Starting phenix.real_space_refine on Thu Feb 22 02:03:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab8_15314/02_2024/8ab8_15314_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab8_15314/02_2024/8ab8_15314.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab8_15314/02_2024/8ab8_15314_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab8_15314/02_2024/8ab8_15314_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab8_15314/02_2024/8ab8_15314_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab8_15314/02_2024/8ab8_15314.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab8_15314/02_2024/8ab8_15314.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab8_15314/02_2024/8ab8_15314_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab8_15314/02_2024/8ab8_15314_updated.pdb" } resolution = 2.6 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 21041 2.51 5 N 5294 2.21 5 O 6075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 4": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P GLU 137": "OE1" <-> "OE2" Residue "P GLU 178": "OE1" <-> "OE2" Residue "P GLU 213": "OE1" <-> "OE2" Residue "P PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 220": "OE1" <-> "OE2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G ARG 61": "NH1" <-> "NH2" Residue "G GLU 66": "OE1" <-> "OE2" Residue "G ARG 70": "NH1" <-> "NH2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G GLU 96": "OE1" <-> "OE2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F GLU 121": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A 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 "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 "I GLU 34": "OE1" <-> "OE2" Residue "N ARG 4": "NH1" <-> "NH2" Residue "N ARG 70": "NH1" <-> "NH2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "N TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 110": "NH1" <-> "NH2" Residue "N PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N 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 112": "OE1" <-> "OE2" Residue "R GLU 123": "OE1" <-> "OE2" Residue "Q GLU 88": "OE1" <-> "OE2" Residue "Q GLU 118": "OE1" <-> "OE2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "Q GLU 126": "OE1" <-> "OE2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "L GLU 141": "OE1" <-> "OE2" Residue "L ARG 188": "NH1" <-> "NH2" Residue "L GLU 354": "OE1" <-> "OE2" Residue "L ARG 384": "NH1" <-> "NH2" Residue "L GLU 424": "OE1" <-> "OE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M GLU 78": "OE1" <-> "OE2" Residue "M TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 117": "OE1" <-> "OE2" Residue "M ARG 140": "NH1" <-> "NH2" Residue "M GLU 150": "OE1" <-> "OE2" Residue "M ARG 234": "NH1" <-> "NH2" Residue "M GLU 313": "OE1" <-> "OE2" Residue "M GLU 350": "OE1" <-> "OE2" Residue "M GLU 376": "OE1" <-> "OE2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "O ARG 132": "NH1" <-> "NH2" Residue "O ARG 136": "NH1" <-> "NH2" Residue "O GLU 164": "OE1" <-> "OE2" Residue "O ARG 170": "NH1" <-> "NH2" Residue "O ARG 189": "NH1" <-> "NH2" Residue "O ARG 207": "NH1" <-> "NH2" Residue "O TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 250": "NH1" <-> "NH2" Residue "O GLU 260": "OE1" <-> "OE2" Residue "O ARG 289": "NH1" <-> "NH2" Residue "O ARG 321": "NH1" <-> "NH2" Residue "S PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 34": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32550 Number of models: 1 Model: "" Number of chains: 33 Chain: "C" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "P" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1445 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 11, 'TRANS': 174} Chain: "G" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "A" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "B" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "D" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "I" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "J" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "N" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "E" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 452 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} 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: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 271 Unusual residues: {'CDL': 1, 'DCQ': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "P" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {'FES': 1, 'LMT': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 111 Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "J" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 248 Unusual residues: {'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 111 Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 30.131 51.898 36.540 1.00 94.04 S ATOM 4207 SG CYS P 187 32.524 48.942 36.024 1.00 92.14 S Time building chain proxies: 19.23, per 1000 atoms: 0.59 Number of scatterers: 32550 At special positions: 0 Unit cell: (119.691, 129.735, 164.052, 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 6075 8.00 N 5294 7.00 C 21041 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=2.05 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: 14.10 Conformation dependent library (CDL) restraints added in 5.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 301 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 190 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 170 " 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 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7482 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: 6.20 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: 3.938A pdb=" N PHE C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY C 33 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR C 46 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY C 47 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 3.633A 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: 3.751A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 135 removed outlier: 3.564A pdb=" N LEU C 134 " --> pdb=" O MET C 130 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 Processing helix chain 'C' and resid 151 through 153 No H-bonds generated for 'chain 'C' and resid 151 through 153' 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: 4.058A pdb=" N THR C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 246 removed outlier: 6.875A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.890A 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: 3.870A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LEU C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.975A 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: 4.120A 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: 3.649A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN P 90 " --> pdb=" O ASP P 86 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N MET P 91 " --> pdb=" O PHE P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 99 Processing helix chain 'P' and resid 132 through 138 Processing helix chain 'P' and resid 152 through 155 No H-bonds generated for 'chain 'P' and resid 152 through 155' Processing helix chain 'G' and resid 4 through 16 Processing helix chain 'G' and resid 18 through 35 Proline residue: G 26 - end of helix Processing helix chain 'G' and resid 37 through 40 Processing helix chain 'G' and resid 44 through 47 Processing helix chain 'G' and resid 53 through 60 Processing helix chain 'G' and resid 64 through 83 Processing helix chain 'G' and resid 89 through 91 No H-bonds generated for 'chain 'G' and resid 89 through 91' Processing helix chain 'G' and resid 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: 3.692A pdb=" N ASN G 121 " --> pdb=" O ASP G 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 88 Processing helix chain 'F' and resid 92 through 110 Processing helix chain 'F' and resid 124 through 137 Processing helix chain 'F' and resid 139 through 145 removed outlier: 3.599A pdb=" N VAL F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.542A pdb=" N HIS A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 4.194A 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: 3.838A pdb=" N VAL A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Proline residue: A 124 - end of helix removed outlier: 3.832A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 154 removed outlier: 4.021A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.795A 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: 3.537A 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: 3.510A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 4.047A 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: 3.658A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 395 removed outlier: 3.563A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.353A 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: 3.689A pdb=" N ASP A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 4.005A 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: 3.656A pdb=" N LYS B 116 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU B 117 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 129 through 141 Processing helix chain 'B' and resid 144 through 157 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 200 through 210 Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.701A 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: 3.725A 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: 3.602A 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 81 removed outlier: 4.408A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) Proline residue: H 62 - end of helix removed outlier: 3.510A pdb=" N TYR H 81 " --> pdb=" O ASN H 77 " (cutoff:3.500A) 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: 5.173A pdb=" N HIS I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LYS I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 49 removed outlier: 3.517A pdb=" N LYS J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 3.538A 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: 3.928A pdb=" N PHE N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLY N 33 " --> pdb=" O TRP N 30 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR N 46 " --> pdb=" O GLN N 43 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY N 47 " --> pdb=" O LEU N 44 " (cutoff:3.500A) removed outlier: 3.625A 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: 3.754A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 135 removed outlier: 3.565A pdb=" N LEU N 134 " --> pdb=" O MET N 130 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 138 through 153 removed outlier: 3.621A pdb=" N LEU N 150 " --> pdb=" O VAL N 146 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL N 151 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER N 152 " --> pdb=" O CYS N 148 " (cutoff:3.500A) removed outlier: 4.311A 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: 4.059A pdb=" N THR N 203 " --> pdb=" O ILE N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 246 removed outlier: 6.873A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.896A 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: 3.859A pdb=" N ILE N 299 " --> pdb=" O MET N 295 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU N 302 " --> pdb=" O ALA N 298 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU N 303 " --> pdb=" O ILE N 299 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE N 304 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 3.970A 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: 4.120A 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: 3.647A pdb=" N SER E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N MET E 91 " --> pdb=" O PHE E 87 " (cutoff:3.500A) 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: 3.696A 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: 3.605A 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: 3.837A pdb=" N VAL L 123 " --> pdb=" O LYS L 120 " (cutoff:3.500A) Proline residue: L 124 - end of helix removed outlier: 3.836A pdb=" N VAL L 127 " --> pdb=" O PRO L 124 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU L 134 " --> pdb=" O ALA L 131 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN L 135 " --> pdb=" O ASP L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 156 removed outlier: 4.019A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU L 156 " --> pdb=" O THR L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 160 No H-bonds generated for 'chain 'L' and resid 158 through 160' Processing helix chain 'L' and resid 162 through 174 Processing helix chain 'L' and resid 179 through 181 No H-bonds generated for 'chain 'L' and resid 179 through 181' Processing helix chain 'L' and resid 188 through 193 removed outlier: 3.538A pdb=" N THR L 193 " --> pdb=" O GLU L 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 206 Processing helix chain 'L' and resid 209 through 211 No H-bonds generated for 'chain 'L' and resid 209 through 211' Processing helix chain 'L' and resid 222 through 232 Processing helix chain 'L' and resid 294 through 304 removed outlier: 3.510A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 312 through 316 removed outlier: 4.046A pdb=" N ARG L 315 " --> pdb=" O GLY L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 320 through 328 Processing helix chain 'L' and resid 359 through 375 removed outlier: 3.662A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 395 removed outlier: 3.689A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.324A 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: 3.683A pdb=" N ASP L 468 " --> pdb=" O ARG L 464 " (cutoff:3.500A) removed outlier: 4.005A 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: 3.628A pdb=" N VAL M 108 " --> pdb=" O PRO M 105 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS M 116 " --> pdb=" O ASN M 113 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU M 117 " --> pdb=" O VAL M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 127 Processing helix chain 'M' and resid 129 through 141 Processing helix chain 'M' and resid 144 through 157 Processing helix chain 'M' and resid 160 through 162 No H-bonds generated for 'chain 'M' and resid 160 through 162' Processing helix chain 'M' and resid 175 through 185 Processing helix chain 'M' and resid 188 through 190 No H-bonds generated for 'chain 'M' and resid 188 through 190' Processing helix chain 'M' and resid 200 through 210 Processing helix chain 'M' and resid 254 through 263 removed outlier: 3.700A 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: 3.912A 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: 3.598A 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 81 removed outlier: 4.408A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL S 59 " --> pdb=" O GLN S 55 " (cutoff:3.500A) Proline residue: S 62 - end of helix removed outlier: 3.513A pdb=" N TYR S 81 " --> pdb=" O ASN S 77 " (cutoff:3.500A) 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: 5.164A pdb=" N HIS T 55 " --> pdb=" O LYS T 51 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LYS T 56 " --> pdb=" O ASP T 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 49 removed outlier: 3.598A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.546A 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: 3.925A pdb=" N LYS P 114 " --> pdb=" O HIS P 129 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'P' and resid 185 through 187 removed outlier: 3.508A pdb=" N SER P 192 " --> pdb=" O CYS P 187 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 31 through 34 Processing sheet with id= F, first strand: chain 'A' and resid 266 through 271 Processing sheet with id= G, first strand: chain 'B' and resid 16 through 20 removed outlier: 4.153A 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: 3.630A 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: 4.155A 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: 3.611A 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 1578 hydrogen bonds defined for protein. 4314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.32 Time building geometry restraints manager: 14.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.39: 13344 1.39 - 1.60: 19799 1.60 - 1.82: 187 1.82 - 2.03: 27 2.03 - 2.24: 20 Bond restraints: 33377 Sorted by residual: bond pdb=" C4M DCQ C 507 " pdb=" O4 DCQ C 507 " ideal model delta sigma weight residual 1.427 1.694 -0.267 2.00e-02 2.50e+03 1.78e+02 bond pdb=" C2C HEC D 401 " pdb=" C3C HEC D 401 " ideal model delta sigma weight residual 1.334 1.463 -0.129 2.00e-02 2.50e+03 4.15e+01 bond pdb=" C2B HEC O 401 " pdb=" C3B HEC O 401 " ideal model delta sigma weight residual 1.334 1.462 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C2C HEC O 401 " pdb=" C3C HEC O 401 " ideal model delta sigma weight residual 1.334 1.457 -0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" C2B HEC D 401 " pdb=" C3B HEC D 401 " ideal model delta sigma weight residual 1.334 1.455 -0.121 2.00e-02 2.50e+03 3.65e+01 ... (remaining 33372 not shown) Histogram of bond angle deviations from ideal: 84.02 - 102.98: 398 102.98 - 121.95: 37932 121.95 - 140.91: 7021 140.91 - 159.87: 0 159.87 - 178.84: 12 Bond angle restraints: 45363 Sorted by residual: angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.27 95.98 15.29 1.47e+00 4.63e-01 1.08e+02 angle pdb=" C GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta sigma weight residual 111.27 96.76 14.51 1.47e+00 4.63e-01 9.74e+01 angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 93.36 10.97 1.14e+00 7.69e-01 9.26e+01 angle pdb=" C GLN M 215 " pdb=" CA GLN M 215 " pdb=" CB GLN M 215 " ideal model delta sigma weight residual 109.64 92.66 16.98 1.77e+00 3.19e-01 9.21e+01 angle pdb=" C GLN B 215 " pdb=" CA GLN B 215 " pdb=" CB GLN B 215 " ideal model delta sigma weight residual 109.64 92.76 16.88 1.77e+00 3.19e-01 9.10e+01 ... (remaining 45358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.73: 18923 32.73 - 65.45: 956 65.45 - 98.18: 84 98.18 - 130.91: 1 130.91 - 163.64: 3 Dihedral angle restraints: 19967 sinusoidal: 8354 harmonic: 11613 Sorted by residual: dihedral pdb=" C GLN M 215 " pdb=" N GLN M 215 " pdb=" CA GLN M 215 " pdb=" CB GLN M 215 " ideal model delta harmonic sigma weight residual -122.60 -101.51 -21.09 0 2.50e+00 1.60e-01 7.12e+01 dihedral pdb=" C GLN B 215 " pdb=" N GLN B 215 " pdb=" CA GLN B 215 " pdb=" CB GLN B 215 " ideal model delta harmonic sigma weight residual -122.60 -101.78 -20.82 0 2.50e+00 1.60e-01 6.94e+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 -104.65 -17.95 0 2.50e+00 1.60e-01 5.16e+01 ... (remaining 19964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 4246 0.155 - 0.310: 666 0.310 - 0.465: 40 0.465 - 0.620: 2 0.620 - 0.776: 5 Chirality restraints: 4959 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 -1.80 -0.78 2.00e-01 2.50e+01 1.50e+01 chirality pdb=" CB4 CDL S 702 " pdb=" CB3 CDL S 702 " pdb=" CB6 CDL S 702 " pdb=" OB6 CDL S 702 " both_signs ideal model delta sigma weight residual False -2.57 -1.81 -0.77 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" CB4 CDL H 702 " pdb=" CB3 CDL H 702 " pdb=" CB6 CDL H 702 " pdb=" OB6 CDL H 702 " both_signs ideal model delta sigma weight residual False -2.57 -1.87 -0.71 2.00e-01 2.50e+01 1.25e+01 ... (remaining 4956 not shown) Planarity restraints: 5699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 DCQ C 507 " 0.102 2.00e-02 2.50e+03 1.75e-01 9.19e+02 pdb=" C1M DCQ C 507 " 0.207 2.00e-02 2.50e+03 pdb=" C2 DCQ C 507 " 0.038 2.00e-02 2.50e+03 pdb=" C3 DCQ C 507 " 0.025 2.00e-02 2.50e+03 pdb=" C4 DCQ C 507 " 0.026 2.00e-02 2.50e+03 pdb=" C5 DCQ C 507 " 0.031 2.00e-02 2.50e+03 pdb=" C6 DCQ C 507 " -0.018 2.00e-02 2.50e+03 pdb=" C7 DCQ C 507 " -0.371 2.00e-02 2.50e+03 pdb=" O2 DCQ C 507 " 0.058 2.00e-02 2.50e+03 pdb=" O3 DCQ C 507 " -0.355 2.00e-02 2.50e+03 pdb=" O4 DCQ C 507 " 0.200 2.00e-02 2.50e+03 pdb=" O5 DCQ C 507 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 279 " 0.047 2.00e-02 2.50e+03 3.39e-02 2.30e+01 pdb=" CG TYR C 279 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR C 279 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR C 279 " -0.063 2.00e-02 2.50e+03 pdb=" CE1 TYR C 279 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR C 279 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR C 279 " 0.039 2.00e-02 2.50e+03 pdb=" OH TYR C 279 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC O 401 " -0.018 2.00e-02 2.50e+03 2.79e-02 1.76e+01 pdb=" C2C HEC O 401 " -0.021 2.00e-02 2.50e+03 pdb=" C3C HEC O 401 " 0.006 2.00e-02 2.50e+03 pdb=" C4C HEC O 401 " -0.022 2.00e-02 2.50e+03 pdb=" CAC HEC O 401 " 0.044 2.00e-02 2.50e+03 pdb=" CHC HEC O 401 " 0.054 2.00e-02 2.50e+03 pdb=" CHD HEC O 401 " -0.003 2.00e-02 2.50e+03 pdb=" CMC HEC O 401 " -0.028 2.00e-02 2.50e+03 pdb=" NC HEC O 401 " -0.011 2.00e-02 2.50e+03 ... (remaining 5696 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 273 2.63 - 3.20: 28987 3.20 - 3.77: 54176 3.77 - 4.33: 79211 4.33 - 4.90: 121546 Nonbonded interactions: 284193 Sorted by model distance: nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.069 2.520 nonbonded pdb=" NE2 HIS N 82 " pdb="FE HEM N 501 " model vdw 2.077 3.080 nonbonded pdb=" NE2 HIS C 82 " pdb="FE HEM C 501 " model vdw 2.101 3.080 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.181 3.080 nonbonded pdb=" OB3 CDL S 701 " pdb=" O1 CDL S 702 " model vdw 2.224 2.440 ... (remaining 284188 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 506)) selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = chain 'H' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = (chain 'J' 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: 1.640 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.430 Check model and map are aligned: 0.480 Set scattering table: 0.290 Process input model: 92.070 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.310 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:14.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9215 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.267 33377 Z= 0.621 Angle : 1.616 19.276 45363 Z= 1.007 Chirality : 0.111 0.776 4959 Planarity : 0.007 0.175 5699 Dihedral : 18.122 163.636 12470 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.47 % Rotamer: Outliers : 3.28 % Allowed : 6.65 % Favored : 90.07 % Cbeta Deviations : 0.91 % 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: -1.23 (0.12), residues: 3953 helix: -0.92 (0.09), residues: 2124 sheet: 0.14 (0.26), residues: 351 loop : -0.62 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.006 TRP C 142 HIS 0.026 0.004 HIS C 253 PHE 0.050 0.006 PHE B 107 TYR 0.063 0.006 TYR C 279 ARG 0.023 0.002 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 459 time to evaluate : 4.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 6 LYS cc_start: 0.9163 (tttt) cc_final: 0.8940 (ttmt) REVERT: C 52 MET cc_start: 0.9436 (mtt) cc_final: 0.9215 (mtt) REVERT: P 105 VAL cc_start: 0.8554 (t) cc_final: 0.8263 (p) REVERT: P 143 VAL cc_start: 0.5239 (OUTLIER) cc_final: 0.4918 (t) REVERT: P 214 TYR cc_start: 0.7813 (p90) cc_final: 0.7606 (p90) REVERT: G 9 LYS cc_start: 0.9194 (mttp) cc_final: 0.8779 (tttm) REVERT: G 66 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8859 (mt-10) REVERT: F 126 GLU cc_start: 0.9001 (mp0) cc_final: 0.8554 (mp0) REVERT: A 87 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8109 (mtp85) REVERT: A 390 LYS cc_start: 0.8939 (tptt) cc_final: 0.8652 (mttt) REVERT: A 433 HIS cc_start: 0.8630 (t70) cc_final: 0.8320 (m-70) REVERT: B 134 GLU cc_start: 0.8969 (tt0) cc_final: 0.8768 (tt0) REVERT: B 139 LYS cc_start: 0.9162 (tttt) cc_final: 0.8917 (tppt) REVERT: B 170 TYR cc_start: 0.8084 (p90) cc_final: 0.7789 (p90) REVERT: B 388 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8172 (tm-30) REVERT: H 78 GLU cc_start: 0.9029 (tt0) cc_final: 0.8675 (mt-10) REVERT: J 13 SER cc_start: 0.8788 (t) cc_final: 0.8583 (p) REVERT: J 75 ILE cc_start: 0.9208 (mm) cc_final: 0.9006 (tp) REVERT: R 9 LYS cc_start: 0.9098 (mttp) cc_final: 0.8843 (ttpt) REVERT: R 85 LYS cc_start: 0.9176 (mttm) cc_final: 0.8968 (mmtt) REVERT: Q 138 THR cc_start: 0.9258 (m) cc_final: 0.9049 (p) REVERT: L 87 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.7266 (mtp85) REVERT: L 240 GLN cc_start: 0.8820 (mp10) cc_final: 0.8387 (mm110) REVERT: M 16 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8941 (p) REVERT: M 19 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8946 (tp30) REVERT: M 205 GLN cc_start: 0.9097 (tm-30) cc_final: 0.8743 (tm130) REVERT: M 370 VAL cc_start: 0.7671 (t) cc_final: 0.7285 (m) REVERT: M 388 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8112 (tm-30) REVERT: U 10 LYS cc_start: 0.9146 (tttm) cc_final: 0.8923 (tptm) REVERT: U 11 LYS cc_start: 0.8844 (tttt) cc_final: 0.8445 (ptpp) outliers start: 109 outliers final: 8 residues processed: 525 average time/residue: 1.6987 time to fit residues: 1033.0963 Evaluate side-chains 331 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 318 time to evaluate : 3.874 ------------------------------------------------------------------------------- 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 116 VAL Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 60 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 330 optimal weight: 6.9990 chunk 296 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 199 optimal weight: 2.9990 chunk 158 optimal weight: 30.0000 chunk 306 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 186 optimal weight: 0.8980 chunk 228 optimal weight: 8.9990 chunk 355 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN C 14 ASN C 22 GLN C 173 ASN C 202 HIS C 332 ASN P 90 ASN P 115 ASN G 84 HIS A 50 GLN A 222 HIS A 332 ASN A 371 ASN B 87 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN B 377 ASN D 93 HIS J 80 ASN N 14 ASN N 22 GLN N 202 HIS N 332 ASN E 90 ASN R 84 HIS Q 131 GLN L 371 ASN M 87 HIS M 241 ASN U 80 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9176 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33377 Z= 0.241 Angle : 0.613 15.197 45363 Z= 0.303 Chirality : 0.042 0.165 4959 Planarity : 0.004 0.042 5699 Dihedral : 14.020 155.228 5302 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 0.99 % Favored : 98.99 % Rotamer: Outliers : 1.65 % Allowed : 10.35 % Favored : 88.00 % 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: 0.85 (0.13), residues: 3953 helix: 0.96 (0.11), residues: 2122 sheet: 0.67 (0.26), residues: 359 loop : 0.12 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 142 HIS 0.009 0.001 HIS C 197 PHE 0.021 0.002 PHE A 334 TYR 0.020 0.002 TYR D 237 ARG 0.007 0.001 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 339 time to evaluate : 3.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 129 HIS cc_start: 0.6731 (t70) cc_final: 0.6170 (t70) REVERT: G 9 LYS cc_start: 0.9129 (mttp) cc_final: 0.8692 (tttm) REVERT: A 87 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.7981 (mtp85) REVERT: A 120 LYS cc_start: 0.9044 (tttt) cc_final: 0.8741 (ptmt) REVERT: A 230 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8635 (tp30) REVERT: A 390 LYS cc_start: 0.9033 (tptt) cc_final: 0.8803 (mttm) REVERT: B 134 GLU cc_start: 0.8923 (tt0) cc_final: 0.8721 (tt0) REVERT: B 139 LYS cc_start: 0.9227 (tttt) cc_final: 0.8964 (tppt) REVERT: B 388 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8096 (tm-30) REVERT: D 163 ASP cc_start: 0.9147 (m-30) cc_final: 0.8654 (p0) REVERT: H 78 GLU cc_start: 0.9144 (tt0) cc_final: 0.8769 (mt-10) REVERT: I 54 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8813 (ttp80) REVERT: R 9 LYS cc_start: 0.9042 (mttp) cc_final: 0.8834 (ttpt) REVERT: R 85 LYS cc_start: 0.9181 (mttm) cc_final: 0.8968 (mmtt) REVERT: L 240 GLN cc_start: 0.8833 (mp10) cc_final: 0.8421 (mm110) REVERT: M 370 VAL cc_start: 0.7777 (t) cc_final: 0.7424 (m) REVERT: M 388 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8252 (tm-30) REVERT: M 392 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8339 (tt0) REVERT: S 76 LYS cc_start: 0.9160 (tptt) cc_final: 0.8919 (tptm) REVERT: U 10 LYS cc_start: 0.9107 (tttm) cc_final: 0.8841 (tptm) REVERT: U 11 LYS cc_start: 0.8827 (tttt) cc_final: 0.8519 (ptpp) outliers start: 55 outliers final: 17 residues processed: 372 average time/residue: 1.6855 time to fit residues: 729.3259 Evaluate side-chains 315 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 295 time to evaluate : 3.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain R residue 117 ASP Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 332 VAL Chi-restraints excluded: chain M residue 392 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 197 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 295 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 355 optimal weight: 0.3980 chunk 384 optimal weight: 0.9980 chunk 316 optimal weight: 4.9990 chunk 352 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 285 optimal weight: 0.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 129 HIS B 316 GLN B 354 ASN B 377 ASN D 93 HIS Q 137 ASN M 295 ASN M 316 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9174 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33377 Z= 0.222 Angle : 0.551 13.733 45363 Z= 0.267 Chirality : 0.041 0.201 4959 Planarity : 0.004 0.052 5699 Dihedral : 12.981 151.125 5283 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.59 % Allowed : 10.95 % Favored : 87.45 % 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: 1.45 (0.13), residues: 3953 helix: 1.49 (0.11), residues: 2130 sheet: 0.78 (0.26), residues: 364 loop : 0.37 (0.17), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 142 HIS 0.007 0.001 HIS N 96 PHE 0.020 0.001 PHE A 334 TYR 0.032 0.001 TYR P 214 ARG 0.003 0.000 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 316 time to evaluate : 3.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 129 HIS cc_start: 0.6899 (t-170) cc_final: 0.6397 (t70) REVERT: P 196 ILE cc_start: 0.7111 (mp) cc_final: 0.6370 (tp) REVERT: G 9 LYS cc_start: 0.9129 (mttp) cc_final: 0.8676 (tttm) REVERT: F 115 ASP cc_start: 0.8555 (p0) cc_final: 0.8225 (t70) REVERT: A 120 LYS cc_start: 0.9044 (tttt) cc_final: 0.8728 (ptmt) REVERT: A 230 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8729 (tp30) REVERT: A 390 LYS cc_start: 0.9002 (tptt) cc_final: 0.8797 (mttm) REVERT: B 139 LYS cc_start: 0.9229 (tttt) cc_final: 0.8973 (tppt) REVERT: B 388 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8077 (tm-30) REVERT: D 163 ASP cc_start: 0.9124 (m-30) cc_final: 0.8618 (p0) REVERT: H 78 GLU cc_start: 0.9146 (tt0) cc_final: 0.8727 (mt-10) REVERT: R 9 LYS cc_start: 0.9077 (mttp) cc_final: 0.8819 (ttpt) REVERT: L 240 GLN cc_start: 0.8834 (mp10) cc_final: 0.8406 (mm110) REVERT: M 370 VAL cc_start: 0.7932 (t) cc_final: 0.7631 (m) REVERT: M 388 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8201 (tm-30) REVERT: M 392 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8390 (tt0) REVERT: U 10 LYS cc_start: 0.9055 (tttm) cc_final: 0.8793 (tptm) REVERT: U 11 LYS cc_start: 0.8829 (tttt) cc_final: 0.8473 (ptpp) outliers start: 53 outliers final: 15 residues processed: 350 average time/residue: 1.7165 time to fit residues: 698.1179 Evaluate side-chains 306 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 290 time to evaluate : 3.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 392 GLN Chi-restraints excluded: chain U residue 58 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 351 optimal weight: 7.9990 chunk 267 optimal weight: 8.9990 chunk 184 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 238 optimal weight: 6.9990 chunk 356 optimal weight: 3.9990 chunk 377 optimal weight: 8.9990 chunk 186 optimal weight: 0.8980 chunk 338 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 377 ASN D 93 HIS N 22 GLN M 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9209 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 33377 Z= 0.380 Angle : 0.603 15.217 45363 Z= 0.291 Chirality : 0.044 0.230 4959 Planarity : 0.004 0.056 5699 Dihedral : 12.971 152.215 5277 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.81 % Allowed : 11.04 % Favored : 87.15 % 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: 1.47 (0.13), residues: 3953 helix: 1.49 (0.11), residues: 2132 sheet: 0.70 (0.26), residues: 364 loop : 0.43 (0.17), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 142 HIS 0.009 0.001 HIS C 96 PHE 0.023 0.002 PHE A 334 TYR 0.030 0.002 TYR P 214 ARG 0.006 0.000 ARG P 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 293 time to evaluate : 3.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 129 HIS cc_start: 0.6952 (t-170) cc_final: 0.6489 (t70) REVERT: G 9 LYS cc_start: 0.9145 (mttp) cc_final: 0.8707 (tttm) REVERT: F 115 ASP cc_start: 0.8592 (p0) cc_final: 0.8282 (t0) REVERT: A 120 LYS cc_start: 0.9045 (tttt) cc_final: 0.8722 (ptmt) REVERT: A 230 GLU cc_start: 0.9125 (mm-30) cc_final: 0.8740 (tp30) REVERT: A 390 LYS cc_start: 0.9021 (tptt) cc_final: 0.8779 (mttm) REVERT: B 139 LYS cc_start: 0.9209 (tttt) cc_final: 0.8952 (tppt) REVERT: B 388 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8074 (tm-30) REVERT: D 163 ASP cc_start: 0.9137 (m-30) cc_final: 0.8627 (p0) REVERT: R 9 LYS cc_start: 0.9088 (mttp) cc_final: 0.8830 (ttpt) REVERT: Q 103 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8432 (tm-30) REVERT: L 240 GLN cc_start: 0.8863 (mp10) cc_final: 0.8424 (mm110) REVERT: L 461 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8548 (p0) REVERT: M 236 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8144 (ttp-170) REVERT: M 370 VAL cc_start: 0.8145 (t) cc_final: 0.7872 (m) REVERT: M 388 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8223 (tm-30) REVERT: M 392 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8382 (tt0) REVERT: U 10 LYS cc_start: 0.9079 (tttm) cc_final: 0.8825 (tptm) REVERT: U 11 LYS cc_start: 0.8716 (tttt) cc_final: 0.8431 (ptpp) outliers start: 60 outliers final: 25 residues processed: 331 average time/residue: 1.6457 time to fit residues: 633.1388 Evaluate side-chains 309 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 281 time to evaluate : 3.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain M residue 392 GLN Chi-restraints excluded: chain U residue 58 GLN Chi-restraints excluded: chain U residue 67 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 314 optimal weight: 9.9990 chunk 214 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 322 optimal weight: 0.3980 chunk 261 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 192 optimal weight: 0.9980 chunk 339 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 GLN B 168 GLN B 354 ASN B 377 ASN N 22 GLN L 161 GLN M 295 ASN U 80 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9177 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33377 Z= 0.205 Angle : 0.521 13.768 45363 Z= 0.250 Chirality : 0.040 0.180 4959 Planarity : 0.004 0.056 5699 Dihedral : 12.512 151.016 5277 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.44 % Allowed : 11.58 % Favored : 86.97 % 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: 1.67 (0.14), residues: 3953 helix: 1.65 (0.11), residues: 2134 sheet: 0.80 (0.26), residues: 364 loop : 0.52 (0.17), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 142 HIS 0.007 0.001 HIS C 197 PHE 0.021 0.001 PHE A 334 TYR 0.028 0.001 TYR P 214 ARG 0.004 0.000 ARG M 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 292 time to evaluate : 3.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 129 HIS cc_start: 0.6936 (t-170) cc_final: 0.6435 (t70) REVERT: G 9 LYS cc_start: 0.9141 (mttp) cc_final: 0.8716 (tttm) REVERT: F 103 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8618 (mt-10) REVERT: F 107 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.9127 (mtpp) REVERT: F 115 ASP cc_start: 0.8610 (p0) cc_final: 0.8279 (t0) REVERT: A 120 LYS cc_start: 0.9037 (tttt) cc_final: 0.8723 (ptmt) REVERT: A 390 LYS cc_start: 0.9016 (tptt) cc_final: 0.8789 (mttm) REVERT: B 139 LYS cc_start: 0.9222 (tttt) cc_final: 0.8972 (tppt) REVERT: B 388 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8070 (tm-30) REVERT: D 163 ASP cc_start: 0.9113 (m-30) cc_final: 0.8622 (p0) REVERT: R 9 LYS cc_start: 0.9077 (mttp) cc_final: 0.8824 (ttpt) REVERT: Q 103 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8431 (tm-30) REVERT: L 240 GLN cc_start: 0.8857 (mp10) cc_final: 0.8397 (mm110) REVERT: L 461 ASP cc_start: 0.8828 (OUTLIER) cc_final: 0.8601 (p0) REVERT: M 370 VAL cc_start: 0.8179 (t) cc_final: 0.7918 (m) REVERT: M 388 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8296 (tm-30) REVERT: U 11 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8409 (ptpp) outliers start: 48 outliers final: 17 residues processed: 320 average time/residue: 1.6930 time to fit residues: 631.3040 Evaluate side-chains 301 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 281 time to evaluate : 3.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 74 SER Chi-restraints excluded: chain U residue 11 LYS Chi-restraints excluded: chain U residue 67 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 127 optimal weight: 0.7980 chunk 340 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 221 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 378 optimal weight: 8.9990 chunk 314 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 125 optimal weight: 8.9990 chunk 198 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN B 168 GLN B 377 ASN M 205 GLN M 295 ASN U 80 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9169 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33377 Z= 0.192 Angle : 0.502 13.020 45363 Z= 0.242 Chirality : 0.040 0.264 4959 Planarity : 0.004 0.054 5699 Dihedral : 12.225 150.277 5277 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.56 % Allowed : 11.64 % Favored : 86.79 % 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: 1.85 (0.14), residues: 3953 helix: 1.79 (0.11), residues: 2124 sheet: 0.90 (0.26), residues: 364 loop : 0.63 (0.17), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 142 HIS 0.007 0.001 HIS C 197 PHE 0.020 0.001 PHE A 334 TYR 0.022 0.001 TYR P 214 ARG 0.002 0.000 ARG P 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 290 time to evaluate : 3.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 129 HIS cc_start: 0.6875 (t-170) cc_final: 0.6397 (t70) REVERT: G 9 LYS cc_start: 0.9130 (mttp) cc_final: 0.8712 (tttm) REVERT: F 103 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8636 (mt-10) REVERT: F 107 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.9131 (mtpp) REVERT: F 115 ASP cc_start: 0.8615 (p0) cc_final: 0.8239 (t0) REVERT: F 126 GLU cc_start: 0.9161 (mp0) cc_final: 0.8827 (mp0) REVERT: A 120 LYS cc_start: 0.9017 (tttt) cc_final: 0.8711 (ptmt) REVERT: A 390 LYS cc_start: 0.9025 (tptt) cc_final: 0.8783 (mttm) REVERT: B 139 LYS cc_start: 0.9221 (tttt) cc_final: 0.8967 (tppt) REVERT: B 388 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8035 (tm-30) REVERT: D 163 ASP cc_start: 0.9164 (m-30) cc_final: 0.8657 (p0) REVERT: J 11 LYS cc_start: 0.8895 (mtpm) cc_final: 0.8632 (pttp) REVERT: R 9 LYS cc_start: 0.9075 (mttp) cc_final: 0.8820 (ttpt) REVERT: Q 103 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8408 (tm-30) REVERT: L 240 GLN cc_start: 0.8859 (mp10) cc_final: 0.8388 (mm110) REVERT: M 236 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7981 (ttp-170) REVERT: M 388 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8297 (tm-30) REVERT: U 10 LYS cc_start: 0.9104 (tptm) cc_final: 0.8886 (tptm) REVERT: U 11 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8401 (ptpp) outliers start: 52 outliers final: 25 residues processed: 319 average time/residue: 1.6310 time to fit residues: 606.7120 Evaluate side-chains 305 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 277 time to evaluate : 4.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain S residue 74 SER Chi-restraints excluded: chain U residue 11 LYS Chi-restraints excluded: chain U residue 67 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 364 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 276 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 318 optimal weight: 0.0170 chunk 211 optimal weight: 1.9990 chunk 376 optimal weight: 0.0970 chunk 235 optimal weight: 0.9990 chunk 229 optimal weight: 0.0170 chunk 173 optimal weight: 4.9990 overall best weight: 0.4254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 GLN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 377 ASN D 90 HIS U 80 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 33377 Z= 0.132 Angle : 0.463 10.958 45363 Z= 0.225 Chirality : 0.039 0.185 4959 Planarity : 0.004 0.053 5699 Dihedral : 11.710 149.292 5277 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.11 % Allowed : 12.55 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.14), residues: 3953 helix: 1.94 (0.11), residues: 2124 sheet: 1.00 (0.27), residues: 364 loop : 0.69 (0.17), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 142 HIS 0.004 0.000 HIS C 197 PHE 0.019 0.001 PHE J 20 TYR 0.019 0.001 TYR P 214 ARG 0.006 0.000 ARG P 201 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 294 time to evaluate : 3.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 GLU cc_start: 0.8873 (tt0) cc_final: 0.8647 (pm20) REVERT: P 129 HIS cc_start: 0.6872 (t-170) cc_final: 0.6355 (t70) REVERT: G 9 LYS cc_start: 0.9130 (mttp) cc_final: 0.8706 (tttm) REVERT: F 115 ASP cc_start: 0.8599 (p0) cc_final: 0.8213 (t0) REVERT: F 126 GLU cc_start: 0.9147 (mp0) cc_final: 0.8815 (mp0) REVERT: A 120 LYS cc_start: 0.9043 (tttt) cc_final: 0.8748 (ptmt) REVERT: A 390 LYS cc_start: 0.9080 (tptt) cc_final: 0.8777 (mttm) REVERT: B 139 LYS cc_start: 0.9217 (tttt) cc_final: 0.8967 (tppt) REVERT: B 388 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8009 (tm-30) REVERT: D 163 ASP cc_start: 0.9131 (m-30) cc_final: 0.8637 (p0) REVERT: I 43 ARG cc_start: 0.8797 (mtm-85) cc_final: 0.8414 (ttp-170) REVERT: J 11 LYS cc_start: 0.8903 (mtpm) cc_final: 0.8636 (pttp) REVERT: R 9 LYS cc_start: 0.9065 (mttp) cc_final: 0.8806 (ttpt) REVERT: Q 103 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8421 (tm-30) REVERT: L 240 GLN cc_start: 0.8859 (mp10) cc_final: 0.8351 (mm110) REVERT: M 388 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8317 (tm-30) REVERT: U 11 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8327 (ptpp) outliers start: 37 outliers final: 19 residues processed: 315 average time/residue: 1.6602 time to fit residues: 608.9143 Evaluate side-chains 301 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 281 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 51 TYR Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 74 SER Chi-restraints excluded: chain U residue 11 LYS Chi-restraints excluded: chain U residue 58 GLN Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 233 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 113 optimal weight: 0.2980 chunk 74 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 239 optimal weight: 0.8980 chunk 256 optimal weight: 6.9990 chunk 186 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 296 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 GLN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 ASN M 295 ASN U 80 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9131 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 33377 Z= 0.143 Angle : 0.464 11.511 45363 Z= 0.225 Chirality : 0.039 0.236 4959 Planarity : 0.004 0.053 5699 Dihedral : 11.446 149.425 5275 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.17 % Allowed : 12.64 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.14), residues: 3953 helix: 2.00 (0.11), residues: 2127 sheet: 1.08 (0.27), residues: 364 loop : 0.75 (0.17), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 142 HIS 0.006 0.001 HIS C 197 PHE 0.018 0.001 PHE A 334 TYR 0.024 0.001 TYR Q 114 ARG 0.002 0.000 ARG P 199 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 285 time to evaluate : 3.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 GLU cc_start: 0.8898 (tt0) cc_final: 0.8665 (pm20) REVERT: P 129 HIS cc_start: 0.6880 (t-170) cc_final: 0.6383 (t70) REVERT: G 9 LYS cc_start: 0.9137 (mttp) cc_final: 0.8708 (tttm) REVERT: F 107 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.9122 (mtpp) REVERT: F 115 ASP cc_start: 0.8612 (p0) cc_final: 0.8224 (t0) REVERT: F 126 GLU cc_start: 0.9152 (mp0) cc_final: 0.8827 (mp0) REVERT: A 120 LYS cc_start: 0.9045 (tttt) cc_final: 0.8745 (ptmt) REVERT: A 390 LYS cc_start: 0.9088 (tptt) cc_final: 0.8772 (mttm) REVERT: B 139 LYS cc_start: 0.9220 (tttt) cc_final: 0.8968 (tppt) REVERT: B 388 GLU cc_start: 0.8571 (tm-30) cc_final: 0.7973 (tm-30) REVERT: D 163 ASP cc_start: 0.9109 (m-30) cc_final: 0.8592 (p0) REVERT: I 43 ARG cc_start: 0.8798 (mtm-85) cc_final: 0.8412 (ttp-170) REVERT: J 11 LYS cc_start: 0.8874 (mtpm) cc_final: 0.8652 (pttp) REVERT: R 9 LYS cc_start: 0.9070 (mttp) cc_final: 0.8804 (ttpt) REVERT: Q 103 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8409 (tm-30) REVERT: L 240 GLN cc_start: 0.8875 (mp10) cc_final: 0.8370 (mm110) REVERT: M 236 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7966 (ttp-170) REVERT: M 388 GLU cc_start: 0.8770 (tm-30) cc_final: 0.8325 (tm-30) REVERT: U 11 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8263 (ptpp) REVERT: U 13 SER cc_start: 0.9056 (t) cc_final: 0.8452 (p) outliers start: 39 outliers final: 21 residues processed: 308 average time/residue: 1.7620 time to fit residues: 629.6088 Evaluate side-chains 307 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 283 time to evaluate : 3.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 51 TYR Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain S residue 74 SER Chi-restraints excluded: chain U residue 11 LYS Chi-restraints excluded: chain U residue 58 GLN Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 342 optimal weight: 0.9980 chunk 361 optimal weight: 0.0040 chunk 329 optimal weight: 9.9990 chunk 351 optimal weight: 9.9990 chunk 360 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 275 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 317 optimal weight: 2.9990 chunk 332 optimal weight: 0.0010 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 GLN ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 377 ASN U 80 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9127 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 33377 Z= 0.143 Angle : 0.465 11.386 45363 Z= 0.225 Chirality : 0.039 0.238 4959 Planarity : 0.004 0.053 5699 Dihedral : 11.265 149.380 5275 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.90 % Allowed : 13.18 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.14), residues: 3953 helix: 2.04 (0.11), residues: 2129 sheet: 1.13 (0.27), residues: 364 loop : 0.76 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP P 185 HIS 0.006 0.001 HIS C 197 PHE 0.018 0.001 PHE J 20 TYR 0.026 0.001 TYR M 170 ARG 0.002 0.000 ARG R 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 286 time to evaluate : 3.998 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 159 GLU cc_start: 0.8913 (tt0) cc_final: 0.8667 (pm20) REVERT: P 129 HIS cc_start: 0.6844 (t-170) cc_final: 0.6149 (t-90) REVERT: P 199 ARG cc_start: 0.7629 (mtt-85) cc_final: 0.6496 (mtt-85) REVERT: G 9 LYS cc_start: 0.9134 (mttp) cc_final: 0.8707 (tttm) REVERT: F 115 ASP cc_start: 0.8613 (p0) cc_final: 0.8227 (t0) REVERT: F 126 GLU cc_start: 0.9152 (mp0) cc_final: 0.8833 (mp0) REVERT: A 120 LYS cc_start: 0.9050 (tttt) cc_final: 0.8747 (ptmt) REVERT: A 390 LYS cc_start: 0.9085 (tptt) cc_final: 0.8773 (mttm) REVERT: B 139 LYS cc_start: 0.9220 (tttt) cc_final: 0.8969 (tppt) REVERT: B 388 GLU cc_start: 0.8591 (tm-30) cc_final: 0.7987 (tm-30) REVERT: D 163 ASP cc_start: 0.9119 (m-30) cc_final: 0.8606 (p0) REVERT: I 43 ARG cc_start: 0.8798 (mtm-85) cc_final: 0.8432 (ttp-170) REVERT: J 11 LYS cc_start: 0.8863 (mtpm) cc_final: 0.8655 (pttp) REVERT: R 9 LYS cc_start: 0.9072 (mttp) cc_final: 0.8803 (ttpt) REVERT: Q 103 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8405 (tm-30) REVERT: L 240 GLN cc_start: 0.8881 (mp10) cc_final: 0.8364 (mm110) REVERT: M 236 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7985 (ttp-170) REVERT: M 373 ILE cc_start: 0.9124 (pp) cc_final: 0.8901 (mm) REVERT: M 388 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8333 (tm-30) REVERT: U 11 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8191 (ptpp) REVERT: U 13 SER cc_start: 0.9043 (t) cc_final: 0.8433 (p) outliers start: 30 outliers final: 18 residues processed: 305 average time/residue: 1.6786 time to fit residues: 594.8235 Evaluate side-chains 303 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 283 time to evaluate : 3.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 51 TYR Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain S residue 74 SER Chi-restraints excluded: chain U residue 11 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 349 optimal weight: 7.9990 chunk 230 optimal weight: 0.0060 chunk 371 optimal weight: 0.6980 chunk 226 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 chunk 258 optimal weight: 9.9990 chunk 389 optimal weight: 0.2980 chunk 358 optimal weight: 2.9990 chunk 310 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 239 optimal weight: 1.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 GLN ** P 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 ASN M 295 ASN U 80 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 33377 Z= 0.144 Angle : 0.468 11.360 45363 Z= 0.226 Chirality : 0.039 0.208 4959 Planarity : 0.004 0.053 5699 Dihedral : 11.122 149.348 5275 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.66 % Allowed : 13.54 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.14), residues: 3953 helix: 2.07 (0.11), residues: 2127 sheet: 1.14 (0.27), residues: 364 loop : 0.77 (0.17), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP P 185 HIS 0.006 0.001 HIS C 197 PHE 0.018 0.001 PHE A 334 TYR 0.036 0.001 TYR M 170 ARG 0.005 0.000 ARG P 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7906 Ramachandran restraints generated. 3953 Oldfield, 0 Emsley, 3953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 284 time to evaluate : 3.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 159 GLU cc_start: 0.8912 (tt0) cc_final: 0.8667 (pm20) REVERT: P 129 HIS cc_start: 0.6887 (t-170) cc_final: 0.6237 (t-90) REVERT: G 9 LYS cc_start: 0.9138 (mttp) cc_final: 0.8708 (tttm) REVERT: F 115 ASP cc_start: 0.8615 (p0) cc_final: 0.8229 (t0) REVERT: F 126 GLU cc_start: 0.9153 (mp0) cc_final: 0.8843 (mp0) REVERT: A 120 LYS cc_start: 0.9033 (tttt) cc_final: 0.8737 (ptmt) REVERT: A 390 LYS cc_start: 0.9084 (tptt) cc_final: 0.8778 (mttm) REVERT: B 139 LYS cc_start: 0.9219 (tttt) cc_final: 0.8969 (tppt) REVERT: B 388 GLU cc_start: 0.8596 (tm-30) cc_final: 0.7986 (tm-30) REVERT: D 163 ASP cc_start: 0.9111 (m-30) cc_final: 0.8593 (p0) REVERT: I 43 ARG cc_start: 0.8784 (mtm-85) cc_final: 0.8423 (ttp-170) REVERT: J 11 LYS cc_start: 0.8833 (mtpm) cc_final: 0.8618 (pttp) REVERT: E 54 LYS cc_start: 0.9143 (mtpp) cc_final: 0.8890 (ttmp) REVERT: R 9 LYS cc_start: 0.9072 (mttp) cc_final: 0.8802 (ttpt) REVERT: R 22 LYS cc_start: 0.9205 (mtpt) cc_final: 0.8906 (mtmm) REVERT: Q 103 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8406 (tm-30) REVERT: L 240 GLN cc_start: 0.8867 (mp10) cc_final: 0.8358 (mm110) REVERT: M 236 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7980 (ttp-170) REVERT: M 388 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8590 (pp20) REVERT: O 85 MET cc_start: 0.8579 (ptp) cc_final: 0.8376 (ptm) REVERT: U 11 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8113 (ptpp) REVERT: U 13 SER cc_start: 0.9044 (t) cc_final: 0.8444 (p) outliers start: 22 outliers final: 17 residues processed: 299 average time/residue: 1.7586 time to fit residues: 611.9966 Evaluate side-chains 300 residues out of total 3324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 281 time to evaluate : 3.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 51 TYR Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain P residue 222 LEU Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain S residue 74 SER Chi-restraints excluded: chain U residue 11 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 391 random chunks: chunk 190 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 330 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 286 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 310 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 319 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN ** P 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 GLN B 377 ASN U 80 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.073466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.055615 restraints weight = 60084.204| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 1.79 r_work: 0.2544 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2426 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9127 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 33377 Z= 0.282 Angle : 0.540 13.784 45363 Z= 0.259 Chirality : 0.042 0.200 4959 Planarity : 0.004 0.054 5699 Dihedral : 11.534 150.525 5275 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.87 % Allowed : 13.39 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.14), residues: 3953 helix: 1.92 (0.11), residues: 2125 sheet: 1.04 (0.27), residues: 365 loop : 0.77 (0.17), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP P 185 HIS 0.013 0.001 HIS C 197 PHE 0.022 0.002 PHE A 334 TYR 0.039 0.002 TYR M 170 ARG 0.006 0.000 ARG P 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10864.54 seconds wall clock time: 196 minutes 3.73 seconds (11763.73 seconds total)