favored : 87.73 % Cbeta Deviations : 1.55 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.12), residues: 3955 helix: -1.18 (0.09), residues: 2122 sheet: 0.13 (0.26), residues: 347 loop : -0.76 (0.16), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.009 TRP A 474 HIS 0.026 0.005 HIS Q 92 PHE 0.053 0.008 PHE B 107 TYR 0.056 0.009 TYR G 101 ARG 0.031 0.003 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 425 time to evaluate : 4.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 160 ASP cc_start: 0.9311 (m-30) cc_final: 0.8967 (m-30) REVERT: P 126 PHE cc_start: 0.7837 (m-10) cc_final: 0.6790 (m-10) REVERT: P 147 ARG cc_start: 0.4721 (OUTLIER) cc_final: 0.3563 (mtp180) REVERT: P 196 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7001 (mt) REVERT: G 50 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8837 (pm20) REVERT: F 138 THR cc_start: 0.7409 (m) cc_final: 0.7057 (m) REVERT: A 91 GLN cc_start: 0.8922 (tp40) cc_final: 0.8518 (tp40) REVERT: A 144 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8414 (mt) REVERT: A 205 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8444 (tm-30) REVERT: B 251 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8463 (pm20) REVERT: B 268 SER cc_start: 0.7696 (m) cc_final: 0.7287 (p) REVERT: D 164 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8624 (pm20) REVERT: I 35 THR cc_start: 0.9051 (m) cc_final: 0.8778 (p) REVERT: I 38 ASP cc_start: 0.8821 (m-30) cc_final: 0.8541 (m-30) REVERT: J 10 LYS cc_start: 0.9201 (tttm) cc_final: 0.8987 (tptt) REVERT: J 13 SER cc_start: 0.8632 (t) cc_final: 0.8355 (p) REVERT: N 139 MET cc_start: 0.8947 (mmm) cc_final: 0.8727 (tpt) REVERT: N 197 HIS cc_start: 0.9490 (OUTLIER) cc_final: 0.8647 (p-80) REVERT: N 250 LYS cc_start: 0.8440 (ttmt) cc_final: 0.8173 (ttpt) REVERT: R 123 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8363 (tm-30) REVERT: Q 109 GLN cc_start: 0.8369 (mt0) cc_final: 0.7913 (mp10) REVERT: Q 140 ASP cc_start: 0.9027 (m-30) cc_final: 0.8627 (m-30) REVERT: L 35 LEU cc_start: 0.8331 (mt) cc_final: 0.8126 (mp) REVERT: L 91 GLN cc_start: 0.8647 (tp40) cc_final: 0.8348 (tp40) REVERT: O 164 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8813 (pm20) REVERT: O 223 ASP cc_start: 0.8437 (m-30) cc_final: 0.8217 (p0) REVERT: S 71 THR cc_start: 0.8767 (m) cc_final: 0.8458 (p) REVERT: S 86 ARG cc_start: 0.8454 (mtm180) cc_final: 0.8218 (mtp85) REVERT: S 87 HIS cc_start: 0.8315 (m-70) cc_final: 0.7666 (m-70) REVERT: U 55 ARG cc_start: 0.8450 (ttm-80) cc_final: 0.8076 (ttm170) outliers start: 127 outliers final: 9 residues processed: 521 average time/residue: 1.5432 time to fit residues: 941.8784 Evaluate side-chains 237 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 222 time to evaluate : 3.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 147 ARG Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain R residue 17 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain L residue 378 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 5.9990 chunk 297 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 200 optimal weight: 0.4980 chunk 158 optimal weight: 7.9990 chunk 307 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 228 optimal weight: 7.9990 chunk 355 optimal weight: 10.0000 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN C 22 GLN C 73 ASN C 173 ASN C 177 GLN C 332 ASN P 85 GLN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 ASN A 135 GLN A 222 HIS A 332 ASN A 371 ASN B 87 HIS ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN B 316 GLN D 118 GLN D 193 GLN H 42 HIS N 14 ASN N 22 GLN N 177 GLN N 332 ASN Q 131 GLN Q 132 HIS Q 135 ASN ** L 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 196 ASN ** L 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 332 ASN L 371 ASN M 87 HIS ** M 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 GLN M 197 ASN M 215 GLN O 90 HIS O 118 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 33375 Z= 0.254 Angle : 0.675 17.931 45366 Z= 0.326 Chirality : 0.043 0.216 4952 Planarity : 0.005 0.042 5712 Dihedral : 13.840 158.184 5268 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.23 % Allowed : 13.08 % Favored : 84.69 % 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: 0.46 (0.13), residues: 3955 helix: 0.62 (0.11), residues: 2143 sheet: 0.59 (0.27), residues: 355 loop : -0.05 (0.17), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 156 HIS 0.013 0.001 HIS F 96 PHE 0.020 0.002 PHE A 334 TYR 0.025 0.002 TYR P 194 ARG 0.010 0.001 ARG L 146 *********************** 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 307 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 233 time to evaluate : 3.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.8951 (ttp) cc_final: 0.8751 (ttm) REVERT: C 160 ASP cc_start: 0.9338 (m-30) cc_final: 0.9102 (m-30) REVERT: P 126 PHE cc_start: 0.7646 (m-10) cc_final: 0.6934 (m-10) REVERT: P 147 ARG cc_start: 0.4836 (OUTLIER) cc_final: 0.3333 (ttt180) REVERT: P 202 ARG cc_start: 0.8758 (ttp80) cc_final: 0.8491 (ttm110) REVERT: P 222 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8432 (tp) REVERT: F 84 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8709 (mm-30) REVERT: A 231 LYS cc_start: 0.9206 (tttt) cc_final: 0.8960 (tptp) REVERT: A 275 MET cc_start: 0.8692 (ttm) cc_final: 0.8440 (ttm) REVERT: B 306 ILE cc_start: 0.8822 (mt) cc_final: 0.8617 (mp) REVERT: D 164 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8398 (pm20) REVERT: D 166 ASN cc_start: 0.8514 (m110) cc_final: 0.8011 (m110) REVERT: H 78 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8333 (pp20) REVERT: J 10 LYS cc_start: 0.9219 (tttm) cc_final: 0.8909 (tptt) REVERT: J 13 SER cc_start: 0.8756 (t) cc_final: 0.8453 (p) REVERT: J 74 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7106 (mp0) REVERT: N 283 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8432 (mtm110) REVERT: E 55 ASP cc_start: 0.9091 (p0) cc_final: 0.8875 (p0) REVERT: E 96 ASP cc_start: 0.9003 (p0) cc_final: 0.8753 (p0) REVERT: R 123 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8614 (tm-30) REVERT: Q 130 LEU cc_start: 0.9341 (tp) cc_final: 0.9091 (tp) REVERT: L 91 GLN cc_start: 0.8735 (tp40) cc_final: 0.8416 (tp40) REVERT: M 269 MET cc_start: 0.8528 (ptm) cc_final: 0.7723 (ppp) REVERT: M 334 GLU cc_start: 0.9372 (tp30) cc_final: 0.9018 (mm-30) REVERT: S 51 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.6533 (ptm-80) REVERT: S 68 TYR cc_start: 0.8493 (t80) cc_final: 0.8153 (t80) REVERT: S 91 LYS cc_start: 0.8377 (mttm) cc_final: 0.8082 (mmtm) REVERT: U 73 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7356 (ptt-90) outliers start: 74 outliers final: 15 residues processed: 286 average time/residue: 1.6563 time to fit residues: 557.1341 Evaluate side-chains 209 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 188 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 147 ARG Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain J residue 74 GLU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain L residue 223 ASP Chi-restraints excluded: chain L residue 378 SER Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.0070 chunk 110 optimal weight: 2.9990 chunk 296 optimal weight: 10.0000 chunk 242 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 356 optimal weight: 5.9990 chunk 385 optimal weight: 10.0000 chunk 317 optimal weight: 5.9990 chunk 353 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 286 optimal weight: 30.0000 overall best weight: 2.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN F 132 HIS A 364 HIS B 92 HIS D 193 GLN N 138 GLN N 341 GLN N 343 HIS R 84 HIS L 136 HIS ** M 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 316 GLN S 77 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 33375 Z= 0.290 Angle : 0.673 32.972 45366 Z= 0.306 Chirality : 0.043 0.221 4952 Planarity : 0.004 0.061 5712 Dihedral : 12.475 146.848 5247 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.53 % Allowed : 13.23 % Favored : 84.24 % 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: 1.10 (0.13), residues: 3955 helix: 1.15 (0.11), residues: 2139 sheet: 0.65 (0.27), residues: 359 loop : 0.31 (0.17), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 280 HIS 0.018 0.001 HIS F 96 PHE 0.018 0.002 PHE F 94 TYR 0.019 0.002 TYR L 444 ARG 0.010 0.001 ARG P 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 200 time to evaluate : 3.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.8971 (ttp) cc_final: 0.8755 (ttm) REVERT: C 160 ASP cc_start: 0.9327 (m-30) cc_final: 0.9120 (m-30) REVERT: P 126 PHE cc_start: 0.8007 (m-10) cc_final: 0.7424 (m-10) REVERT: P 216 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7907 (t80) REVERT: P 222 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8365 (tp) REVERT: F 84 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8698 (mm-30) REVERT: F 88 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8672 (mp0) REVERT: F 95 LYS cc_start: 0.8339 (tptt) cc_final: 0.8027 (tppt) REVERT: F 126 GLU cc_start: 0.8511 (mp0) cc_final: 0.7843 (mm-30) REVERT: B 58 GLU cc_start: 0.9394 (OUTLIER) cc_final: 0.9056 (tt0) REVERT: B 183 ARG cc_start: 0.9415 (OUTLIER) cc_final: 0.9209 (mmt90) REVERT: H 78 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8503 (pp20) REVERT: J 10 LYS cc_start: 0.9312 (tttm) cc_final: 0.8935 (tptt) REVERT: N 283 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8029 (mtt90) REVERT: N 341 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8883 (pp30) REVERT: N 365 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9062 (mp) REVERT: E 54 LYS cc_start: 0.9237 (tppt) cc_final: 0.8888 (tttt) REVERT: E 55 ASP cc_start: 0.9200 (p0) cc_final: 0.8911 (p0) REVERT: E 96 ASP cc_start: 0.9169 (p0) cc_final: 0.8905 (p0) REVERT: R 123 GLU cc_start: 0.8985 (tm-30) cc_final: 0.8758 (tm-30) REVERT: Q 99 ASP cc_start: 0.8710 (m-30) cc_final: 0.8206 (p0) REVERT: L 87 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.8031 (ptp-170) REVERT: O 164 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8793 (pm20) REVERT: S 51 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.6467 (ptm-80) REVERT: S 75 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8735 (tm-30) REVERT: S 76 LYS cc_start: 0.8954 (tptm) cc_final: 0.8676 (tppt) REVERT: S 78 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8404 (tm-30) outliers start: 84 outliers final: 18 residues processed: 264 average time/residue: 1.6437 time to fit residues: 509.3527 Evaluate side-chains 199 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 171 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain N residue 147 ILE Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain N residue 341 GLN Chi-restraints excluded: chain N residue 365 ILE Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 386 LEU Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 75 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 3.9990 chunk 268 optimal weight: 8.9990 chunk 185 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 239 optimal weight: 6.9990 chunk 357 optimal weight: 8.9990 chunk 378 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 339 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 45 ASN G 84 HIS A 50 GLN D 193 GLN I 49 GLN N 341 GLN N 343 HIS R 45 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 33375 Z= 0.364 Angle : 0.642 17.027 45366 Z= 0.304 Chirality : 0.043 0.175 4952 Planarity : 0.004 0.046 5712 Dihedral : 12.363 147.800 5238 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.26 % Allowed : 14.29 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.13), residues: 3955 helix: 1.17 (0.11), residues: 2151 sheet: 0.47 (0.27), residues: 357 loop : 0.34 (0.17), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 156 HIS 0.012 0.001 HIS N 343 PHE 0.018 0.002 PHE P 126 TYR 0.052 0.002 TYR Q 114 ARG 0.015 0.000 ARG Q 104 *********************** 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 252 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 177 time to evaluate : 4.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.9014 (ttp) cc_final: 0.8809 (ttm) REVERT: C 139 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8387 (tpt) REVERT: P 185 TRP cc_start: 0.7906 (m-90) cc_final: 0.7288 (m-90) REVERT: G 16 LYS cc_start: 0.9403 (mmmt) cc_final: 0.9030 (pptt) REVERT: F 95 LYS cc_start: 0.8613 (tptt) cc_final: 0.8317 (tppt) REVERT: F 121 GLU cc_start: 0.8097 (tp30) cc_final: 0.7857 (tp30) REVERT: F 126 GLU cc_start: 0.8798 (mp0) cc_final: 0.8129 (mm-30) REVERT: B 60 PHE cc_start: 0.9467 (OUTLIER) cc_final: 0.8744 (t80) REVERT: H 78 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8578 (pp20) REVERT: J 10 LYS cc_start: 0.9360 (tttm) cc_final: 0.8956 (tptt) REVERT: N 139 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8643 (tpt) REVERT: N 283 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.7838 (mtt90) REVERT: N 345 GLU cc_start: 0.9431 (OUTLIER) cc_final: 0.9113 (mp0) REVERT: N 365 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.9091 (mp) REVERT: E 55 ASP cc_start: 0.9256 (p0) cc_final: 0.8958 (p0) REVERT: R 123 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8633 (tm-30) REVERT: Q 121 GLU cc_start: 0.7873 (tt0) cc_final: 0.7517 (tp30) REVERT: Q 122 ASP cc_start: 0.7217 (p0) cc_final: 0.6545 (p0) REVERT: Q 125 GLU cc_start: 0.9068 (tp30) cc_final: 0.8854 (tt0) REVERT: M 334 GLU cc_start: 0.9536 (tp30) cc_final: 0.9077 (pm20) REVERT: S 75 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8791 (tm-30) REVERT: S 76 LYS cc_start: 0.9112 (tptm) cc_final: 0.8864 (tppt) REVERT: S 78 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8440 (tm-30) outliers start: 75 outliers final: 25 residues processed: 234 average time/residue: 1.5549 time to fit residues: 428.8583 Evaluate side-chains 191 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 3.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain N residue 139 MET Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain N residue 345 GLU Chi-restraints excluded: chain N residue 365 ILE Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 272 SER Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain S residue 75 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 282 optimal weight: 7.9990 chunk 156 optimal weight: 8.9990 chunk 323 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 340 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN B 196 ASN D 193 GLN ** H 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9061 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 33375 Z= 0.319 Angle : 0.597 17.201 45366 Z= 0.282 Chirality : 0.042 0.171 4952 Planarity : 0.004 0.047 5712 Dihedral : 11.931 146.807 5235 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.05 % Allowed : 14.98 % Favored : 82.98 % 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: 1.28 (0.13), residues: 3955 helix: 1.32 (0.11), residues: 2149 sheet: 0.28 (0.26), residues: 358 loop : 0.47 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 142 HIS 0.007 0.001 HIS N 96 PHE 0.021 0.002 PHE N 234 TYR 0.015 0.001 TYR D 117 ARG 0.008 0.000 ARG N 70 *********************** 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 239 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 171 time to evaluate : 3.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.9008 (ttp) cc_final: 0.8777 (ttm) REVERT: P 185 TRP cc_start: 0.7900 (m-90) cc_final: 0.7588 (m-90) REVERT: P 216 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7842 (t80) REVERT: G 16 LYS cc_start: 0.9414 (mmmt) cc_final: 0.9015 (pptt) REVERT: G 50 GLU cc_start: 0.8747 (pm20) cc_final: 0.8489 (pp20) REVERT: F 95 LYS cc_start: 0.8711 (tptt) cc_final: 0.8348 (tppt) REVERT: F 121 GLU cc_start: 0.8186 (tp30) cc_final: 0.7899 (tp30) REVERT: F 125 GLU cc_start: 0.9282 (mm-30) cc_final: 0.8767 (mt-10) REVERT: A 223 ASP cc_start: 0.9369 (OUTLIER) cc_final: 0.8882 (t0) REVERT: H 78 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8543 (pp20) REVERT: J 10 LYS cc_start: 0.9366 (tttm) cc_final: 0.8880 (tptt) REVERT: N 255 ASP cc_start: 0.9164 (p0) cc_final: 0.8901 (p0) REVERT: N 283 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8128 (mtt90) REVERT: N 341 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8698 (pp30) REVERT: N 345 GLU cc_start: 0.9321 (OUTLIER) cc_final: 0.9103 (mp0) REVERT: E 54 LYS cc_start: 0.9115 (tppt) cc_final: 0.8837 (mtpt) REVERT: E 55 ASP cc_start: 0.9246 (p0) cc_final: 0.8946 (p0) REVERT: R 123 GLU cc_start: 0.9194 (tm-30) cc_final: 0.8776 (tm-30) REVERT: Q 84 GLU cc_start: 0.9421 (mm-30) cc_final: 0.9208 (mm-30) REVERT: Q 121 GLU cc_start: 0.8309 (tt0) cc_final: 0.7918 (tp30) REVERT: Q 122 ASP cc_start: 0.7764 (p0) cc_final: 0.7124 (p0) REVERT: Q 125 GLU cc_start: 0.9063 (tp30) cc_final: 0.8752 (tt0) REVERT: M 101 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8568 (mttp) REVERT: S 51 ARG cc_start: 0.9283 (OUTLIER) cc_final: 0.6428 (ptm-80) REVERT: S 75 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8832 (tm-30) REVERT: S 78 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8450 (tm-30) outliers start: 68 outliers final: 21 residues processed: 223 average time/residue: 1.5983 time to fit residues: 419.2852 Evaluate side-chains 181 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 152 time to evaluate : 3.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain N residue 341 GLN Chi-restraints excluded: chain N residue 345 GLU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 101 LYS Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 75 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 0.9990 chunk 341 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 222 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 379 optimal weight: 5.9990 chunk 314 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 199 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN D 193 GLN ** M 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.5445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 33375 Z= 0.230 Angle : 0.551 15.002 45366 Z= 0.261 Chirality : 0.041 0.179 4952 Planarity : 0.004 0.046 5712 Dihedral : 11.795 147.907 5235 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.68 % Allowed : 15.67 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.14), residues: 3955 helix: 1.43 (0.11), residues: 2149 sheet: 0.26 (0.26), residues: 356 loop : 0.54 (0.18), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 142 HIS 0.005 0.001 HIS M 87 PHE 0.017 0.001 PHE A 334 TYR 0.016 0.001 TYR D 117 ARG 0.005 0.000 ARG N 70 *********************** 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 223 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 167 time to evaluate : 3.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.9000 (ttp) cc_final: 0.8785 (ttm) REVERT: P 216 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7790 (t80) REVERT: G 16 LYS cc_start: 0.9406 (mmmt) cc_final: 0.9041 (pptt) REVERT: G 50 GLU cc_start: 0.8777 (pm20) cc_final: 0.8410 (pp20) REVERT: F 95 LYS cc_start: 0.8713 (tptt) cc_final: 0.8439 (tppt) REVERT: F 96 HIS cc_start: 0.7949 (p90) cc_final: 0.7690 (p-80) REVERT: F 121 GLU cc_start: 0.8087 (tp30) cc_final: 0.7812 (tp30) REVERT: F 125 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8862 (mt-10) REVERT: F 126 GLU cc_start: 0.9106 (mp0) cc_final: 0.8141 (mm-30) REVERT: A 223 ASP cc_start: 0.9380 (OUTLIER) cc_final: 0.8900 (t0) REVERT: H 78 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8563 (pp20) REVERT: J 10 LYS cc_start: 0.9373 (tttm) cc_final: 0.8879 (tptt) REVERT: N 255 ASP cc_start: 0.9135 (p0) cc_final: 0.8896 (p0) REVERT: N 283 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.7957 (mtt90) REVERT: E 54 LYS cc_start: 0.9117 (tppt) cc_final: 0.8824 (mtpt) REVERT: E 55 ASP cc_start: 0.9266 (p0) cc_final: 0.8956 (p0) REVERT: R 112 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8877 (tt0) REVERT: R 123 GLU cc_start: 0.9238 (tm-30) cc_final: 0.8850 (tm-30) REVERT: Q 121 GLU cc_start: 0.8358 (tt0) cc_final: 0.7899 (tp30) REVERT: Q 122 ASP cc_start: 0.7835 (p0) cc_final: 0.7238 (p0) REVERT: Q 125 GLU cc_start: 0.9032 (tp30) cc_final: 0.8782 (tt0) REVERT: L 99 MET cc_start: 0.9015 (ttp) cc_final: 0.8656 (pp-130) REVERT: M 197 ASN cc_start: 0.8898 (t0) cc_final: 0.8298 (t160) REVERT: S 75 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8834 (tm-30) REVERT: S 78 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8410 (tm-30) REVERT: U 69 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8269 (pm20) outliers start: 56 outliers final: 17 residues processed: 213 average time/residue: 1.6296 time to fit residues: 407.6472 Evaluate side-chains 179 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 3.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 270 VAL Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain R residue 55 MET Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 179 LYS Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain U residue 69 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 216 optimal weight: 3.9990 chunk 276 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 chunk 319 optimal weight: 8.9990 chunk 211 optimal weight: 0.9990 chunk 377 optimal weight: 0.9980 chunk 236 optimal weight: 0.0470 chunk 230 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN D 193 GLN O 90 HIS O 269 GLN S 77 ASN T 49 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 33375 Z= 0.216 Angle : 0.543 15.062 45366 Z= 0.257 Chirality : 0.040 0.181 4952 Planarity : 0.004 0.047 5712 Dihedral : 11.591 148.077 5235 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.35 % Allowed : 15.94 % Favored : 82.71 % 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: 1.52 (0.14), residues: 3955 helix: 1.49 (0.11), residues: 2149 sheet: 0.31 (0.27), residues: 354 loop : 0.65 (0.18), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 142 HIS 0.005 0.001 HIS N 96 PHE 0.017 0.001 PHE A 334 TYR 0.019 0.001 TYR F 114 ARG 0.005 0.000 ARG P 202 *********************** 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 202 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 157 time to evaluate : 3.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.9015 (ttp) cc_final: 0.8801 (ttm) REVERT: P 164 MET cc_start: 0.9038 (ptm) cc_final: 0.8513 (ppp) REVERT: P 216 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7813 (t80) REVERT: G 16 LYS cc_start: 0.9401 (mmmt) cc_final: 0.9061 (pptt) REVERT: G 50 GLU cc_start: 0.8789 (pm20) cc_final: 0.8420 (pp20) REVERT: F 95 LYS cc_start: 0.8719 (tptt) cc_final: 0.8461 (tppt) REVERT: F 96 HIS cc_start: 0.7882 (p90) cc_final: 0.7660 (p-80) REVERT: F 121 GLU cc_start: 0.8127 (tp30) cc_final: 0.7850 (tp30) REVERT: F 125 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8864 (mt-10) REVERT: F 126 GLU cc_start: 0.9130 (mp0) cc_final: 0.8818 (mp0) REVERT: H 78 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8588 (pp20) REVERT: J 10 LYS cc_start: 0.9375 (tttm) cc_final: 0.8832 (tptt) REVERT: N 255 ASP cc_start: 0.9108 (p0) cc_final: 0.8892 (p0) REVERT: N 283 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.7882 (mtt90) REVERT: N 341 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8362 (pp30) REVERT: E 54 LYS cc_start: 0.9116 (tppt) cc_final: 0.8827 (mtpt) REVERT: E 55 ASP cc_start: 0.9288 (p0) cc_final: 0.8990 (p0) REVERT: R 112 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8867 (tt0) REVERT: R 123 GLU cc_start: 0.9246 (tm-30) cc_final: 0.8867 (tm-30) REVERT: Q 121 GLU cc_start: 0.8457 (tt0) cc_final: 0.7746 (tm-30) REVERT: Q 122 ASP cc_start: 0.7908 (p0) cc_final: 0.6907 (p0) REVERT: Q 125 GLU cc_start: 0.9005 (tp30) cc_final: 0.8780 (tt0) REVERT: L 99 MET cc_start: 0.9001 (ttp) cc_final: 0.8644 (pp-130) REVERT: L 390 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8707 (mtpm) REVERT: M 197 ASN cc_start: 0.8887 (t0) cc_final: 0.8255 (t160) REVERT: O 85 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8470 (pmm) REVERT: O 90 HIS cc_start: 0.9162 (OUTLIER) cc_final: 0.8885 (m-70) REVERT: S 75 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.8824 (tm-30) REVERT: S 78 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8373 (tm-30) REVERT: U 69 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8271 (pm20) outliers start: 45 outliers final: 16 residues processed: 195 average time/residue: 1.7025 time to fit residues: 387.6077 Evaluate side-chains 175 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 150 time to evaluate : 3.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 270 VAL Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain N residue 341 GLN Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain O residue 85 MET Chi-restraints excluded: chain O residue 90 HIS Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain U residue 69 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 225 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 83 HIS D 193 GLN D 236 ASN M 92 HIS M 197 ASN O 90 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 33375 Z= 0.274 Angle : 0.576 15.861 45366 Z= 0.268 Chirality : 0.041 0.186 4952 Planarity : 0.004 0.046 5712 Dihedral : 11.577 147.958 5235 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.20 % Allowed : 16.30 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.14), residues: 3955 helix: 1.50 (0.11), residues: 2147 sheet: 0.29 (0.27), residues: 354 loop : 0.69 (0.18), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 142 HIS 0.019 0.001 HIS O 90 PHE 0.017 0.001 PHE L 334 TYR 0.016 0.001 TYR D 117 ARG 0.004 0.000 ARG P 202 *********************** 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 192 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 152 time to evaluate : 3.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 164 MET cc_start: 0.9074 (ptm) cc_final: 0.8486 (ppp) REVERT: P 216 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7811 (t80) REVERT: G 16 LYS cc_start: 0.9412 (mmmt) cc_final: 0.9061 (pptt) REVERT: G 50 GLU cc_start: 0.8795 (pm20) cc_final: 0.8423 (pp20) REVERT: F 95 LYS cc_start: 0.8770 (tptt) cc_final: 0.8510 (tppt) REVERT: F 96 HIS cc_start: 0.8041 (p90) cc_final: 0.7818 (p-80) REVERT: F 121 GLU cc_start: 0.8104 (tp30) cc_final: 0.7839 (tp30) REVERT: F 125 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8862 (mt-10) REVERT: H 78 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8565 (pp20) REVERT: J 10 LYS cc_start: 0.9366 (tttm) cc_final: 0.8838 (tptt) REVERT: N 255 ASP cc_start: 0.9098 (p0) cc_final: 0.8889 (p0) REVERT: N 283 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8026 (mtt90) REVERT: E 54 LYS cc_start: 0.9147 (tppt) cc_final: 0.8855 (mtpt) REVERT: E 55 ASP cc_start: 0.9288 (p0) cc_final: 0.9010 (p0) REVERT: R 123 GLU cc_start: 0.9244 (tm-30) cc_final: 0.8832 (tm-30) REVERT: Q 99 ASP cc_start: 0.8893 (m-30) cc_final: 0.8524 (p0) REVERT: Q 121 GLU cc_start: 0.8554 (tt0) cc_final: 0.7699 (tm-30) REVERT: Q 122 ASP cc_start: 0.8018 (p0) cc_final: 0.6848 (p0) REVERT: L 99 MET cc_start: 0.9032 (ttp) cc_final: 0.8665 (pp-130) REVERT: L 390 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8729 (mtpm) REVERT: M 364 MET cc_start: 0.8927 (mmm) cc_final: 0.8684 (mmt) REVERT: S 75 GLU cc_start: 0.9197 (OUTLIER) cc_final: 0.8840 (tm-30) REVERT: S 78 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8402 (tm-30) REVERT: U 69 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8282 (pm20) outliers start: 40 outliers final: 19 residues processed: 186 average time/residue: 1.7573 time to fit residues: 381.2996 Evaluate side-chains 174 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 150 time to evaluate : 3.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 270 VAL Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain R residue 55 MET Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain O residue 90 HIS Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain U residue 69 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 9.9990 chunk 361 optimal weight: 0.1980 chunk 330 optimal weight: 10.0000 chunk 352 optimal weight: 8.9990 chunk 211 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 276 optimal weight: 20.0000 chunk 108 optimal weight: 0.5980 chunk 318 optimal weight: 1.9990 chunk 332 optimal weight: 0.9990 chunk 350 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 332 ASN O 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33375 Z= 0.178 Angle : 0.538 14.211 45366 Z= 0.255 Chirality : 0.040 0.192 4952 Planarity : 0.003 0.046 5712 Dihedral : 11.405 148.280 5235 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.84 % Allowed : 16.54 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.14), residues: 3955 helix: 1.54 (0.11), residues: 2151 sheet: 0.35 (0.27), residues: 356 loop : 0.75 (0.18), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 142 HIS 0.010 0.001 HIS O 90 PHE 0.016 0.001 PHE L 334 TYR 0.022 0.001 TYR F 114 ARG 0.009 0.000 ARG F 104 *********************** 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 186 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 158 time to evaluate : 3.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 164 MET cc_start: 0.9079 (ptm) cc_final: 0.8532 (ppp) REVERT: P 216 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7829 (t80) REVERT: G 16 LYS cc_start: 0.9411 (mmmt) cc_final: 0.9066 (pptt) REVERT: G 50 GLU cc_start: 0.8819 (pm20) cc_final: 0.8429 (pp20) REVERT: F 95 LYS cc_start: 0.8799 (tptt) cc_final: 0.8533 (tppt) REVERT: F 96 HIS cc_start: 0.8063 (p90) cc_final: 0.7825 (p-80) REVERT: F 121 GLU cc_start: 0.8061 (tp30) cc_final: 0.7758 (tp30) REVERT: F 125 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8888 (mt-10) REVERT: F 126 GLU cc_start: 0.9203 (mp0) cc_final: 0.8922 (mp0) REVERT: H 78 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8583 (pp20) REVERT: J 10 LYS cc_start: 0.9336 (tttm) cc_final: 0.8776 (tptt) REVERT: N 283 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.7828 (mtt90) REVERT: E 54 LYS cc_start: 0.9108 (tppt) cc_final: 0.8811 (mtpt) REVERT: E 55 ASP cc_start: 0.9287 (p0) cc_final: 0.9002 (p0) REVERT: R 123 GLU cc_start: 0.9243 (tm-30) cc_final: 0.8880 (tm-30) REVERT: Q 99 ASP cc_start: 0.8906 (m-30) cc_final: 0.8293 (p0) REVERT: Q 100 GLU cc_start: 0.8437 (pp20) cc_final: 0.8182 (pp20) REVERT: Q 121 GLU cc_start: 0.8587 (tt0) cc_final: 0.7725 (tm-30) REVERT: Q 122 ASP cc_start: 0.8022 (p0) cc_final: 0.6858 (p0) REVERT: L 99 MET cc_start: 0.8991 (ttp) cc_final: 0.8631 (pp-130) REVERT: L 390 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8715 (mtpm) REVERT: S 51 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.6291 (ptm-80) REVERT: S 75 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8865 (tm-30) REVERT: S 78 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8392 (tm-30) REVERT: U 69 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8247 (pm20) outliers start: 28 outliers final: 15 residues processed: 182 average time/residue: 1.8111 time to fit residues: 383.4931 Evaluate side-chains 171 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain P residue 119 LYS Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 270 VAL Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain R residue 55 MET Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 179 LYS Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain U residue 69 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 5.9990 chunk 372 optimal weight: 0.0000 chunk 227 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 258 optimal weight: 1.9990 chunk 390 optimal weight: 0.7980 chunk 359 optimal weight: 3.9990 chunk 310 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 240 optimal weight: 0.0770 chunk 190 optimal weight: 4.9990 overall best weight: 0.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 343 HIS R 45 ASN M 92 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 33375 Z= 0.154 Angle : 0.527 13.708 45366 Z= 0.251 Chirality : 0.039 0.191 4952 Planarity : 0.004 0.049 5712 Dihedral : 11.183 148.486 5235 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.66 % Allowed : 16.93 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.14), residues: 3955 helix: 1.61 (0.11), residues: 2141 sheet: 0.42 (0.27), residues: 354 loop : 0.80 (0.18), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 142 HIS 0.008 0.001 HIS B 92 PHE 0.016 0.001 PHE L 334 TYR 0.014 0.001 TYR D 117 ARG 0.007 0.000 ARG N 70 ********************** 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 183 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 3.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 164 MET cc_start: 0.9090 (ptm) cc_final: 0.8570 (ppp) REVERT: P 216 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.7811 (t80) REVERT: G 16 LYS cc_start: 0.9413 (mmmt) cc_final: 0.9066 (pptt) REVERT: G 50 GLU cc_start: 0.8839 (pm20) cc_final: 0.8447 (pp20) REVERT: F 95 LYS cc_start: 0.8804 (tptt) cc_final: 0.8573 (tptp) REVERT: F 121 GLU cc_start: 0.8118 (tp30) cc_final: 0.7821 (tp30) REVERT: F 125 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8848 (mt-10) REVERT: H 78 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8578 (pp20) REVERT: J 10 LYS cc_start: 0.9315 (tttm) cc_final: 0.8757 (tptt) REVERT: N 283 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8000 (mtt90) REVERT: E 55 ASP cc_start: 0.9281 (p0) cc_final: 0.8998 (p0) REVERT: R 123 GLU cc_start: 0.9241 (tm-30) cc_final: 0.8831 (tm-30) REVERT: Q 100 GLU cc_start: 0.8411 (pp20) cc_final: 0.8055 (pt0) REVERT: Q 121 GLU cc_start: 0.8617 (tt0) cc_final: 0.7735 (tm-30) REVERT: Q 122 ASP cc_start: 0.8047 (p0) cc_final: 0.6898 (p0) REVERT: L 99 MET cc_start: 0.8987 (ttp) cc_final: 0.8630 (pp-130) REVERT: M 197 ASN cc_start: 0.8905 (t0) cc_final: 0.8125 (t0) REVERT: S 75 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8858 (tm-30) REVERT: S 78 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8371 (tm-30) REVERT: U 69 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8232 (pm20) outliers start: 22 outliers final: 12 residues processed: 180 average time/residue: 1.7515 time to fit residues: 370.0713 Evaluate side-chains 171 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 162 LEU Chi-restraints excluded: chain P residue 216 PHE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 17 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain D residue 166 ASN Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain N residue 242 LEU Chi-restraints excluded: chain N residue 270 VAL Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain O residue 297 ILE Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain U residue 69 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 7.9990 chunk 331 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 286 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 311 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 319 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 57 optimal weight: 0.5980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 343 HIS R 45 ASN M 92 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.059777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.047251 restraints weight = 108480.943| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.34 r_work: 0.2792 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.5871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33375 Z= 0.183 Angle : 0.545 14.318 45366 Z= 0.255 Chirality : 0.040 0.195 4952 Planarity : 0.004 0.054 5712 Dihedral : 11.090 148.395 5235 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.57 % Allowed : 17.14 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.14), residues: 3955 helix: 1.66 (0.11), residues: 2129 sheet: 0.43 (0.27), residues: 354 loop : 0.83 (0.18), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP P 120 HIS 0.011 0.001 HIS F 96 PHE 0.016 0.001 PHE L 334 TYR 0.023 0.001 TYR F 114 ARG 0.007 0.000 ARG N 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9191.10 seconds wall clock time: 168 minutes 7.42 seconds (10087.42 seconds total)