Starting phenix.real_space_refine on Thu Feb 22 01:04:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aba_15316/02_2024/8aba_15316_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aba_15316/02_2024/8aba_15316.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aba_15316/02_2024/8aba_15316_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aba_15316/02_2024/8aba_15316_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aba_15316/02_2024/8aba_15316_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aba_15316/02_2024/8aba_15316.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aba_15316/02_2024/8aba_15316.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aba_15316/02_2024/8aba_15316_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aba_15316/02_2024/8aba_15316_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 8 7.16 5 P 30 5.49 5 S 102 5.16 5 C 21031 2.51 5 N 5296 2.21 5 O 6073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 4": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C 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 "A GLU 457": "OE1" <-> "OE2" Residue "A TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B GLU 350": "OE1" <-> "OE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "D ARG 189": "NH1" <-> "NH2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "D TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D ARG 321": "NH1" <-> "NH2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "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 "E ARG 56": "NH1" <-> "NH2" Residue "R GLU 12": "OE1" <-> "OE2" Residue "R GLU 50": "OE1" <-> "OE2" Residue "R GLU 51": "OE1" <-> "OE2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R ARG 61": "NH1" <-> "NH2" Residue "R GLU 66": "OE1" <-> "OE2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R ARG 73": "NH1" <-> "NH2" Residue "R ARG 76": "NH1" <-> "NH2" Residue "R GLU 96": "OE1" <-> "OE2" Residue "R GLU 110": "OE1" <-> "OE2" Residue "R GLU 123": "OE1" <-> "OE2" Residue "Q GLU 88": "OE1" <-> "OE2" Residue "Q GLU 118": "OE1" <-> "OE2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "Q GLU 126": "OE1" <-> "OE2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "L GLU 141": "OE1" <-> "OE2" Residue "L ARG 188": "NH1" <-> "NH2" Residue "L GLU 354": "OE1" <-> "OE2" Residue "L ARG 384": "NH1" <-> "NH2" Residue "L GLU 424": "OE1" <-> "OE2" Residue "L GLU 457": "OE1" <-> "OE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M GLU 78": "OE1" <-> "OE2" Residue "M TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 117": "OE1" <-> "OE2" Residue "M ARG 140": "NH1" <-> "NH2" Residue "M GLU 150": "OE1" <-> "OE2" Residue "M ARG 234": "NH1" <-> "NH2" Residue "M GLU 313": "OE1" <-> "OE2" Residue "M GLU 350": "OE1" <-> "OE2" Residue "M GLU 376": "OE1" <-> "OE2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "O ARG 132": "NH1" <-> "NH2" Residue "O ARG 136": "NH1" <-> "NH2" Residue "O GLU 164": "OE1" <-> "OE2" Residue "O ARG 170": "NH1" <-> "NH2" Residue "O ARG 189": "NH1" <-> "NH2" Residue "O ARG 207": "NH1" <-> "NH2" Residue "O TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 250": "NH1" <-> "NH2" Residue "O GLU 260": "OE1" <-> "OE2" Residue "O ARG 289": "NH1" <-> "NH2" Residue "O ARG 321": "NH1" <-> "NH2" Residue "S PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 34": "OE1" <-> "OE2" Residue "U TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32540 Number of models: 1 Model: "" Number of chains: 31 Chain: "C" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "P" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1445 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 11, 'TRANS': 174} Chain: "G" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "A" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "B" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "D" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "I" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "J" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "N" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "E" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "R" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "Q" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "L" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "M" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "O" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "S" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "T" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "U" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "C" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 248 Unusual residues: {'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "P" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'FES': 1, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "A" 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: 115 Unresolved non-hydrogen dihedrals: 111 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: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 59 Unusual residues: {'LMT': 1, 'XP4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "N" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 298 Unusual residues: {'CDL': 2, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 127 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 29.901 46.532 27.632 1.00284.47 S ATOM 4207 SG CYS P 187 32.231 44.484 25.278 1.00237.01 S Time building chain proxies: 17.42, per 1000 atoms: 0.54 Number of scatterers: 32540 At special positions: 0 Unit cell: (118.833, 128.805, 165.369, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 8 26.01 S 102 16.00 P 30 15.00 O 6073 8.00 N 5296 7.00 C 21031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS P 173 " - pdb=" SG CYS P 189 " distance=2.04 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.06 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.07 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.06 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.92 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 301 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 170 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 190 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 187 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 168 " Number of angles added : 3 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7486 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 185 helices and 15 sheets defined 54.3% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.11 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: 3.909A pdb=" N PHE C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY C 33 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR C 46 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.578A 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: 3.709A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 135 removed outlier: 4.163A pdb=" N VAL C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 153 removed outlier: 3.575A pdb=" N LEU C 150 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL C 151 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER C 152 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA C 153 " --> pdb=" O ASN C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 166 Processing helix chain 'C' and resid 173 through 203 Proline residue: C 187 - end of helix removed outlier: 4.030A pdb=" N THR C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 246 removed outlier: 6.769A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.829A 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: 3.807A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LEU C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.936A 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: 4.043A 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: 3.611A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN P 90 " --> pdb=" O ASP P 86 " (cutoff:3.500A) removed outlier: 4.889A 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: 3.625A 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: 3.579A 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: 3.519A pdb=" N HIS A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 4.216A 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: 3.831A pdb=" N VAL A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Proline residue: A 124 - end of helix removed outlier: 3.871A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 154 removed outlier: 3.996A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.774A 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: 3.573A pdb=" N THR A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 206 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.985A 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: 3.583A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 395 removed outlier: 3.564A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.411A 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: 3.664A pdb=" N ASP A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.980A 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: 3.638A pdb=" N LYS B 116 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU B 117 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 129 through 141 Processing helix chain 'B' and resid 144 through 157 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 200 through 210 removed outlier: 3.514A pdb=" N THR B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.718A 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: 3.686A 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: 3.514A pdb=" N PHE D 215 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 282 Processing helix chain 'D' and resid 286 through 319 Proline residue: D 317 - end of helix Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 40 through 81 removed outlier: 4.417A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) Proline residue: H 62 - end of helix Processing helix chain 'H' and resid 86 through 92 Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 44 Processing helix chain 'I' and resid 50 through 56 removed outlier: 4.946A pdb=" N HIS I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 49 removed outlier: 3.535A pdb=" N LYS J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 3.576A 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: 3.907A pdb=" N PHE N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY N 33 " --> pdb=" O TRP N 30 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR N 46 " --> pdb=" O GLN N 43 " (cutoff:3.500A) removed outlier: 3.569A 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: 3.712A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 135 removed outlier: 4.158A pdb=" N VAL N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 138 through 153 removed outlier: 3.568A pdb=" N LEU N 150 " --> pdb=" O VAL N 146 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL N 151 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER N 152 " --> pdb=" O CYS N 148 " (cutoff:3.500A) removed outlier: 4.288A 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: 4.025A pdb=" N THR N 203 " --> pdb=" O ILE N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 246 removed outlier: 6.779A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.823A 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: 3.815A pdb=" N ILE N 299 " --> pdb=" O MET N 295 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU N 302 " --> pdb=" O ALA N 298 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU N 303 " --> pdb=" O ILE N 299 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE N 304 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 3.929A 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: 4.044A 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: 3.608A pdb=" N SER E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASN E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N MET E 91 " --> pdb=" O PHE E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 98 No H-bonds generated for 'chain 'E' and resid 95 through 98' Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 35 Proline residue: R 26 - end of helix Processing helix chain 'R' and resid 37 through 40 Processing helix chain 'R' and resid 44 through 47 Processing helix chain 'R' and resid 53 through 60 Processing helix chain 'R' and resid 64 through 83 Processing helix chain 'R' and resid 89 through 91 No H-bonds generated for 'chain 'R' and resid 89 through 91' Processing helix chain 'R' and resid 103 through 121 removed outlier: 3.635A 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: 3.586A pdb=" N VAL Q 145 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 72 through 79 Processing helix chain 'L' and resid 89 through 99 Processing helix chain 'L' and resid 120 through 135 removed outlier: 3.831A pdb=" N VAL L 123 " --> pdb=" O LYS L 120 " (cutoff:3.500A) Proline residue: L 124 - end of helix removed outlier: 3.865A pdb=" N VAL L 127 " --> pdb=" O PRO L 124 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU L 134 " --> pdb=" O ALA L 131 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN L 135 " --> pdb=" O ASP L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 154 removed outlier: 3.989A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 160 No H-bonds generated for 'chain 'L' and resid 158 through 160' Processing helix chain 'L' and resid 162 through 174 Processing helix chain 'L' and resid 179 through 181 No H-bonds generated for 'chain 'L' and resid 179 through 181' Processing helix chain 'L' and resid 188 through 191 No H-bonds generated for 'chain 'L' and resid 188 through 191' Processing helix chain 'L' and resid 196 through 206 Processing helix chain 'L' and resid 209 through 211 No H-bonds generated for 'chain 'L' and resid 209 through 211' Processing helix chain 'L' and resid 222 through 232 Processing helix chain 'L' and resid 294 through 304 Processing helix chain 'L' and resid 312 through 316 removed outlier: 3.978A pdb=" N ARG L 315 " --> pdb=" O GLY L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 320 through 327 Processing helix chain 'L' and resid 359 through 375 removed outlier: 3.582A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 395 removed outlier: 3.624A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.394A 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: 3.659A pdb=" N ASP L 468 " --> pdb=" O ARG L 464 " (cutoff:3.500A) removed outlier: 3.980A 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: 3.626A pdb=" N VAL M 108 " --> pdb=" O PRO M 105 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS M 116 " --> pdb=" O ASN M 113 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU M 117 " --> pdb=" O VAL M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 127 Processing helix chain 'M' and resid 129 through 141 Processing helix chain 'M' and resid 144 through 157 Processing helix chain 'M' and resid 160 through 162 No H-bonds generated for 'chain 'M' and resid 160 through 162' Processing helix chain 'M' and resid 175 through 185 Processing helix chain 'M' and resid 188 through 190 No H-bonds generated for 'chain 'M' and resid 188 through 190' Processing helix chain 'M' and resid 200 through 210 removed outlier: 3.512A pdb=" N THR M 209 " --> pdb=" O GLN M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 263 removed outlier: 3.712A 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: 3.894A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 375 through 377 No H-bonds generated for 'chain 'M' and resid 375 through 377' Processing helix chain 'M' and resid 383 through 394 Processing helix chain 'M' and resid 407 through 409 No H-bonds generated for 'chain 'M' and resid 407 through 409' Processing helix chain 'M' and resid 413 through 415 No H-bonds generated for 'chain 'M' and resid 413 through 415' Processing helix chain 'O' and resid 87 through 90 No H-bonds generated for 'chain 'O' and resid 87 through 90' Processing helix chain 'O' and resid 110 through 122 Processing helix chain 'O' and resid 124 through 126 No H-bonds generated for 'chain 'O' and resid 124 through 126' Processing helix chain 'O' and resid 135 through 138 No H-bonds generated for 'chain 'O' and resid 135 through 138' Processing helix chain 'O' and resid 145 through 153 Processing helix chain 'O' and resid 185 through 192 Processing helix chain 'O' and resid 210 through 218 removed outlier: 3.517A pdb=" N PHE O 215 " --> pdb=" O ASP O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 267 through 282 Processing helix chain 'O' and resid 286 through 319 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 31 through 33 No H-bonds generated for 'chain 'S' and resid 31 through 33' Processing helix chain 'S' and resid 40 through 81 removed outlier: 4.419A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL S 59 " --> pdb=" O GLN S 55 " (cutoff:3.500A) Proline residue: S 62 - end of helix Processing helix chain 'S' and resid 86 through 92 Processing helix chain 'T' and resid 5 through 11 Processing helix chain 'T' and resid 15 through 44 Processing helix chain 'T' and resid 50 through 56 removed outlier: 4.937A pdb=" N HIS T 55 " --> pdb=" O LYS T 51 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS T 56 " --> pdb=" O ASP T 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 49 removed outlier: 3.593A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.568A 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: 3.873A pdb=" N LYS P 114 " --> pdb=" O HIS P 129 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'P' and resid 185 through 187 Processing sheet with id= E, first strand: chain 'A' and resid 31 through 34 Processing sheet with id= F, first strand: chain 'A' and resid 266 through 271 Processing sheet with id= G, first strand: chain 'B' and resid 16 through 20 removed outlier: 4.051A 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: 3.563A 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: 4.044A 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: 3.559A 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 1583 hydrogen bonds defined for protein. 4326 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: 10.40 Time building geometry restraints manager: 14.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 13593 1.41 - 1.61: 19561 1.61 - 1.82: 174 1.82 - 2.03: 19 2.03 - 2.24: 20 Bond restraints: 33367 Sorted by residual: bond pdb=" N TYR S 9 " pdb=" CA TYR S 9 " ideal model delta sigma weight residual 1.458 1.638 -0.180 1.90e-02 2.77e+03 9.00e+01 bond pdb=" N TYR H 9 " pdb=" CA TYR H 9 " ideal model delta sigma weight residual 1.458 1.637 -0.179 1.90e-02 2.77e+03 8.86e+01 bond pdb=" C31 CDL A3001 " pdb=" CA7 CDL A3001 " ideal model delta sigma weight residual 1.500 1.615 -0.115 1.50e-02 4.44e+03 5.89e+01 bond pdb=" N ALA T 4 " pdb=" CA ALA T 4 " ideal model delta sigma weight residual 1.458 1.600 -0.142 1.90e-02 2.77e+03 5.60e+01 bond pdb=" N ALA I 4 " pdb=" CA ALA I 4 " ideal model delta sigma weight residual 1.458 1.596 -0.138 1.90e-02 2.77e+03 5.30e+01 ... (remaining 33362 not shown) Histogram of bond angle deviations from ideal: 83.16 - 102.43: 330 102.43 - 121.71: 37850 121.71 - 140.98: 7160 140.98 - 160.26: 0 160.26 - 179.53: 12 Bond angle restraints: 45352 Sorted by residual: angle pdb=" CG ARG B 90 " pdb=" CD ARG B 90 " pdb=" NE ARG B 90 " ideal model delta sigma weight residual 112.00 89.71 22.29 2.20e+00 2.07e-01 1.03e+02 angle pdb=" CG ARG M 90 " pdb=" CD ARG M 90 " pdb=" NE ARG M 90 " ideal model delta sigma weight residual 112.00 91.29 20.71 2.20e+00 2.07e-01 8.86e+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 93.98 10.35 1.14e+00 7.69e-01 8.24e+01 angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.14 97.13 14.01 1.56e+00 4.11e-01 8.07e+01 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 93.70 10.63 1.20e+00 6.94e-01 7.85e+01 ... (remaining 45347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.42: 18764 31.42 - 62.83: 1083 62.83 - 94.25: 112 94.25 - 125.66: 1 125.66 - 157.08: 3 Dihedral angle restraints: 19963 sinusoidal: 8344 harmonic: 11619 Sorted by residual: dihedral pdb=" C GLU O 283 " pdb=" N GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta harmonic sigma weight residual -122.60 -104.74 -17.86 0 2.50e+00 1.60e-01 5.11e+01 dihedral pdb=" C2B HEC O 401 " pdb=" C3B HEC O 401 " pdb=" CAB HEC O 401 " pdb=" CBB HEC O 401 " ideal model delta sinusoidal sigma weight residual 60.00 -3.75 63.75 2 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" C2B HEC D 401 " pdb=" C3B HEC D 401 " pdb=" CAB HEC D 401 " pdb=" CBB HEC D 401 " ideal model delta sinusoidal sigma weight residual 60.00 -2.96 62.96 2 1.00e+01 1.00e-02 3.81e+01 ... (remaining 19960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 4605 0.199 - 0.398: 342 0.398 - 0.596: 11 0.596 - 0.795: 0 0.795 - 0.994: 4 Chirality restraints: 4962 Sorted by residual: chirality pdb=" CB4 CDL H 702 " pdb=" CB3 CDL H 702 " pdb=" CB6 CDL H 702 " pdb=" OB6 CDL H 702 " both_signs ideal model delta sigma weight residual False -2.57 -1.58 -0.99 2.00e-01 2.50e+01 2.47e+01 chirality pdb=" CB4 CDL N 506 " pdb=" CB3 CDL N 506 " pdb=" CB6 CDL N 506 " pdb=" OB6 CDL N 506 " both_signs ideal model delta sigma weight residual False -2.57 -1.62 -0.96 2.00e-01 2.50e+01 2.28e+01 chirality pdb=" CB4 CDL C 505 " pdb=" CB3 CDL C 505 " pdb=" CB6 CDL C 505 " pdb=" OB6 CDL C 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.65 -0.92 2.00e-01 2.50e+01 2.12e+01 ... (remaining 4959 not shown) Planarity restraints: 5700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A HEC D 401 " -0.015 2.00e-02 2.50e+03 3.21e-02 2.32e+01 pdb=" C2A HEC D 401 " -0.025 2.00e-02 2.50e+03 pdb=" C3A HEC D 401 " -0.031 2.00e-02 2.50e+03 pdb=" C4A HEC D 401 " -0.032 2.00e-02 2.50e+03 pdb=" CAA HEC D 401 " 0.051 2.00e-02 2.50e+03 pdb=" CHA HEC D 401 " 0.011 2.00e-02 2.50e+03 pdb=" CHB HEC D 401 " 0.060 2.00e-02 2.50e+03 pdb=" CMA HEC D 401 " -0.010 2.00e-02 2.50e+03 pdb=" NA HEC D 401 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC O 401 " -0.027 2.00e-02 2.50e+03 2.96e-02 1.98e+01 pdb=" C2C HEC O 401 " -0.021 2.00e-02 2.50e+03 pdb=" C3C HEC O 401 " 0.001 2.00e-02 2.50e+03 pdb=" C4C HEC O 401 " -0.014 2.00e-02 2.50e+03 pdb=" CAC HEC O 401 " 0.047 2.00e-02 2.50e+03 pdb=" CHC HEC O 401 " 0.058 2.00e-02 2.50e+03 pdb=" CHD HEC O 401 " -0.006 2.00e-02 2.50e+03 pdb=" CMC HEC O 401 " -0.027 2.00e-02 2.50e+03 pdb=" NC HEC O 401 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 474 " 0.057 2.00e-02 2.50e+03 2.74e-02 1.88e+01 pdb=" CG TRP A 474 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP A 474 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 474 " -0.022 2.00e-02 2.50e+03 pdb=" NE1 TRP A 474 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 474 " -0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP A 474 " -0.039 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 474 " 0.024 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 474 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 474 " 0.021 2.00e-02 2.50e+03 ... (remaining 5697 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 313 2.63 - 3.20: 29439 3.20 - 3.77: 53800 3.77 - 4.33: 80114 4.33 - 4.90: 122220 Nonbonded interactions: 285886 Sorted by model distance: nonbonded pdb=" NE2 HIS C 82 " pdb="FE HEM C 501 " model vdw 2.064 3.080 nonbonded pdb=" NE2 HIS N 82 " pdb="FE HEM N 501 " model vdw 2.090 3.080 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.131 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.162 2.520 nonbonded pdb=" SD MET O 248 " pdb="FE HEC O 401 " model vdw 2.171 3.360 ... (remaining 285881 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' and (resid 26 through 474 or resid 3001 through 3002)) } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = (chain 'C' and (resid 1 through 383 or resid 501 through 503)) selection = (chain 'N' and (resid 1 through 383 or resid 501 through 503)) } ncs_group { reference = chain 'D' selection = (chain 'O' and (resid 85 through 328 or resid 401)) } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = (chain 'H' and resid 9 through 93) selection = chain 'S' } ncs_group { reference = (chain 'I' and resid 4 through 57) 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 11.650 Check model and map are aligned: 0.500 Set scattering table: 0.310 Process input model: 91.210 Find NCS groups from input model: 2.070 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9211 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.221 33367 Z= 0.707 Angle : 1.765 22.287 45352 Z= 1.105 Chirality : 0.112 0.994 4962 Planarity : 0.007 0.081 5700 Dihedral : 18.438 157.081 12462 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.58 % Allowed : 8.24 % Favored : 88.18 % Cbeta Deviations : 1.02 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.12), residues: 3955 helix: -1.23 (0.09), residues: 2141 sheet: 0.01 (0.25), residues: 357 loop : -0.70 (0.16), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.007 TRP A 474 HIS 0.027 0.004 HIS Q 92 PHE 0.046 0.006 PHE B 107 TYR 0.041 0.007 TYR O 120 ARG 0.031 0.002 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 486 time to evaluate : 3.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 369 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8929 (ttm) REVERT: P 92 SER cc_start: 0.9643 (t) cc_final: 0.9262 (p) REVERT: P 114 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8661 (mmmm) REVERT: P 158 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8277 (ttmm) REVERT: P 164 MET cc_start: 0.9097 (mtm) cc_final: 0.8782 (mtm) REVERT: P 213 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: F 91 CYS cc_start: 0.8785 (m) cc_final: 0.8585 (m) REVERT: F 116 HIS cc_start: 0.8910 (m-70) cc_final: 0.8429 (m90) REVERT: A 141 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8687 (tp30) REVERT: A 275 MET cc_start: 0.9391 (mtp) cc_final: 0.9186 (mtp) REVERT: B 364 MET cc_start: 0.9204 (tpp) cc_final: 0.8985 (mmm) REVERT: D 224 GLU cc_start: 0.9344 (tt0) cc_final: 0.9101 (pm20) REVERT: D 248 MET cc_start: 0.9306 (ttp) cc_final: 0.8576 (ttp) REVERT: H 57 LEU cc_start: 0.8989 (mt) cc_final: 0.8665 (tp) REVERT: H 76 LYS cc_start: 0.9087 (tptm) cc_final: 0.8817 (tppt) REVERT: I 30 ASP cc_start: 0.9438 (t70) cc_final: 0.9169 (t0) REVERT: I 43 ARG cc_start: 0.9167 (mtm110) cc_final: 0.8658 (ttp80) REVERT: J 13 SER cc_start: 0.9256 (t) cc_final: 0.8971 (p) REVERT: J 58 GLN cc_start: 0.9333 (tp40) cc_final: 0.8662 (tm-30) REVERT: J 63 LYS cc_start: 0.9057 (mmtp) cc_final: 0.8725 (mptt) REVERT: J 80 ASN cc_start: 0.9340 (t0) cc_final: 0.9035 (t0) REVERT: N 186 MET cc_start: 0.9544 (tpp) cc_final: 0.9290 (mmt) REVERT: N 287 ASP cc_start: 0.8786 (t0) cc_final: 0.8346 (t70) REVERT: E 55 ASP cc_start: 0.8898 (OUTLIER) cc_final: 0.8435 (p0) REVERT: R 44 MET cc_start: 0.9540 (tmm) cc_final: 0.9320 (tmm) REVERT: R 50 GLU cc_start: 0.9084 (pt0) cc_final: 0.8799 (pm20) REVERT: Q 95 LYS cc_start: 0.9415 (tptt) cc_final: 0.9209 (tptp) REVERT: Q 113 ASP cc_start: 0.9288 (m-30) cc_final: 0.8953 (t0) REVERT: Q 122 ASP cc_start: 0.8692 (p0) cc_final: 0.8412 (p0) REVERT: Q 126 GLU cc_start: 0.9293 (mp0) cc_final: 0.8578 (mp0) REVERT: L 29 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8996 (ptmm) REVERT: L 48 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8897 (tt) REVERT: L 159 ASN cc_start: 0.7654 (p0) cc_final: 0.7411 (p0) REVERT: L 405 GLU cc_start: 0.9288 (mt-10) cc_final: 0.9035 (tm-30) REVERT: M 197 ASN cc_start: 0.8927 (t0) cc_final: 0.8679 (t0) REVERT: M 341 TYR cc_start: 0.9210 (t80) cc_final: 0.8795 (t80) REVERT: M 345 LYS cc_start: 0.9457 (OUTLIER) cc_final: 0.9218 (ttmm) REVERT: S 22 LYS cc_start: 0.9409 (tttt) cc_final: 0.9206 (tttm) REVERT: U 10 LYS cc_start: 0.9506 (tttm) cc_final: 0.9288 (tptm) REVERT: U 13 SER cc_start: 0.9290 (t) cc_final: 0.9088 (p) REVERT: U 58 GLN cc_start: 0.9378 (tp40) cc_final: 0.9169 (tt0) REVERT: U 74 GLU cc_start: 0.8966 (mp0) cc_final: 0.8522 (pp20) outliers start: 119 outliers final: 13 residues processed: 563 average time/residue: 0.5140 time to fit residues: 439.1110 Evaluate side-chains 356 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 334 time to evaluate : 4.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain P residue 114 LYS Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain N residue 178 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 345 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 5.9990 chunk 297 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 101 optimal weight: 7.9990 chunk 200 optimal weight: 0.0970 chunk 158 optimal weight: 0.0170 chunk 307 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 186 optimal weight: 3.9990 chunk 228 optimal weight: 0.6980 chunk 355 optimal weight: 6.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN C 22 GLN C 173 ASN C 202 HIS C 332 ASN P 85 GLN P 90 ASN G 54 ASN G 84 HIS A 192 GLN A 222 HIS A 371 ASN B 87 HIS B 197 ASN I 49 GLN N 14 ASN N 202 HIS N 332 ASN E 90 ASN L 332 ASN L 371 ASN M 87 HIS ** M 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 GLN M 197 ASN M 316 GLN M 377 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9132 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 33367 Z= 0.177 Angle : 0.595 15.954 45352 Z= 0.294 Chirality : 0.041 0.175 4962 Planarity : 0.004 0.038 5700 Dihedral : 14.252 154.166 5323 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.32 % Allowed : 11.16 % Favored : 87.52 % 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: 0.59 (0.13), residues: 3955 helix: 0.78 (0.11), residues: 2132 sheet: 0.42 (0.27), residues: 368 loop : -0.02 (0.17), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP N 156 HIS 0.006 0.001 HIS C 197 PHE 0.019 0.002 PHE L 334 TYR 0.026 0.002 TYR F 114 ARG 0.005 0.001 ARG Q 104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 377 time to evaluate : 3.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 255 ASP cc_start: 0.9406 (m-30) cc_final: 0.9156 (m-30) REVERT: P 164 MET cc_start: 0.8795 (mtm) cc_final: 0.8509 (mtm) REVERT: P 213 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8062 (mp0) REVERT: F 77 ASP cc_start: 0.8902 (t0) cc_final: 0.8607 (t0) REVERT: F 107 LYS cc_start: 0.9369 (ttmt) cc_final: 0.9088 (tptp) REVERT: F 114 TYR cc_start: 0.8727 (t80) cc_final: 0.8186 (t80) REVERT: F 120 LYS cc_start: 0.9339 (mttp) cc_final: 0.8795 (mmtp) REVERT: B 60 PHE cc_start: 0.9604 (OUTLIER) cc_final: 0.9288 (t80) REVERT: D 224 GLU cc_start: 0.9387 (tt0) cc_final: 0.9145 (pm20) REVERT: D 248 MET cc_start: 0.8527 (ttp) cc_final: 0.7976 (ttp) REVERT: H 57 LEU cc_start: 0.9019 (mt) cc_final: 0.8782 (tp) REVERT: H 76 LYS cc_start: 0.9010 (tptm) cc_final: 0.8668 (tppt) REVERT: I 43 ARG cc_start: 0.9064 (mtm110) cc_final: 0.8658 (ttp80) REVERT: J 13 SER cc_start: 0.9232 (t) cc_final: 0.8989 (p) REVERT: J 80 ASN cc_start: 0.9309 (t0) cc_final: 0.8968 (t0) REVERT: N 16 TYR cc_start: 0.9050 (m-80) cc_final: 0.8755 (m-80) REVERT: N 287 ASP cc_start: 0.8437 (t0) cc_final: 0.8055 (t0) REVERT: E 55 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8438 (p0) REVERT: R 31 TYR cc_start: 0.9042 (t80) cc_final: 0.8824 (t80) REVERT: R 51 GLU cc_start: 0.9539 (mp0) cc_final: 0.9196 (mp0) REVERT: R 117 ASP cc_start: 0.9202 (m-30) cc_final: 0.8869 (t0) REVERT: Q 113 ASP cc_start: 0.9288 (m-30) cc_final: 0.9047 (t0) REVERT: L 29 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.9033 (ptmm) REVERT: L 48 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8689 (tt) REVERT: M 60 PHE cc_start: 0.9629 (OUTLIER) cc_final: 0.9230 (t80) REVERT: S 22 LYS cc_start: 0.9241 (tttt) cc_final: 0.8981 (tttm) outliers start: 44 outliers final: 15 residues processed: 414 average time/residue: 0.4831 time to fit residues: 311.4972 Evaluate side-chains 340 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 320 time to evaluate : 4.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 74 SER Chi-restraints excluded: chain U residue 79 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 296 optimal weight: 6.9990 chunk 242 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 356 optimal weight: 0.7980 chunk 385 optimal weight: 0.0370 chunk 317 optimal weight: 0.9990 chunk 353 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 286 optimal weight: 30.0000 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN A 364 HIS B 168 GLN B 316 GLN D 93 HIS N 22 GLN N 177 GLN M 392 GLN O 90 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9137 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33367 Z= 0.179 Angle : 0.522 12.664 45352 Z= 0.255 Chirality : 0.040 0.169 4962 Planarity : 0.004 0.045 5700 Dihedral : 12.949 150.761 5285 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.11 % Allowed : 11.64 % Favored : 87.25 % 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: 1.31 (0.13), residues: 3955 helix: 1.40 (0.11), residues: 2141 sheet: 0.69 (0.27), residues: 368 loop : 0.26 (0.17), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 142 HIS 0.012 0.001 HIS D 93 PHE 0.016 0.001 PHE L 334 TYR 0.017 0.001 TYR F 114 ARG 0.013 0.000 ARG P 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 331 time to evaluate : 3.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 255 ASP cc_start: 0.9431 (m-30) cc_final: 0.9162 (m-30) REVERT: P 213 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8233 (mp0) REVERT: G 117 ASP cc_start: 0.9040 (m-30) cc_final: 0.8717 (t0) REVERT: F 107 LYS cc_start: 0.9356 (ttmt) cc_final: 0.9079 (tptp) REVERT: F 114 TYR cc_start: 0.8611 (t80) cc_final: 0.7999 (t80) REVERT: F 120 LYS cc_start: 0.9306 (mttp) cc_final: 0.8696 (mmtp) REVERT: F 126 GLU cc_start: 0.9301 (mp0) cc_final: 0.9049 (mp0) REVERT: B 60 PHE cc_start: 0.9597 (OUTLIER) cc_final: 0.9286 (t80) REVERT: B 83 LYS cc_start: 0.9467 (mmtm) cc_final: 0.9251 (mtmt) REVERT: B 213 ASP cc_start: 0.9475 (m-30) cc_final: 0.9060 (t0) REVERT: D 224 GLU cc_start: 0.9423 (tt0) cc_final: 0.9109 (pm20) REVERT: H 57 LEU cc_start: 0.8988 (mt) cc_final: 0.8756 (tp) REVERT: H 76 LYS cc_start: 0.9009 (tptm) cc_final: 0.8674 (tppt) REVERT: I 43 ARG cc_start: 0.9027 (mtm110) cc_final: 0.8665 (ttp80) REVERT: J 13 SER cc_start: 0.9251 (t) cc_final: 0.9028 (p) REVERT: J 80 ASN cc_start: 0.9285 (t0) cc_final: 0.8936 (t0) REVERT: N 287 ASP cc_start: 0.8386 (t0) cc_final: 0.7964 (t0) REVERT: E 55 ASP cc_start: 0.8796 (OUTLIER) cc_final: 0.8513 (p0) REVERT: R 117 ASP cc_start: 0.9199 (m-30) cc_final: 0.8910 (t0) REVERT: L 29 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.9056 (ptmm) REVERT: M 60 PHE cc_start: 0.9606 (OUTLIER) cc_final: 0.9140 (t80) REVERT: S 22 LYS cc_start: 0.9290 (tttt) cc_final: 0.9030 (tttm) outliers start: 37 outliers final: 19 residues processed: 357 average time/residue: 0.4748 time to fit residues: 269.3395 Evaluate side-chains 331 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 307 time to evaluate : 3.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 168 CYS Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain S residue 28 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 7.9990 chunk 268 optimal weight: 10.0000 chunk 185 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 239 optimal weight: 2.9990 chunk 357 optimal weight: 0.9990 chunk 378 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 339 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN B 168 GLN B 316 GLN N 22 GLN E 85 GLN L 50 GLN O 236 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9204 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 33367 Z= 0.467 Angle : 0.636 19.457 45352 Z= 0.299 Chirality : 0.044 0.160 4962 Planarity : 0.004 0.050 5700 Dihedral : 12.627 150.147 5275 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.65 % Allowed : 12.18 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.13), residues: 3955 helix: 1.46 (0.11), residues: 2124 sheet: 0.56 (0.27), residues: 368 loop : 0.39 (0.17), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 142 HIS 0.011 0.001 HIS N 96 PHE 0.017 0.002 PHE N 240 TYR 0.017 0.002 TYR C 16 ARG 0.006 0.000 ARG P 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 304 time to evaluate : 3.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 255 ASP cc_start: 0.9501 (m-30) cc_final: 0.9199 (m-30) REVERT: P 150 GLN cc_start: 0.8835 (tt0) cc_final: 0.8605 (tt0) REVERT: P 213 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8123 (mp0) REVERT: F 107 LYS cc_start: 0.9354 (ttmt) cc_final: 0.9079 (tptp) REVERT: B 60 PHE cc_start: 0.9639 (OUTLIER) cc_final: 0.9358 (t80) REVERT: B 213 ASP cc_start: 0.9439 (m-30) cc_final: 0.9086 (t0) REVERT: D 224 GLU cc_start: 0.9471 (tt0) cc_final: 0.9151 (pm20) REVERT: H 57 LEU cc_start: 0.9003 (mt) cc_final: 0.8765 (tp) REVERT: H 76 LYS cc_start: 0.9076 (tptm) cc_final: 0.8743 (tppt) REVERT: I 43 ARG cc_start: 0.8991 (mtm110) cc_final: 0.8633 (ttp80) REVERT: J 80 ASN cc_start: 0.9316 (t0) cc_final: 0.9006 (t0) REVERT: N 287 ASP cc_start: 0.8431 (t0) cc_final: 0.8006 (t0) REVERT: E 55 ASP cc_start: 0.9003 (OUTLIER) cc_final: 0.8782 (p0) REVERT: R 117 ASP cc_start: 0.9212 (m-30) cc_final: 0.8955 (t0) REVERT: L 29 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9062 (ptmm) REVERT: M 60 PHE cc_start: 0.9661 (OUTLIER) cc_final: 0.9228 (t80) REVERT: S 22 LYS cc_start: 0.9461 (tttt) cc_final: 0.9179 (tttm) REVERT: U 11 LYS cc_start: 0.9076 (mtpp) cc_final: 0.8765 (mtmm) outliers start: 55 outliers final: 36 residues processed: 346 average time/residue: 0.4579 time to fit residues: 254.9960 Evaluate side-chains 338 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 297 time to evaluate : 3.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 168 CYS Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain H residue 18 SER Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 239 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 301 SER Chi-restraints excluded: chain O residue 307 SER Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 71 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 8.9990 chunk 215 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 282 optimal weight: 6.9990 chunk 156 optimal weight: 8.9990 chunk 323 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 193 optimal weight: 0.9990 chunk 340 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 GLN B 168 GLN B 316 GLN N 22 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9179 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33367 Z= 0.271 Angle : 0.535 16.925 45352 Z= 0.253 Chirality : 0.041 0.151 4962 Planarity : 0.004 0.049 5700 Dihedral : 12.240 149.921 5275 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.44 % Allowed : 12.21 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.14), residues: 3955 helix: 1.61 (0.11), residues: 2128 sheet: 0.50 (0.27), residues: 368 loop : 0.43 (0.17), residues: 1459 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 0.013 0.001 PHE A 334 TYR 0.016 0.001 TYR O 117 ARG 0.006 0.000 ARG P 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 315 time to evaluate : 3.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 255 ASP cc_start: 0.9481 (m-30) cc_final: 0.9162 (m-30) REVERT: P 150 GLN cc_start: 0.8829 (tt0) cc_final: 0.8571 (tt0) REVERT: P 201 ARG cc_start: 0.8772 (mmm-85) cc_final: 0.8541 (mmm-85) REVERT: P 213 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8256 (mp0) REVERT: G 117 ASP cc_start: 0.9028 (m-30) cc_final: 0.8720 (t0) REVERT: F 107 LYS cc_start: 0.9350 (ttmt) cc_final: 0.9059 (tptp) REVERT: F 120 LYS cc_start: 0.9344 (mttp) cc_final: 0.8785 (mmtp) REVERT: B 60 PHE cc_start: 0.9611 (OUTLIER) cc_final: 0.9326 (t80) REVERT: B 64 ASN cc_start: 0.9310 (m-40) cc_final: 0.9071 (m-40) REVERT: B 83 LYS cc_start: 0.9494 (mmtm) cc_final: 0.9228 (mtmt) REVERT: B 85 TYR cc_start: 0.9440 (m-80) cc_final: 0.9196 (m-80) REVERT: B 213 ASP cc_start: 0.9426 (m-30) cc_final: 0.9116 (t0) REVERT: D 224 GLU cc_start: 0.9477 (tt0) cc_final: 0.9164 (pm20) REVERT: H 57 LEU cc_start: 0.8988 (mt) cc_final: 0.8772 (tp) REVERT: H 76 LYS cc_start: 0.9039 (tptm) cc_final: 0.8707 (tppt) REVERT: I 43 ARG cc_start: 0.8942 (mtm110) cc_final: 0.8574 (ttp80) REVERT: J 58 GLN cc_start: 0.9264 (tp40) cc_final: 0.8626 (tm-30) REVERT: J 80 ASN cc_start: 0.9307 (t0) cc_final: 0.8995 (t0) REVERT: N 287 ASP cc_start: 0.8375 (t0) cc_final: 0.7951 (t0) REVERT: R 117 ASP cc_start: 0.9182 (m-30) cc_final: 0.8933 (t0) REVERT: L 29 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.9074 (ptmm) REVERT: M 60 PHE cc_start: 0.9643 (OUTLIER) cc_final: 0.9202 (t80) REVERT: M 339 ARG cc_start: 0.9449 (OUTLIER) cc_final: 0.9111 (ttp-110) REVERT: S 22 LYS cc_start: 0.9435 (tttt) cc_final: 0.9145 (tttm) REVERT: U 11 LYS cc_start: 0.9086 (mtpp) cc_final: 0.8864 (mtmm) outliers start: 48 outliers final: 36 residues processed: 350 average time/residue: 0.4477 time to fit residues: 251.0727 Evaluate side-chains 349 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 308 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain P residue 168 CYS Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 29 LYS Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 272 SER Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 339 ARG Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 301 SER Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 71 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 8.9990 chunk 341 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 222 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 379 optimal weight: 6.9990 chunk 314 optimal weight: 4.9990 chunk 175 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 125 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN B 168 GLN B 316 GLN N 22 GLN L 74 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9202 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 33367 Z= 0.396 Angle : 0.588 18.612 45352 Z= 0.277 Chirality : 0.043 0.156 4962 Planarity : 0.004 0.051 5700 Dihedral : 12.099 149.701 5273 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.77 % Allowed : 12.45 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.14), residues: 3955 helix: 1.58 (0.11), residues: 2122 sheet: 0.45 (0.27), residues: 368 loop : 0.45 (0.17), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 142 HIS 0.009 0.001 HIS C 197 PHE 0.016 0.001 PHE N 240 TYR 0.017 0.002 TYR O 117 ARG 0.006 0.000 ARG P 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 311 time to evaluate : 3.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 255 ASP cc_start: 0.9500 (m-30) cc_final: 0.9169 (m-30) REVERT: P 150 GLN cc_start: 0.8889 (tt0) cc_final: 0.8612 (tt0) REVERT: P 201 ARG cc_start: 0.8857 (mmm-85) cc_final: 0.8621 (mmm-85) REVERT: P 213 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: F 107 LYS cc_start: 0.9351 (ttmt) cc_final: 0.9065 (tptp) REVERT: F 120 LYS cc_start: 0.9334 (mttp) cc_final: 0.8763 (mmtp) REVERT: B 60 PHE cc_start: 0.9627 (OUTLIER) cc_final: 0.9373 (t80) REVERT: B 64 ASN cc_start: 0.9323 (m-40) cc_final: 0.9076 (m-40) REVERT: B 213 ASP cc_start: 0.9431 (m-30) cc_final: 0.9118 (t0) REVERT: D 224 GLU cc_start: 0.9494 (tt0) cc_final: 0.9183 (pm20) REVERT: H 57 LEU cc_start: 0.9006 (mt) cc_final: 0.8774 (tp) REVERT: H 76 LYS cc_start: 0.9071 (tptm) cc_final: 0.8744 (tppt) REVERT: I 43 ARG cc_start: 0.8914 (mtm110) cc_final: 0.8520 (ttp80) REVERT: J 58 GLN cc_start: 0.9268 (tp40) cc_final: 0.8615 (tm-30) REVERT: J 80 ASN cc_start: 0.9324 (t0) cc_final: 0.9013 (t0) REVERT: N 287 ASP cc_start: 0.8436 (t0) cc_final: 0.8005 (t0) REVERT: R 117 ASP cc_start: 0.9176 (m-30) cc_final: 0.8941 (t0) REVERT: M 60 PHE cc_start: 0.9673 (OUTLIER) cc_final: 0.9268 (t80) REVERT: M 339 ARG cc_start: 0.9465 (OUTLIER) cc_final: 0.8803 (ttp80) REVERT: S 22 LYS cc_start: 0.9490 (tttt) cc_final: 0.9197 (tttm) outliers start: 59 outliers final: 44 residues processed: 356 average time/residue: 0.4681 time to fit residues: 265.7522 Evaluate side-chains 351 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 303 time to evaluate : 3.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 369 MET Chi-restraints excluded: chain P residue 71 SER Chi-restraints excluded: chain P residue 76 SER Chi-restraints excluded: chain P residue 118 ILE Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain P residue 168 CYS Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain R residue 11 SER Chi-restraints excluded: chain R residue 32 VAL Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 140 ASP Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 121 ASP Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 194 ILE Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 272 SER Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 339 ARG Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 307 SER Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 71 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 216 optimal weight: 0.7980 chunk 276 optimal weight: 8.9990 chunk 214 optimal weight: 0.8980 chunk 319 optimal weight: 0.0970 chunk 211 optimal weight: 0.9980 chunk 377 optimal weight: 2.9990 chunk 236 optimal weight: 0.0470 chunk 230 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 135 ASN B 168 GLN B 316 GLN N 22 GLN N 343 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9143 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 33367 Z= 0.137 Angle : 0.487 11.764 45352 Z= 0.235 Chirality : 0.039 0.165 4962 Planarity : 0.004 0.050 5700 Dihedral : 11.545 149.362 5269 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.93 % Allowed : 13.32 % 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: 1.69 (0.14), residues: 3955 helix: 1.75 (0.11), residues: 2125 sheet: 0.57 (0.27), residues: 366 loop : 0.48 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 142 HIS 0.005 0.001 HIS B 87 PHE 0.015 0.001 PHE A 334 TYR 0.022 0.001 TYR P 214 ARG 0.006 0.000 ARG Q 144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 331 time to evaluate : 3.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 255 ASP cc_start: 0.9474 (m-30) cc_final: 0.9126 (m-30) REVERT: P 150 GLN cc_start: 0.8919 (tt0) cc_final: 0.8654 (tt0) REVERT: P 201 ARG cc_start: 0.8859 (mmm-85) cc_final: 0.8641 (mmm-85) REVERT: P 213 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8232 (mp0) REVERT: G 117 ASP cc_start: 0.8988 (m-30) cc_final: 0.8686 (t0) REVERT: F 107 LYS cc_start: 0.9359 (ttmt) cc_final: 0.9044 (tptp) REVERT: F 131 GLN cc_start: 0.9314 (mm-40) cc_final: 0.9093 (mm110) REVERT: B 60 PHE cc_start: 0.9579 (OUTLIER) cc_final: 0.9327 (t80) REVERT: B 83 LYS cc_start: 0.9466 (mmtm) cc_final: 0.9239 (mtpt) REVERT: B 213 ASP cc_start: 0.9439 (m-30) cc_final: 0.9133 (t0) REVERT: D 224 GLU cc_start: 0.9483 (tt0) cc_final: 0.9192 (pm20) REVERT: H 57 LEU cc_start: 0.8994 (mt) cc_final: 0.8775 (tp) REVERT: H 76 LYS cc_start: 0.9016 (tptm) cc_final: 0.8699 (tppt) REVERT: I 43 ARG cc_start: 0.8883 (mtm110) cc_final: 0.8492 (ttp80) REVERT: J 11 LYS cc_start: 0.9260 (ttmm) cc_final: 0.8897 (tmtt) REVERT: J 58 GLN cc_start: 0.9262 (tp40) cc_final: 0.8621 (tm-30) REVERT: J 80 ASN cc_start: 0.9307 (t0) cc_final: 0.8994 (t0) REVERT: N 287 ASP cc_start: 0.8352 (t0) cc_final: 0.7939 (t0) REVERT: R 117 ASP cc_start: 0.9153 (m-30) cc_final: 0.8920 (t0) REVERT: M 60 PHE cc_start: 0.9623 (OUTLIER) cc_final: 0.9218 (t80) REVERT: S 22 LYS cc_start: 0.9435 (tttt) cc_final: 0.9150 (tttm) REVERT: U 11 LYS cc_start: 0.8883 (mtmm) cc_final: 0.8675 (mtpp) outliers start: 31 outliers final: 22 residues processed: 353 average time/residue: 0.4738 time to fit residues: 266.8717 Evaluate side-chains 341 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 316 time to evaluate : 4.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain N residue 255 ASP Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 183 THR 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 O residue 201 SER Chi-restraints excluded: chain O residue 301 SER Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 71 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 225 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 74 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 240 optimal weight: 0.0570 chunk 257 optimal weight: 6.9990 chunk 186 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 296 optimal weight: 1.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN B 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9150 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33367 Z= 0.172 Angle : 0.493 12.286 45352 Z= 0.237 Chirality : 0.039 0.150 4962 Planarity : 0.004 0.050 5700 Dihedral : 11.296 149.165 5265 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.02 % Allowed : 13.50 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.14), residues: 3955 helix: 1.85 (0.11), residues: 2125 sheet: 0.64 (0.26), residues: 368 loop : 0.54 (0.17), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 142 HIS 0.005 0.001 HIS C 197 PHE 0.022 0.001 PHE E 64 TYR 0.021 0.001 TYR P 214 ARG 0.008 0.000 ARG P 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 323 time to evaluate : 3.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 255 ASP cc_start: 0.9487 (m-30) cc_final: 0.9140 (m-30) REVERT: P 128 ARG cc_start: 0.8371 (tpt90) cc_final: 0.7949 (tpt90) REVERT: P 150 GLN cc_start: 0.8917 (tt0) cc_final: 0.8648 (tt0) REVERT: P 201 ARG cc_start: 0.8857 (mmm-85) cc_final: 0.8654 (mmm-85) REVERT: P 213 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8295 (mp0) REVERT: G 117 ASP cc_start: 0.8978 (m-30) cc_final: 0.8715 (t0) REVERT: F 107 LYS cc_start: 0.9363 (ttmt) cc_final: 0.9036 (tptp) REVERT: F 131 GLN cc_start: 0.9323 (mm-40) cc_final: 0.9075 (mm110) REVERT: B 60 PHE cc_start: 0.9588 (OUTLIER) cc_final: 0.9382 (t80) REVERT: B 83 LYS cc_start: 0.9464 (mmtm) cc_final: 0.9236 (mtpt) REVERT: B 213 ASP cc_start: 0.9452 (m-30) cc_final: 0.9140 (t0) REVERT: D 224 GLU cc_start: 0.9491 (tt0) cc_final: 0.9195 (pm20) REVERT: D 248 MET cc_start: 0.8517 (ttp) cc_final: 0.8136 (ttp) REVERT: H 57 LEU cc_start: 0.9002 (mt) cc_final: 0.8784 (tp) REVERT: H 76 LYS cc_start: 0.9013 (tptm) cc_final: 0.8700 (tppt) REVERT: I 43 ARG cc_start: 0.8876 (mtm110) cc_final: 0.8566 (ttp-170) REVERT: J 11 LYS cc_start: 0.9272 (ttmm) cc_final: 0.8934 (tmtt) REVERT: J 58 GLN cc_start: 0.9265 (tp40) cc_final: 0.8620 (tm-30) REVERT: J 80 ASN cc_start: 0.9307 (t0) cc_final: 0.8989 (t0) REVERT: N 287 ASP cc_start: 0.8367 (t0) cc_final: 0.7954 (t0) REVERT: R 117 ASP cc_start: 0.9165 (m-30) cc_final: 0.8935 (t0) REVERT: Q 112 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8732 (tp30) REVERT: M 60 PHE cc_start: 0.9626 (OUTLIER) cc_final: 0.9212 (t80) REVERT: S 22 LYS cc_start: 0.9455 (tttt) cc_final: 0.9170 (tttm) outliers start: 34 outliers final: 24 residues processed: 346 average time/residue: 0.4575 time to fit residues: 254.6074 Evaluate side-chains 340 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 313 time to evaluate : 3.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 235 HIS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain D residue 90 HIS Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 139 MET Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 183 THR 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 O residue 201 SER Chi-restraints excluded: chain O residue 301 SER Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 71 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 9.9990 chunk 361 optimal weight: 0.9980 chunk 330 optimal weight: 2.9990 chunk 352 optimal weight: 8.9990 chunk 211 optimal weight: 0.9990 chunk 153 optimal weight: 6.9990 chunk 276 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 318 optimal weight: 4.9990 chunk 332 optimal weight: 0.9990 chunk 350 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 GLN D 90 HIS O 269 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9149 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33367 Z= 0.184 Angle : 0.503 11.982 45352 Z= 0.242 Chirality : 0.039 0.151 4962 Planarity : 0.004 0.050 5700 Dihedral : 11.170 149.092 5265 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.87 % Allowed : 14.02 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.14), residues: 3955 helix: 1.88 (0.11), residues: 2125 sheet: 0.67 (0.26), residues: 368 loop : 0.57 (0.17), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 142 HIS 0.006 0.001 HIS C 197 PHE 0.018 0.001 PHE E 64 TYR 0.028 0.001 TYR P 194 ARG 0.007 0.000 ARG Q 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 320 time to evaluate : 4.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 255 ASP cc_start: 0.9481 (m-30) cc_final: 0.9138 (m-30) REVERT: P 150 GLN cc_start: 0.8912 (tt0) cc_final: 0.8641 (tt0) REVERT: P 213 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8305 (mp0) REVERT: G 117 ASP cc_start: 0.8974 (m-30) cc_final: 0.8710 (t0) REVERT: F 107 LYS cc_start: 0.9366 (ttmt) cc_final: 0.9027 (tptp) REVERT: F 131 GLN cc_start: 0.9319 (mm-40) cc_final: 0.9066 (mm110) REVERT: B 60 PHE cc_start: 0.9588 (OUTLIER) cc_final: 0.9381 (t80) REVERT: B 83 LYS cc_start: 0.9466 (mmtm) cc_final: 0.9253 (mtpt) REVERT: B 213 ASP cc_start: 0.9455 (m-30) cc_final: 0.9146 (t0) REVERT: D 224 GLU cc_start: 0.9501 (tt0) cc_final: 0.9220 (pm20) REVERT: D 248 MET cc_start: 0.8525 (ttp) cc_final: 0.8156 (ttp) REVERT: H 57 LEU cc_start: 0.8989 (mt) cc_final: 0.8782 (tp) REVERT: H 76 LYS cc_start: 0.9008 (tptm) cc_final: 0.8694 (tppt) REVERT: I 43 ARG cc_start: 0.8868 (mtm110) cc_final: 0.8566 (ttp-170) REVERT: J 11 LYS cc_start: 0.9269 (ttmm) cc_final: 0.8945 (tmtt) REVERT: J 58 GLN cc_start: 0.9267 (tp40) cc_final: 0.8625 (tm-30) REVERT: J 80 ASN cc_start: 0.9304 (t0) cc_final: 0.8984 (t0) REVERT: N 287 ASP cc_start: 0.8364 (t0) cc_final: 0.7951 (t0) REVERT: R 117 ASP cc_start: 0.9161 (m-30) cc_final: 0.8932 (t0) REVERT: Q 99 ASP cc_start: 0.9290 (m-30) cc_final: 0.8825 (p0) REVERT: M 60 PHE cc_start: 0.9627 (OUTLIER) cc_final: 0.9208 (t80) REVERT: S 22 LYS cc_start: 0.9458 (tttt) cc_final: 0.9171 (tttm) outliers start: 29 outliers final: 22 residues processed: 340 average time/residue: 0.4800 time to fit residues: 261.5537 Evaluate side-chains 336 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 311 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 139 MET Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 183 THR 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 O residue 201 SER Chi-restraints excluded: chain O residue 301 SER Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 2.9990 chunk 372 optimal weight: 0.7980 chunk 227 optimal weight: 0.0570 chunk 176 optimal weight: 9.9990 chunk 258 optimal weight: 0.7980 chunk 390 optimal weight: 10.0000 chunk 359 optimal weight: 0.8980 chunk 310 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 240 optimal weight: 0.6980 chunk 190 optimal weight: 4.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 343 HIS B 168 GLN D 90 HIS R 84 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9128 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 33367 Z= 0.145 Angle : 0.485 10.559 45352 Z= 0.235 Chirality : 0.039 0.165 4962 Planarity : 0.004 0.051 5700 Dihedral : 10.876 148.938 5265 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.87 % Allowed : 13.92 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.14), residues: 3955 helix: 1.94 (0.11), residues: 2123 sheet: 0.71 (0.26), residues: 368 loop : 0.63 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP T 50 HIS 0.004 0.000 HIS B 87 PHE 0.029 0.001 PHE P 186 TYR 0.022 0.001 TYR P 214 ARG 0.007 0.000 ARG Q 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 321 time to evaluate : 4.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 255 ASP cc_start: 0.9471 (m-30) cc_final: 0.9132 (m-30) REVERT: P 61 ASN cc_start: 0.8974 (t0) cc_final: 0.8383 (t0) REVERT: P 128 ARG cc_start: 0.8384 (tpt90) cc_final: 0.7926 (tpt90) REVERT: P 150 GLN cc_start: 0.8939 (tt0) cc_final: 0.8659 (tt0) REVERT: P 164 MET cc_start: 0.8201 (tpp) cc_final: 0.7872 (tpt) REVERT: P 213 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8289 (mp0) REVERT: G 117 ASP cc_start: 0.8977 (m-30) cc_final: 0.8717 (t0) REVERT: F 120 LYS cc_start: 0.9341 (mttp) cc_final: 0.8888 (mmtp) REVERT: F 131 GLN cc_start: 0.9290 (mm-40) cc_final: 0.9043 (mm110) REVERT: B 60 PHE cc_start: 0.9581 (OUTLIER) cc_final: 0.9368 (t80) REVERT: B 213 ASP cc_start: 0.9435 (m-30) cc_final: 0.9133 (t0) REVERT: D 224 GLU cc_start: 0.9493 (tt0) cc_final: 0.9221 (pm20) REVERT: D 248 MET cc_start: 0.8435 (ttp) cc_final: 0.8141 (ttp) REVERT: H 57 LEU cc_start: 0.8990 (mt) cc_final: 0.8765 (tp) REVERT: H 76 LYS cc_start: 0.8999 (tptm) cc_final: 0.8688 (tppt) REVERT: I 43 ARG cc_start: 0.8868 (mtm110) cc_final: 0.8563 (ttp-170) REVERT: J 11 LYS cc_start: 0.9269 (ttmm) cc_final: 0.8973 (tmtt) REVERT: J 58 GLN cc_start: 0.9262 (tp40) cc_final: 0.8558 (tm-30) REVERT: J 80 ASN cc_start: 0.9302 (t0) cc_final: 0.8980 (t0) REVERT: N 287 ASP cc_start: 0.8322 (t0) cc_final: 0.7907 (t0) REVERT: N 369 MET cc_start: 0.8935 (mtm) cc_final: 0.8496 (mmt) REVERT: N 374 GLU cc_start: 0.9034 (tt0) cc_final: 0.8796 (mt-10) REVERT: R 117 ASP cc_start: 0.9148 (m-30) cc_final: 0.8926 (t0) REVERT: Q 99 ASP cc_start: 0.9292 (m-30) cc_final: 0.8818 (p0) REVERT: M 60 PHE cc_start: 0.9615 (OUTLIER) cc_final: 0.9249 (t80) REVERT: M 163 ASN cc_start: 0.9025 (m-40) cc_final: 0.8800 (m110) REVERT: S 22 LYS cc_start: 0.9443 (tttt) cc_final: 0.9160 (tttm) outliers start: 29 outliers final: 21 residues processed: 342 average time/residue: 0.4723 time to fit residues: 259.7938 Evaluate side-chains 333 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 309 time to evaluate : 3.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 130 ARG Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain G residue 6 SER Chi-restraints excluded: chain F residue 116 HIS Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain N residue 14 ASN Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 139 MET Chi-restraints excluded: chain R residue 97 GLU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 159 ASN Chi-restraints excluded: chain L residue 183 THR 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 O residue 201 SER Chi-restraints excluded: chain O residue 301 SER Chi-restraints excluded: chain S residue 28 THR Chi-restraints excluded: chain S residue 61 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 0.8980 chunk 331 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 286 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 311 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 319 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 GLN D 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.067310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.051544 restraints weight = 75433.555| |-----------------------------------------------------------------------------| r_work (start): 0.2631 rms_B_bonded: 2.35 r_work: 0.2501 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2361 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33367 Z= 0.208 Angle : 0.505 12.171 45352 Z= 0.242 Chirality : 0.040 0.152 4962 Planarity : 0.004 0.050 5700 Dihedral : 10.795 148.963 5265 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.87 % Allowed : 13.95 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.14), residues: 3955 helix: 1.94 (0.11), residues: 2127 sheet: 0.71 (0.26), residues: 368 loop : 0.66 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 142 HIS 0.007 0.001 HIS C 197 PHE 0.024 0.001 PHE P 186 TYR 0.024 0.001 TYR P 194 ARG 0.007 0.000 ARG P 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7086.33 seconds wall clock time: 131 minutes 1.87 seconds (7861.87 seconds total)