Starting phenix.real_space_refine on Fri Mar 22 06:33:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abf_15319/03_2024/8abf_15319_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abf_15319/03_2024/8abf_15319.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abf_15319/03_2024/8abf_15319_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abf_15319/03_2024/8abf_15319_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abf_15319/03_2024/8abf_15319_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abf_15319/03_2024/8abf_15319.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abf_15319/03_2024/8abf_15319.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abf_15319/03_2024/8abf_15319_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abf_15319/03_2024/8abf_15319_updated.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 8 7.16 5 P 30 5.49 5 S 102 5.16 5 C 21031 2.51 5 N 5296 2.21 5 O 6073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 4": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C GLU 272": "OE1" <-> "OE2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P GLU 137": "OE1" <-> "OE2" Residue "P GLU 178": "OE1" <-> "OE2" Residue "P GLU 213": "OE1" <-> "OE2" Residue "P PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 220": "OE1" <-> "OE2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G ARG 61": "NH1" <-> "NH2" Residue "G GLU 66": "OE1" <-> "OE2" Residue "G ARG 70": "NH1" <-> "NH2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G GLU 96": "OE1" <-> "OE2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F GLU 121": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D ARG 321": "NH1" <-> "NH2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "N ARG 4": "NH1" <-> "NH2" Residue "N ARG 70": "NH1" <-> "NH2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "N PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 110": "NH1" <-> "NH2" Residue "N ARG 283": "NH1" <-> "NH2" Residue "N ARG 310": "NH1" <-> "NH2" Residue "N ARG 314": "NH1" <-> "NH2" Residue "N TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "R GLU 12": "OE1" <-> "OE2" Residue "R GLU 50": "OE1" <-> "OE2" Residue "R GLU 51": "OE1" <-> "OE2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R ARG 61": "NH1" <-> "NH2" Residue "R GLU 66": "OE1" <-> "OE2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R ARG 73": "NH1" <-> "NH2" Residue "R ARG 76": "NH1" <-> "NH2" Residue "R GLU 96": "OE1" <-> "OE2" Residue "R GLU 110": "OE1" <-> "OE2" Residue "R GLU 112": "OE1" <-> "OE2" Residue "R GLU 123": "OE1" <-> "OE2" Residue "Q GLU 88": "OE1" <-> "OE2" Residue "Q GLU 118": "OE1" <-> "OE2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "Q GLU 126": "OE1" <-> "OE2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "L GLU 141": "OE1" <-> "OE2" Residue "L ARG 188": "NH1" <-> "NH2" Residue "L GLU 354": "OE1" <-> "OE2" Residue "L ARG 384": "NH1" <-> "NH2" Residue "L GLU 424": "OE1" <-> "OE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M GLU 78": "OE1" <-> "OE2" Residue "M 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 PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 250": "NH1" <-> "NH2" Residue "O GLU 260": "OE1" <-> "OE2" Residue "O ARG 289": "NH1" <-> "NH2" Residue "O ARG 321": "NH1" <-> "NH2" Residue "S PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 34": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32540 Number of models: 1 Model: "" Number of chains: 33 Chain: "C" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "P" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1445 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 11, 'TRANS': 174} Chain: "G" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "A" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "B" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "D" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "I" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "J" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "N" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "E" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "R" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "Q" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "L" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "M" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "O" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "S" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "T" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "U" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "C" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 248 Unusual residues: {'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "P" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {'FES': 1, 'LMT': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 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: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 248 Unusual residues: {'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 111 Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 29.402 46.555 29.358 1.00138.94 S ATOM 4207 SG CYS P 187 31.996 44.352 27.417 1.00153.13 S Time building chain proxies: 16.80, per 1000 atoms: 0.52 Number of scatterers: 32540 At special positions: 0 Unit cell: (119.691, 129.735, 165.726, 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=2.06 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.07 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.41 Conformation dependent library (CDL) restraints added in 5.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES P 301 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 170 " pdb="FE2 FES P 301 " - pdb=" ND1 HIS P 190 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 168 " pdb="FE1 FES P 301 " - pdb=" SG CYS P 187 " Number of angles added : 3 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7486 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 186 helices and 15 sheets defined 54.5% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.96 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: 3.963A pdb=" N PHE C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY C 33 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR C 46 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.634A 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 103 removed outlier: 3.761A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 135 removed outlier: 3.527A pdb=" N LEU C 134 " --> pdb=" O MET C 130 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N VAL C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 153 removed outlier: 3.606A pdb=" N LEU C 150 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL C 151 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER C 152 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 4.369A 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: 4.073A pdb=" N THR C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 246 removed outlier: 6.910A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.859A 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: 3.821A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.971A 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: 4.138A 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: 3.608A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN P 90 " --> pdb=" O ASP P 86 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N MET P 91 " --> pdb=" O PHE P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 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: 3.667A pdb=" N ASN G 121 " --> pdb=" O ASP G 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 88 Processing helix chain 'F' and resid 92 through 110 Processing helix chain 'F' and resid 124 through 137 Processing helix chain 'F' and resid 139 through 145 removed outlier: 3.579A 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: 3.518A pdb=" N HIS A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 4.200A 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: 3.853A pdb=" N VAL A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Proline residue: A 124 - end of helix removed outlier: 3.809A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 156 removed outlier: 4.027A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.504A pdb=" N THR A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 206 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.521A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 4.007A 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: 3.637A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 395 removed outlier: 3.513A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.281A 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: 3.661A pdb=" N ASP A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET A 469 " --> pdb=" O ILE A 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 70 through 79 Processing helix chain 'B' and resid 101 through 117 Proline residue: B 105 - end of helix removed outlier: 3.636A pdb=" N LYS B 116 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU B 117 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 129 through 141 Processing helix chain 'B' and resid 144 through 157 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 200 through 210 Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.724A pdb=" N LEU B 263 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 removed outlier: 3.895A pdb=" N THR B 282 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 330 Processing helix chain 'B' and resid 334 through 353 Processing helix chain 'B' and resid 355 through 367 removed outlier: 3.639A 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: 3.548A pdb=" N PHE D 215 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 282 Processing helix chain 'D' and resid 286 through 319 Proline residue: D 317 - end of helix Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 40 through 80 removed outlier: 4.362A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) Proline residue: H 62 - end of helix Processing helix chain 'H' and resid 86 through 92 Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 44 Processing helix chain 'I' and resid 50 through 56 removed outlier: 5.150A pdb=" N HIS I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LYS I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 49 removed outlier: 3.563A pdb=" N TRP J 31 " --> pdb=" O THR J 27 " (cutoff:3.500A) Proline residue: J 33 - end of helix Processing helix chain 'J' and resid 54 through 59 Processing helix chain 'J' and resid 61 through 63 No H-bonds generated for 'chain 'J' and resid 61 through 63' Processing helix chain 'J' and resid 67 through 71 Processing helix chain 'J' and resid 77 through 79 No H-bonds generated for 'chain 'J' and resid 77 through 79' Processing helix chain 'N' and resid 3 through 6 No H-bonds generated for 'chain 'N' and resid 3 through 6' Processing helix chain 'N' and resid 8 through 17 Processing helix chain 'N' and resid 28 through 52 removed outlier: 3.951A pdb=" N PHE N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY N 33 " --> pdb=" O TRP N 30 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR N 46 " --> pdb=" O GLN N 43 " (cutoff:3.500A) removed outlier: 3.655A 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 103 removed outlier: 3.770A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 135 removed outlier: 3.546A pdb=" N LEU N 134 " --> pdb=" O MET N 130 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 138 through 153 removed outlier: 3.602A pdb=" N LEU N 150 " --> pdb=" O VAL N 146 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL N 151 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER N 152 " --> pdb=" O CYS N 148 " (cutoff:3.500A) removed outlier: 4.367A 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: 4.067A pdb=" N THR N 203 " --> pdb=" O ILE N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 246 removed outlier: 6.907A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.862A 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: 3.816A pdb=" N ILE N 299 " --> pdb=" O MET N 295 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU N 302 " --> pdb=" O ALA N 298 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU N 303 " --> pdb=" O ILE N 299 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE N 304 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 3.974A 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: 4.132A 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: 3.639A pdb=" N SER E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N MET E 91 " --> pdb=" O PHE E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 98 No H-bonds generated for 'chain 'E' and resid 95 through 98' Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 35 Proline residue: R 26 - end of helix Processing helix chain 'R' and resid 37 through 40 Processing helix chain 'R' and resid 44 through 47 Processing helix chain 'R' and resid 53 through 60 Processing helix chain 'R' and resid 64 through 83 Processing helix chain 'R' and resid 89 through 91 No H-bonds generated for 'chain 'R' and resid 89 through 91' Processing helix chain 'R' and resid 95 through 97 No H-bonds generated for 'chain 'R' and resid 95 through 97' Processing helix chain 'R' and resid 103 through 121 removed outlier: 3.671A 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: 3.579A pdb=" N VAL Q 145 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 72 through 79 removed outlier: 3.507A pdb=" N HIS L 78 " --> pdb=" O HIS L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 99 Processing helix chain 'L' and resid 120 through 135 removed outlier: 3.843A pdb=" N VAL L 123 " --> pdb=" O LYS L 120 " (cutoff:3.500A) Proline residue: L 124 - end of helix removed outlier: 3.807A pdb=" N VAL L 127 " --> pdb=" O PRO L 124 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU L 134 " --> pdb=" O ALA L 131 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN L 135 " --> pdb=" O ASP L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 156 removed outlier: 4.020A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU L 156 " --> pdb=" O THR L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 160 No H-bonds generated for 'chain 'L' and resid 158 through 160' Processing helix chain 'L' and resid 162 through 174 Processing helix chain 'L' and resid 179 through 181 No H-bonds generated for 'chain 'L' and resid 179 through 181' Processing helix chain 'L' and resid 188 through 191 No H-bonds generated for 'chain 'L' and resid 188 through 191' Processing helix chain 'L' and resid 196 through 206 Processing helix chain 'L' and resid 209 through 211 No H-bonds generated for 'chain 'L' and resid 209 through 211' Processing helix chain 'L' and resid 222 through 232 Processing helix chain 'L' and resid 294 through 304 removed outlier: 3.506A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 312 through 316 removed outlier: 4.020A 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: 3.628A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 395 removed outlier: 3.706A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.258A 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: 3.669A pdb=" N ASP L 468 " --> pdb=" O ARG L 464 " (cutoff:3.500A) removed outlier: 3.995A 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: 3.631A 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: 4.262A pdb=" N GLU M 117 " --> pdb=" O VAL M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 127 Processing helix chain 'M' and resid 129 through 141 Processing helix chain 'M' and resid 144 through 157 Processing helix chain 'M' and resid 160 through 162 No H-bonds generated for 'chain 'M' and resid 160 through 162' Processing helix chain 'M' and resid 175 through 185 Processing helix chain 'M' and resid 188 through 190 No H-bonds generated for 'chain 'M' and resid 188 through 190' Processing helix chain 'M' and resid 200 through 210 Processing helix chain 'M' and resid 254 through 263 removed outlier: 3.727A 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: 3.892A 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 removed outlier: 3.500A pdb=" N LEU M 393 " --> pdb=" O ALA M 389 " (cutoff:3.500A) Processing helix chain 'M' and resid 407 through 409 No H-bonds generated for 'chain 'M' and resid 407 through 409' Processing helix chain 'M' and resid 413 through 415 No H-bonds generated for 'chain 'M' and resid 413 through 415' Processing helix chain 'O' and resid 87 through 90 No H-bonds generated for 'chain 'O' and resid 87 through 90' Processing helix chain 'O' and resid 110 through 122 Processing helix chain 'O' and resid 124 through 126 No H-bonds generated for 'chain 'O' and resid 124 through 126' Processing helix chain 'O' and resid 135 through 138 Processing helix chain 'O' and resid 145 through 153 Processing helix chain 'O' and resid 185 through 192 Processing helix chain 'O' and resid 210 through 218 removed outlier: 3.557A pdb=" N PHE O 215 " --> pdb=" O ASP O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 267 through 282 Processing helix chain 'O' and resid 286 through 319 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 31 through 33 No H-bonds generated for 'chain 'S' and resid 31 through 33' Processing helix chain 'S' and resid 40 through 80 removed outlier: 4.360A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL S 59 " --> pdb=" O GLN S 55 " (cutoff:3.500A) Proline residue: S 62 - end of helix Processing helix chain 'S' and resid 86 through 92 Processing helix chain 'T' and resid 5 through 11 Processing helix chain 'T' and resid 15 through 44 Processing helix chain 'T' and resid 50 through 56 removed outlier: 5.169A pdb=" N HIS T 55 " --> pdb=" O LYS T 51 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LYS T 56 " --> pdb=" O ASP T 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 49 removed outlier: 3.582A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.565A 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: 3.884A pdb=" N LYS P 114 " --> pdb=" O HIS P 129 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'P' and resid 185 through 187 removed outlier: 3.515A pdb=" N SER P 192 " --> pdb=" O CYS P 187 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 31 through 34 Processing sheet with id= F, first strand: chain 'A' and resid 266 through 271 Processing sheet with id= G, first strand: chain 'B' and resid 16 through 20 removed outlier: 4.179A 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: 3.599A 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: 4.154A 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: 3.577A 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 1584 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: 11.56 Time building geometry restraints manager: 14.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.40: 13535 1.40 - 1.61: 19622 1.61 - 1.82: 163 1.82 - 2.03: 27 2.03 - 2.24: 20 Bond restraints: 33367 Sorted by residual: bond pdb=" C2C HEC D 401 " pdb=" C3C HEC D 401 " ideal model delta sigma weight residual 1.334 1.462 -0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C2C HEC O 401 " pdb=" C3C HEC O 401 " ideal model delta sigma weight residual 1.334 1.461 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C2B HEC O 401 " pdb=" C3B HEC O 401 " ideal model delta sigma weight residual 1.334 1.449 -0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C3B HEC D 401 " pdb=" CAB HEC D 401 " ideal model delta sigma weight residual 1.544 1.429 0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C2A HEC O 401 " pdb=" C3A HEC O 401 " ideal model delta sigma weight residual 1.334 1.448 -0.114 2.00e-02 2.50e+03 3.25e+01 ... (remaining 33362 not shown) Histogram of bond angle deviations from ideal: 84.94 - 103.82: 699 103.82 - 122.70: 40037 122.70 - 141.57: 4604 141.57 - 160.45: 0 160.45 - 179.32: 12 Bond angle restraints: 45352 Sorted by residual: angle pdb=" C GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta sigma weight residual 111.27 93.83 17.44 1.47e+00 4.63e-01 1.41e+02 angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 91.45 12.88 1.14e+00 7.69e-01 1.28e+02 angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.27 94.76 16.51 1.47e+00 4.63e-01 1.26e+02 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 91.40 12.93 1.20e+00 6.94e-01 1.16e+02 angle pdb=" CG ARG O 289 " pdb=" CD ARG O 289 " pdb=" NE ARG O 289 " ideal model delta sigma weight residual 112.00 92.16 19.84 2.20e+00 2.07e-01 8.14e+01 ... (remaining 45347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.17: 18965 33.17 - 66.34: 915 66.34 - 99.51: 79 99.51 - 132.68: 1 132.68 - 165.85: 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 -103.26 -19.34 0 2.50e+00 1.60e-01 5.98e+01 dihedral pdb=" C GLU D 283 " pdb=" N GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta harmonic sigma weight residual -122.60 -103.42 -19.18 0 2.50e+00 1.60e-01 5.89e+01 dihedral pdb=" C GLN M 215 " pdb=" N GLN M 215 " pdb=" CA GLN M 215 " pdb=" CB GLN M 215 " ideal model delta harmonic sigma weight residual -122.60 -105.01 -17.59 0 2.50e+00 1.60e-01 4.95e+01 ... (remaining 19960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.217: 4690 0.217 - 0.434: 263 0.434 - 0.651: 4 0.651 - 0.868: 3 0.868 - 1.085: 2 Chirality restraints: 4962 Sorted by residual: chirality pdb=" CB VAL C 146 " pdb=" CA VAL C 146 " pdb=" CG1 VAL C 146 " pdb=" CG2 VAL C 146 " both_signs ideal model delta sigma weight residual False -2.63 -1.54 -1.08 2.00e-01 2.50e+01 2.94e+01 chirality pdb=" CB4 CDL N 505 " pdb=" CB3 CDL N 505 " pdb=" CB6 CDL N 505 " pdb=" OB6 CDL N 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.64 -0.93 2.00e-01 2.50e+01 2.17e+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 -1.71 -0.87 2.00e-01 2.50e+01 1.88e+01 ... (remaining 4959 not shown) Planarity restraints: 5700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 76 " 0.347 9.50e-02 1.11e+02 1.59e-01 2.72e+01 pdb=" NE ARG R 76 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG R 76 " 0.057 2.00e-02 2.50e+03 pdb=" NH1 ARG R 76 " -0.022 2.00e-02 2.50e+03 pdb=" NH2 ARG R 76 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 76 " -0.341 9.50e-02 1.11e+02 1.56e-01 2.58e+01 pdb=" NE ARG G 76 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG G 76 " -0.054 2.00e-02 2.50e+03 pdb=" NH1 ARG G 76 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG G 76 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS N 96 " -0.053 2.00e-02 2.50e+03 4.02e-02 2.43e+01 pdb=" CG HIS N 96 " 0.063 2.00e-02 2.50e+03 pdb=" ND1 HIS N 96 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 HIS N 96 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 HIS N 96 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 HIS N 96 " -0.039 2.00e-02 2.50e+03 ... (remaining 5697 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 359 2.64 - 3.21: 29629 3.21 - 3.77: 53895 3.77 - 4.34: 78862 4.34 - 4.90: 121571 Nonbonded interactions: 284316 Sorted by model distance: nonbonded pdb=" NE2 HIS N 183 " pdb="FE HEM N 501 " model vdw 2.075 3.080 nonbonded pdb=" NE2 HIS C 183 " pdb="FE HEM C 501 " model vdw 2.076 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.076 2.520 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.118 3.080 nonbonded pdb=" NE2 HIS C 96 " pdb="FE HEM C 502 " model vdw 2.239 3.080 ... (remaining 284311 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' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = chain 'H' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = (chain 'J' and resid 8 through 82) selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.810 Check model and map are aligned: 0.520 Set scattering table: 0.330 Process input model: 92.290 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.400 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:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9244 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.186 33367 Z= 0.672 Angle : 1.753 19.843 45352 Z= 1.081 Chirality : 0.113 1.085 4962 Planarity : 0.009 0.159 5700 Dihedral : 18.076 165.854 12462 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.22 % Allowed : 7.22 % Favored : 89.56 % Cbeta Deviations : 1.47 % 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: -1.13 (0.12), residues: 3955 helix: -0.78 (0.09), residues: 2145 sheet: 0.05 (0.25), residues: 351 loop : -0.62 (0.16), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.009 TRP L 474 HIS 0.022 0.005 HIS N 57 PHE 0.063 0.008 PHE B 107 TYR 0.055 0.008 TYR O 120 ARG 0.061 0.003 ARG R 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 474 time to evaluate : 3.487 Fit side-chains revert: symmetry clash REVERT: P 106 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.6582 (mmmt) REVERT: P 131 THR cc_start: 0.7604 (p) cc_final: 0.7262 (p) REVERT: P 134 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8405 (mm-30) REVERT: P 158 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.7053 (tttt) REVERT: P 178 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7047 (mm-30) REVERT: P 182 PHE cc_start: 0.7567 (m-80) cc_final: 0.7313 (m-80) REVERT: F 84 GLU cc_start: 0.8690 (tt0) cc_final: 0.8280 (tp30) REVERT: F 88 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7858 (mm-30) REVERT: F 131 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8951 (mm-40) REVERT: A 68 TYR cc_start: 0.8770 (m-80) cc_final: 0.8563 (m-80) REVERT: A 153 ARG cc_start: 0.8364 (ttp-110) cc_final: 0.7917 (ttt-90) REVERT: A 390 LYS cc_start: 0.9050 (tptt) cc_final: 0.8658 (mttp) REVERT: B 236 ARG cc_start: 0.8453 (ttm110) cc_final: 0.7768 (tpp-160) REVERT: N 288 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8674 (tttt) REVERT: E 55 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7896 (p0) REVERT: L 48 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8721 (tp) REVERT: L 51 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.8947 (p) REVERT: L 87 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8511 (mtt90) REVERT: L 97 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8894 (mm-30) REVERT: L 153 ARG cc_start: 0.8313 (ttp-110) cc_final: 0.7802 (ttt90) REVERT: M 16 SER cc_start: 0.8793 (OUTLIER) cc_final: 0.8495 (p) REVERT: M 236 ARG cc_start: 0.8647 (mtt90) cc_final: 0.8243 (mmm160) REVERT: M 356 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8376 (t0) REVERT: S 78 GLU cc_start: 0.8853 (tt0) cc_final: 0.8585 (tm-30) REVERT: U 73 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8742 (mtt180) outliers start: 107 outliers final: 10 residues processed: 539 average time/residue: 1.7260 time to fit residues: 1071.3163 Evaluate side-chains 353 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 332 time to evaluate : 3.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 106 LYS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 158 LYS Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 288 LYS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 97 GLU Chi-restraints excluded: chain L residue 185 LEU Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 356 ASP Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 9.9990 chunk 297 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 307 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 355 optimal weight: 0.4980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 90 ASN ** P 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 HIS F 137 ASN A 50 GLN A 74 HIS A 222 HIS A 332 ASN A 371 ASN B 87 HIS B 197 ASN B 377 ASN N 14 ASN N 202 HIS N 332 ASN E 90 ASN R 84 HIS L 50 GLN L 332 ASN L 371 ASN M 87 HIS M 197 ASN O 90 HIS O 93 HIS U 80 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9179 moved from start: 0.1843 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= 0.195 Angle : 0.609 16.052 45352 Z= 0.298 Chirality : 0.042 0.153 4962 Planarity : 0.004 0.038 5700 Dihedral : 14.122 156.770 5317 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.77 % Allowed : 10.53 % Favored : 87.70 % 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: 0.81 (0.13), residues: 3955 helix: 0.98 (0.11), residues: 2140 sheet: 0.47 (0.26), residues: 365 loop : 0.06 (0.17), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 156 HIS 0.008 0.001 HIS C 197 PHE 0.021 0.002 PHE L 334 TYR 0.020 0.002 TYR D 237 ARG 0.005 0.001 ARG O 289 *********************** 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 419 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 360 time to evaluate : 3.936 Fit side-chains revert: symmetry clash REVERT: P 195 ASP cc_start: 0.7988 (t0) cc_final: 0.7620 (m-30) REVERT: F 84 GLU cc_start: 0.8718 (tt0) cc_final: 0.8343 (tp30) REVERT: F 88 GLU cc_start: 0.8457 (mm-30) cc_final: 0.7686 (mm-30) REVERT: A 153 ARG cc_start: 0.8739 (ttp-110) cc_final: 0.8324 (ttt-90) REVERT: A 240 GLN cc_start: 0.8483 (mp10) cc_final: 0.8220 (pm20) REVERT: A 390 LYS cc_start: 0.9088 (tptt) cc_final: 0.8870 (mttt) REVERT: A 397 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8195 (mt) REVERT: B 236 ARG cc_start: 0.8172 (ttm110) cc_final: 0.7714 (tpp-160) REVERT: B 251 GLU cc_start: 0.8453 (pm20) cc_final: 0.8054 (pm20) REVERT: H 57 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8776 (tt) REVERT: J 15 LYS cc_start: 0.8744 (mtmm) cc_final: 0.8477 (ptmm) REVERT: J 69 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6993 (pm20) REVERT: R 33 LYS cc_start: 0.9395 (ttpt) cc_final: 0.9176 (ttpt) REVERT: Q 84 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8469 (mt-10) REVERT: Q 95 LYS cc_start: 0.8972 (tptt) cc_final: 0.8771 (tttp) REVERT: Q 96 HIS cc_start: 0.9026 (t-90) cc_final: 0.8585 (t70) REVERT: L 51 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.8982 (p) REVERT: M 60 PHE cc_start: 0.9572 (OUTLIER) cc_final: 0.8971 (t80) REVERT: O 248 MET cc_start: 0.8937 (ttp) cc_final: 0.8413 (ttm) REVERT: S 78 GLU cc_start: 0.8886 (tt0) cc_final: 0.8503 (tm-30) outliers start: 59 outliers final: 14 residues processed: 402 average time/residue: 1.7243 time to fit residues: 802.1128 Evaluate side-chains 336 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 316 time to evaluate : 3.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 398 ASP Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain O residue 230 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.0040 chunk 110 optimal weight: 6.9990 chunk 296 optimal weight: 6.9990 chunk 242 optimal weight: 6.9990 chunk 98 optimal weight: 0.0170 chunk 356 optimal weight: 4.9990 chunk 385 optimal weight: 0.0170 chunk 317 optimal weight: 0.1980 chunk 353 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 overall best weight: 1.0470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 85 GLN P 129 HIS ** P 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 ASN B 316 GLN B 354 ASN B 377 ASN M 316 GLN U 80 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9168 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33367 Z= 0.167 Angle : 0.531 14.092 45352 Z= 0.256 Chirality : 0.040 0.167 4962 Planarity : 0.004 0.043 5700 Dihedral : 13.015 152.323 5275 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.50 % Allowed : 11.19 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.13), residues: 3955 helix: 1.52 (0.11), residues: 2131 sheet: 0.74 (0.26), residues: 365 loop : 0.38 (0.17), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 142 HIS 0.008 0.001 HIS C 197 PHE 0.021 0.001 PHE L 334 TYR 0.014 0.001 TYR D 237 ARG 0.006 0.000 ARG P 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 337 time to evaluate : 3.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 195 ASP cc_start: 0.7833 (t0) cc_final: 0.7600 (m-30) REVERT: G 112 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8448 (tt0) REVERT: F 84 GLU cc_start: 0.8730 (tt0) cc_final: 0.8518 (tp30) REVERT: F 96 HIS cc_start: 0.9188 (t-170) cc_final: 0.8623 (t-90) REVERT: F 103 GLU cc_start: 0.8871 (tp30) cc_final: 0.8604 (tm-30) REVERT: F 109 GLN cc_start: 0.9074 (mt0) cc_final: 0.8870 (mt0) REVERT: F 110 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8014 (pp20) REVERT: A 87 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8157 (ptp90) REVERT: A 153 ARG cc_start: 0.8803 (ttp-110) cc_final: 0.8325 (ttt-90) REVERT: A 240 GLN cc_start: 0.8497 (mp10) cc_final: 0.8111 (pm20) REVERT: A 390 LYS cc_start: 0.9052 (tptt) cc_final: 0.8843 (mttt) REVERT: A 397 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8260 (mt) REVERT: B 205 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8203 (tm-30) REVERT: B 251 GLU cc_start: 0.8437 (pm20) cc_final: 0.8098 (pm20) REVERT: D 258 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8600 (tp30) REVERT: H 57 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8831 (tt) REVERT: J 69 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6887 (pm20) REVERT: R 12 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8392 (mt-10) REVERT: R 33 LYS cc_start: 0.9400 (ttpt) cc_final: 0.9185 (ttpt) REVERT: Q 84 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8484 (mt-10) REVERT: Q 96 HIS cc_start: 0.9076 (t-90) cc_final: 0.8662 (t70) REVERT: Q 100 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8362 (mt-10) REVERT: L 51 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8858 (p) REVERT: M 60 PHE cc_start: 0.9551 (OUTLIER) cc_final: 0.8931 (t80) REVERT: O 248 MET cc_start: 0.8872 (ttp) cc_final: 0.8326 (ttm) REVERT: S 78 GLU cc_start: 0.8872 (tt0) cc_final: 0.8509 (tm-30) outliers start: 50 outliers final: 14 residues processed: 369 average time/residue: 1.7282 time to fit residues: 740.0655 Evaluate side-chains 337 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 313 time to evaluate : 3.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain Q residue 84 GLU Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 60 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 6.9990 chunk 268 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 chunk 239 optimal weight: 2.9990 chunk 357 optimal weight: 5.9990 chunk 378 optimal weight: 6.9990 chunk 186 optimal weight: 0.9990 chunk 339 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN B 316 GLN B 354 ASN B 377 ASN M 215 GLN M 316 GLN U 80 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9235 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 33367 Z= 0.426 Angle : 0.639 16.284 45352 Z= 0.311 Chirality : 0.046 0.155 4962 Planarity : 0.005 0.050 5700 Dihedral : 13.003 152.978 5271 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.89 % Allowed : 10.44 % Favored : 87.67 % 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: 1.49 (0.13), residues: 3955 helix: 1.45 (0.11), residues: 2120 sheet: 0.71 (0.26), residues: 363 loop : 0.57 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 142 HIS 0.017 0.001 HIS C 197 PHE 0.024 0.002 PHE L 334 TYR 0.023 0.002 TYR C 225 ARG 0.005 0.001 ARG I 54 *********************** 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 382 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 319 time to evaluate : 3.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 195 ASP cc_start: 0.7733 (t0) cc_final: 0.7501 (m-30) REVERT: G 112 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8591 (tt0) REVERT: F 84 GLU cc_start: 0.8771 (tt0) cc_final: 0.8557 (tp30) REVERT: F 88 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8287 (mm-30) REVERT: F 110 GLU cc_start: 0.8292 (pt0) cc_final: 0.7956 (pp20) REVERT: A 87 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8410 (ptp90) REVERT: A 153 ARG cc_start: 0.8835 (ttp-110) cc_final: 0.8364 (ttt-90) REVERT: A 240 GLN cc_start: 0.8460 (mp10) cc_final: 0.8119 (pm20) REVERT: A 390 LYS cc_start: 0.9087 (tptt) cc_final: 0.8809 (mttt) REVERT: A 397 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8219 (mt) REVERT: B 205 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8320 (tm-30) REVERT: B 251 GLU cc_start: 0.8483 (pm20) cc_final: 0.8111 (pm20) REVERT: D 258 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8676 (tp30) REVERT: H 57 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8834 (tt) REVERT: J 69 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6987 (pm20) REVERT: E 55 ASP cc_start: 0.8769 (p0) cc_final: 0.8507 (p0) REVERT: Q 84 GLU cc_start: 0.8772 (tp30) cc_final: 0.8545 (tt0) REVERT: Q 96 HIS cc_start: 0.9067 (t-90) cc_final: 0.8595 (t-170) REVERT: Q 100 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8356 (mt-10) REVERT: O 248 MET cc_start: 0.9187 (ttp) cc_final: 0.8983 (ttp) REVERT: S 78 GLU cc_start: 0.8892 (tt0) cc_final: 0.8524 (tm-30) outliers start: 63 outliers final: 23 residues processed: 362 average time/residue: 1.7100 time to fit residues: 716.4809 Evaluate side-chains 337 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 308 time to evaluate : 3.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 472 MET Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 175 THR Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain O residue 230 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 282 optimal weight: 0.8980 chunk 156 optimal weight: 9.9990 chunk 323 optimal weight: 0.9990 chunk 261 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 193 optimal weight: 3.9990 chunk 340 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 HIS B 316 GLN B 354 ASN B 377 ASN U 80 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9201 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 33367 Z= 0.234 Angle : 0.535 14.654 45352 Z= 0.257 Chirality : 0.041 0.157 4962 Planarity : 0.004 0.050 5700 Dihedral : 12.355 151.782 5266 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.32 % Allowed : 11.43 % 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: 1.71 (0.13), residues: 3955 helix: 1.65 (0.11), residues: 2119 sheet: 0.84 (0.26), residues: 363 loop : 0.62 (0.17), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 142 HIS 0.009 0.001 HIS C 197 PHE 0.023 0.001 PHE L 334 TYR 0.015 0.001 TYR N 225 ARG 0.003 0.000 ARG P 128 *********************** 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 364 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 320 time to evaluate : 4.041 Fit side-chains revert: symmetry clash REVERT: P 150 GLN cc_start: 0.6651 (mt0) cc_final: 0.6397 (mt0) REVERT: P 195 ASP cc_start: 0.7532 (t0) cc_final: 0.7331 (m-30) REVERT: G 112 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8451 (tt0) REVERT: F 84 GLU cc_start: 0.8761 (tt0) cc_final: 0.8553 (tp30) REVERT: F 103 GLU cc_start: 0.8835 (tp30) cc_final: 0.8566 (tm-30) REVERT: F 110 GLU cc_start: 0.8280 (pt0) cc_final: 0.7924 (pp20) REVERT: A 153 ARG cc_start: 0.8815 (ttp-110) cc_final: 0.8327 (ttt-90) REVERT: A 240 GLN cc_start: 0.8439 (mp10) cc_final: 0.8089 (pm20) REVERT: A 390 LYS cc_start: 0.9083 (tptt) cc_final: 0.8760 (mttp) REVERT: A 397 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8231 (mt) REVERT: B 205 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8252 (tm-30) REVERT: B 251 GLU cc_start: 0.8478 (pm20) cc_final: 0.8224 (pm20) REVERT: D 258 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8639 (tp30) REVERT: H 57 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8840 (tt) REVERT: J 69 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6956 (pm20) REVERT: E 55 ASP cc_start: 0.8785 (p0) cc_final: 0.8523 (p0) REVERT: R 12 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8432 (mt-10) REVERT: Q 84 GLU cc_start: 0.8764 (tp30) cc_final: 0.8540 (tt0) REVERT: Q 96 HIS cc_start: 0.9077 (t-90) cc_final: 0.8737 (t70) REVERT: Q 100 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8383 (mt-10) REVERT: S 78 GLU cc_start: 0.8878 (tt0) cc_final: 0.8513 (tm-30) outliers start: 44 outliers final: 17 residues processed: 348 average time/residue: 1.7677 time to fit residues: 710.8356 Evaluate side-chains 336 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 314 time to evaluate : 3.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain O residue 230 VAL 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: 2.9990 chunk 341 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 222 optimal weight: 0.6980 chunk 93 optimal weight: 8.9990 chunk 379 optimal weight: 6.9990 chunk 314 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 HIS B 354 ASN B 377 ASN ** U 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9213 moved from start: 0.2317 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= 0.275 Angle : 0.558 15.411 45352 Z= 0.267 Chirality : 0.042 0.160 4962 Planarity : 0.004 0.051 5700 Dihedral : 12.149 151.871 5265 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.29 % Allowed : 11.64 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.13), residues: 3955 helix: 1.68 (0.11), residues: 2123 sheet: 0.91 (0.26), residues: 363 loop : 0.64 (0.17), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 142 HIS 0.013 0.001 HIS C 197 PHE 0.023 0.002 PHE L 334 TYR 0.018 0.002 TYR N 225 ARG 0.008 0.000 ARG I 54 *********************** 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 366 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 323 time to evaluate : 6.489 Fit side-chains revert: symmetry clash REVERT: P 150 GLN cc_start: 0.6677 (mt0) cc_final: 0.6357 (mt0) REVERT: G 112 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8464 (tt0) REVERT: F 84 GLU cc_start: 0.8774 (tt0) cc_final: 0.8535 (tp30) REVERT: F 88 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8297 (mm-30) REVERT: F 110 GLU cc_start: 0.8283 (pt0) cc_final: 0.7918 (pp20) REVERT: A 153 ARG cc_start: 0.8846 (ttp-110) cc_final: 0.8352 (ttt-90) REVERT: A 240 GLN cc_start: 0.8446 (mp10) cc_final: 0.8091 (pm20) REVERT: A 390 LYS cc_start: 0.9095 (tptt) cc_final: 0.8754 (mttp) REVERT: A 397 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8255 (mt) REVERT: B 205 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8261 (tm-30) REVERT: D 258 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8653 (tp30) REVERT: H 57 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8834 (tt) REVERT: J 69 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6992 (pm20) REVERT: E 55 ASP cc_start: 0.8933 (p0) cc_final: 0.8697 (p0) REVERT: Q 84 GLU cc_start: 0.8774 (tp30) cc_final: 0.8464 (mt-10) REVERT: Q 96 HIS cc_start: 0.9066 (t-90) cc_final: 0.8715 (t70) REVERT: Q 112 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8091 (mm-30) REVERT: S 78 GLU cc_start: 0.8894 (tt0) cc_final: 0.8562 (tm-30) outliers start: 43 outliers final: 23 residues processed: 352 average time/residue: 1.7362 time to fit residues: 712.7442 Evaluate side-chains 343 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 314 time to evaluate : 3.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain P residue 196 ILE Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 165 LEU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain Q residue 112 GLU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain O residue 230 VAL 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: 0.5980 chunk 42 optimal weight: 2.9990 chunk 216 optimal weight: 8.9990 chunk 276 optimal weight: 0.5980 chunk 214 optimal weight: 1.9990 chunk 319 optimal weight: 4.9990 chunk 211 optimal weight: 0.7980 chunk 377 optimal weight: 3.9990 chunk 236 optimal weight: 0.0000 chunk 230 optimal weight: 0.5980 chunk 174 optimal weight: 0.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 HIS F 109 GLN B 354 ASN B 377 ASN D 236 ASN M 316 GLN U 80 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9152 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 33367 Z= 0.142 Angle : 0.485 12.408 45352 Z= 0.232 Chirality : 0.039 0.174 4962 Planarity : 0.004 0.049 5700 Dihedral : 11.398 150.720 5265 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.96 % Allowed : 12.09 % Favored : 86.95 % 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: 1.88 (0.11), residues: 2116 sheet: 1.03 (0.27), residues: 363 loop : 0.66 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 161 HIS 0.004 0.001 HIS M 87 PHE 0.019 0.001 PHE L 334 TYR 0.011 0.001 TYR A 114 ARG 0.004 0.000 ARG P 128 *********************** 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 363 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 331 time to evaluate : 4.095 Fit side-chains REVERT: P 150 GLN cc_start: 0.6670 (mt0) cc_final: 0.6326 (mt0) REVERT: G 112 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8548 (tt0) REVERT: F 84 GLU cc_start: 0.8761 (tt0) cc_final: 0.8538 (tp30) REVERT: F 88 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8325 (mm-30) REVERT: F 103 GLU cc_start: 0.8811 (tp30) cc_final: 0.8570 (tm-30) REVERT: F 110 GLU cc_start: 0.8380 (pt0) cc_final: 0.7994 (pp20) REVERT: A 153 ARG cc_start: 0.8835 (ttp-110) cc_final: 0.8364 (ttt-90) REVERT: A 390 LYS cc_start: 0.9073 (tptt) cc_final: 0.8765 (mttp) REVERT: B 31 GLN cc_start: 0.8802 (mt0) cc_final: 0.8525 (mm110) REVERT: B 205 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8246 (tm-30) REVERT: B 251 GLU cc_start: 0.8249 (pm20) cc_final: 0.7999 (pm20) REVERT: D 258 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8612 (tp30) REVERT: H 57 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8849 (tt) REVERT: J 15 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8598 (pttp) REVERT: J 69 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6928 (pm20) REVERT: E 55 ASP cc_start: 0.8880 (p0) cc_final: 0.8645 (p0) REVERT: Q 84 GLU cc_start: 0.8756 (tp30) cc_final: 0.8445 (mt-10) REVERT: Q 96 HIS cc_start: 0.9029 (t-90) cc_final: 0.8785 (t70) REVERT: Q 112 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8124 (mm-30) REVERT: L 48 LEU cc_start: 0.8968 (tp) cc_final: 0.8728 (tp) REVERT: S 78 GLU cc_start: 0.8878 (tt0) cc_final: 0.8603 (tm-30) outliers start: 32 outliers final: 12 residues processed: 350 average time/residue: 1.7442 time to fit residues: 705.7436 Evaluate side-chains 329 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 311 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain Q residue 112 GLU Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain S residue 60 ILE 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: 0.9980 chunk 225 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 240 optimal weight: 6.9990 chunk 257 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 296 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 HIS F 109 GLN B 354 ASN B 377 ASN ** U 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9216 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 33367 Z= 0.324 Angle : 0.579 15.339 45352 Z= 0.276 Chirality : 0.043 0.163 4962 Planarity : 0.004 0.050 5700 Dihedral : 11.858 151.952 5265 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.05 % Allowed : 12.12 % Favored : 86.83 % 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: 1.88 (0.14), residues: 3955 helix: 1.77 (0.11), residues: 2119 sheet: 1.00 (0.26), residues: 363 loop : 0.68 (0.17), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 161 HIS 0.017 0.001 HIS C 197 PHE 0.024 0.002 PHE L 334 TYR 0.022 0.002 TYR N 225 ARG 0.006 0.000 ARG P 201 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 309 time to evaluate : 4.037 Fit side-chains REVERT: G 112 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8453 (tt0) REVERT: F 84 GLU cc_start: 0.8770 (tt0) cc_final: 0.8539 (tp30) REVERT: F 88 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8413 (mm-30) REVERT: F 103 GLU cc_start: 0.8824 (tp30) cc_final: 0.8580 (tm-30) REVERT: A 153 ARG cc_start: 0.8818 (ttp-110) cc_final: 0.8282 (ttt-90) REVERT: B 205 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8259 (tm-30) REVERT: B 251 GLU cc_start: 0.8376 (pm20) cc_final: 0.8163 (pm20) REVERT: D 258 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8645 (tp30) REVERT: H 57 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8837 (tt) REVERT: J 15 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8690 (pttp) REVERT: J 69 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.6983 (pm20) REVERT: R 112 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8479 (tt0) REVERT: Q 84 GLU cc_start: 0.8782 (tp30) cc_final: 0.8479 (mt-10) REVERT: Q 96 HIS cc_start: 0.9051 (t-90) cc_final: 0.8831 (t-90) REVERT: Q 112 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8076 (mm-30) REVERT: M 236 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8108 (ttp-170) REVERT: M 353 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: S 78 GLU cc_start: 0.8894 (tt0) cc_final: 0.8598 (tm-30) outliers start: 35 outliers final: 13 residues processed: 330 average time/residue: 1.7177 time to fit residues: 655.3458 Evaluate side-chains 328 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 306 time to evaluate : 3.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain Q residue 112 GLU Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain M residue 353 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 1.9990 chunk 361 optimal weight: 3.9990 chunk 330 optimal weight: 0.9990 chunk 352 optimal weight: 5.9990 chunk 211 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 276 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 318 optimal weight: 6.9990 chunk 332 optimal weight: 0.9990 chunk 350 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN B 354 ASN B 377 ASN U 80 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9173 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 33367 Z= 0.155 Angle : 0.503 14.116 45352 Z= 0.238 Chirality : 0.039 0.169 4962 Planarity : 0.004 0.050 5700 Dihedral : 11.359 151.371 5265 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.78 % Allowed : 12.57 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.14), residues: 3955 helix: 1.89 (0.11), residues: 2121 sheet: 1.08 (0.27), residues: 363 loop : 0.71 (0.17), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 161 HIS 0.007 0.001 HIS C 197 PHE 0.020 0.001 PHE L 334 TYR 0.012 0.001 TYR G 31 ARG 0.005 0.000 ARG P 201 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 311 time to evaluate : 3.659 Fit side-chains REVERT: G 112 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8290 (tt0) REVERT: F 84 GLU cc_start: 0.8764 (tt0) cc_final: 0.8532 (tp30) REVERT: F 88 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8332 (mm-30) REVERT: F 103 GLU cc_start: 0.8804 (tp30) cc_final: 0.8567 (tm-30) REVERT: F 110 GLU cc_start: 0.8305 (pt0) cc_final: 0.8012 (pp20) REVERT: A 153 ARG cc_start: 0.8831 (ttp-110) cc_final: 0.8327 (ttt-90) REVERT: B 31 GLN cc_start: 0.8834 (mt0) cc_final: 0.8584 (mm110) REVERT: B 205 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8220 (tm-30) REVERT: D 258 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8608 (tp30) REVERT: H 57 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8865 (tt) REVERT: J 15 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8636 (pttp) REVERT: J 69 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6939 (pm20) REVERT: Q 84 GLU cc_start: 0.8794 (tp30) cc_final: 0.8484 (mt-10) REVERT: Q 96 HIS cc_start: 0.9002 (t-90) cc_final: 0.8767 (t-90) REVERT: Q 112 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8041 (mm-30) REVERT: M 353 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8078 (mp0) REVERT: S 78 GLU cc_start: 0.8879 (tt0) cc_final: 0.8605 (tm-30) outliers start: 26 outliers final: 12 residues processed: 326 average time/residue: 1.6907 time to fit residues: 637.3074 Evaluate side-chains 326 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 307 time to evaluate : 3.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 15 LYS Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain Q residue 112 GLU Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain M residue 353 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 3.9990 chunk 372 optimal weight: 4.9990 chunk 227 optimal weight: 0.9980 chunk 176 optimal weight: 7.9990 chunk 258 optimal weight: 0.6980 chunk 390 optimal weight: 0.0980 chunk 359 optimal weight: 5.9990 chunk 310 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 190 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN B 354 ASN B 377 ASN M 377 ASN U 80 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9175 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33367 Z= 0.170 Angle : 0.509 14.275 45352 Z= 0.240 Chirality : 0.039 0.174 4962 Planarity : 0.004 0.049 5700 Dihedral : 11.196 151.214 5265 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.60 % Allowed : 12.72 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.14), residues: 3955 helix: 1.92 (0.11), residues: 2122 sheet: 1.15 (0.27), residues: 363 loop : 0.71 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP P 161 HIS 0.010 0.001 HIS C 197 PHE 0.020 0.001 PHE L 334 TYR 0.015 0.001 TYR N 225 ARG 0.004 0.000 ARG P 201 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 314 time to evaluate : 3.976 Fit side-chains REVERT: G 112 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8564 (tt0) REVERT: F 84 GLU cc_start: 0.8764 (tt0) cc_final: 0.8554 (tp30) REVERT: F 88 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8320 (mm-30) REVERT: F 103 GLU cc_start: 0.8803 (tp30) cc_final: 0.8584 (mm-30) REVERT: F 110 GLU cc_start: 0.8277 (pt0) cc_final: 0.7962 (pp20) REVERT: A 153 ARG cc_start: 0.8849 (ttp-110) cc_final: 0.8343 (ttt-90) REVERT: B 31 GLN cc_start: 0.8837 (mt0) cc_final: 0.8593 (mm110) REVERT: B 205 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8230 (tm-30) REVERT: D 258 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8610 (tp30) REVERT: H 57 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8856 (tt) REVERT: J 69 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6961 (pm20) REVERT: Q 84 GLU cc_start: 0.8785 (tp30) cc_final: 0.8480 (mt-10) REVERT: Q 96 HIS cc_start: 0.8985 (t-90) cc_final: 0.8731 (t-90) REVERT: Q 112 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8027 (mm-30) REVERT: S 78 GLU cc_start: 0.8875 (tt0) cc_final: 0.8610 (tm-30) outliers start: 20 outliers final: 11 residues processed: 327 average time/residue: 1.7501 time to fit residues: 662.1346 Evaluate side-chains 323 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 307 time to evaluate : 3.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 131 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain H residue 57 LEU Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 69 GLU Chi-restraints excluded: chain J residue 73 ARG Chi-restraints excluded: chain Q residue 112 GLU Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 9.9990 chunk 331 optimal weight: 0.0040 chunk 95 optimal weight: 0.8980 chunk 286 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 311 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 319 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 57 optimal weight: 0.0670 overall best weight: 0.5530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN B 354 ASN B 377 ASN M 377 ASN O 93 HIS U 80 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.078854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.059511 restraints weight = 55180.622| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 1.67 r_work: 0.2655 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9139 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 33367 Z= 0.136 Angle : 0.485 13.427 45352 Z= 0.228 Chirality : 0.038 0.175 4962 Planarity : 0.004 0.048 5700 Dihedral : 10.829 150.931 5265 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.54 % Allowed : 12.93 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.14), residues: 3955 helix: 2.01 (0.11), residues: 2124 sheet: 1.20 (0.27), residues: 363 loop : 0.75 (0.17), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP P 161 HIS 0.006 0.001 HIS C 197 PHE 0.018 0.001 PHE A 334 TYR 0.011 0.001 TYR A 114 ARG 0.005 0.000 ARG P 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12054.36 seconds wall clock time: 214 minutes 27.55 seconds (12867.55 seconds total)