Starting phenix.real_space_refine on Thu Feb 22 01:39:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac4_15333/02_2024/8ac4_15333_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac4_15333/02_2024/8ac4_15333.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac4_15333/02_2024/8ac4_15333_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac4_15333/02_2024/8ac4_15333_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac4_15333/02_2024/8ac4_15333_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac4_15333/02_2024/8ac4_15333.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac4_15333/02_2024/8ac4_15333.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac4_15333/02_2024/8ac4_15333_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ac4_15333/02_2024/8ac4_15333_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 8 7.16 5 P 30 5.49 5 S 102 5.16 5 C 21031 2.51 5 N 5296 2.21 5 O 6073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 4": "NH1" <-> "NH2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "P GLU 136": "OE1" <-> "OE2" Residue "P GLU 137": "OE1" <-> "OE2" Residue "P GLU 178": "OE1" <-> "OE2" Residue "P GLU 213": "OE1" <-> "OE2" Residue "P GLU 220": "OE1" <-> "OE2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G ARG 61": "NH1" <-> "NH2" Residue "G GLU 66": "OE1" <-> "OE2" Residue "G ARG 70": "NH1" <-> "NH2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G GLU 96": "OE1" <-> "OE2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F GLU 121": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B GLU 350": "OE1" <-> "OE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "D ARG 189": "NH1" <-> "NH2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "D TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 321": "NH1" <-> "NH2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "N ARG 4": "NH1" <-> "NH2" Residue "N PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 70": "NH1" <-> "NH2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "N ARG 110": "NH1" <-> "NH2" Residue "N PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 283": "NH1" <-> "NH2" Residue "N ARG 310": "NH1" <-> "NH2" Residue "N ARG 314": "NH1" <-> "NH2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "R GLU 12": "OE1" <-> "OE2" Residue "R GLU 50": "OE1" <-> "OE2" Residue "R GLU 51": "OE1" <-> "OE2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R ARG 61": "NH1" <-> "NH2" Residue "R GLU 66": "OE1" <-> "OE2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R ARG 73": "NH1" <-> "NH2" Residue "R ARG 76": "NH1" <-> "NH2" Residue "R GLU 96": "OE1" <-> "OE2" Residue "R GLU 110": "OE1" <-> "OE2" Residue "R GLU 123": "OE1" <-> "OE2" Residue "Q GLU 88": "OE1" <-> "OE2" Residue "Q GLU 118": "OE1" <-> "OE2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "Q GLU 126": "OE1" <-> "OE2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "L GLU 141": "OE1" <-> "OE2" Residue "L ARG 188": "NH1" <-> "NH2" Residue "L GLU 354": "OE1" <-> "OE2" Residue "L ARG 384": "NH1" <-> "NH2" Residue "L GLU 424": "OE1" <-> "OE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M GLU 78": "OE1" <-> "OE2" Residue "M TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 117": "OE1" <-> "OE2" Residue "M ARG 140": "NH1" <-> "NH2" Residue "M GLU 150": "OE1" <-> "OE2" Residue "M ARG 234": "NH1" <-> "NH2" Residue "M GLU 313": "OE1" <-> "OE2" Residue "M GLU 350": "OE1" <-> "OE2" Residue "M GLU 376": "OE1" <-> "OE2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "O ARG 132": "NH1" <-> "NH2" Residue "O ARG 136": "NH1" <-> "NH2" Residue "O GLU 164": "OE1" <-> "OE2" Residue "O ARG 170": "NH1" <-> "NH2" Residue "O ARG 189": "NH1" <-> "NH2" Residue "O ARG 207": "NH1" <-> "NH2" Residue "O TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 250": "NH1" <-> "NH2" Residue "O GLU 260": "OE1" <-> "OE2" Residue "O ARG 289": "NH1" <-> "NH2" Residue "O ARG 321": "NH1" <-> "NH2" Residue "S PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 34": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32540 Number of models: 1 Model: "" Number of chains: 34 Chain: "C" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "P" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1445 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 11, 'TRANS': 174} Chain: "G" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "A" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "B" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "D" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "I" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "J" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "N" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "E" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 465 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "R" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "Q" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "L" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "M" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "O" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "S" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "T" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "U" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "C" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 248 Unusual residues: {'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "P" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {'FES': 1, 'LMT': 1, 'PTY': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 111 Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "J" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 298 Unusual residues: {'CDL': 2, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 127 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 61 Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "U" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'XP4': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4070 SG CYS P 168 34.637 46.742 24.508 1.00164.04 S ATOM 4207 SG CYS P 187 36.885 46.000 21.408 1.00157.45 S Time building chain proxies: 17.24, per 1000 atoms: 0.53 Number of scatterers: 32540 At special positions: 0 Unit cell: (118.854, 129.735, 166.563, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 8 26.01 S 102 16.00 P 30 15.00 O 6073 8.00 N 5296 7.00 C 21031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS P 173 " - pdb=" SG CYS P 189 " distance=2.04 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.06 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.07 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.71 Conformation dependent library (CDL) restraints added in 5.5 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: 184 helices and 15 sheets defined 54.3% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.90 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: 3.915A pdb=" N PHE C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY C 33 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR C 46 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 70 Processing helix chain 'C' and resid 75 through 102 removed outlier: 3.748A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 135 removed outlier: 3.516A pdb=" N LEU C 134 " --> pdb=" O MET C 130 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 153 removed outlier: 4.106A pdb=" N VAL C 151 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER C 152 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 4.351A 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: 4.164A pdb=" N THR C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 246 removed outlier: 6.851A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.777A 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: 3.817A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.988A 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: 4.112A 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: 3.631A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN P 90 " --> pdb=" O ASP P 86 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N MET P 91 " --> pdb=" O PHE P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 98 No H-bonds generated for 'chain 'P' and resid 95 through 98' Processing helix chain 'P' and resid 132 through 138 Processing helix chain 'P' and resid 152 through 155 No H-bonds generated for 'chain 'P' and resid 152 through 155' Processing helix chain 'G' and resid 4 through 16 Processing helix chain 'G' and resid 18 through 35 Proline residue: G 26 - end of helix Processing helix chain 'G' and resid 37 through 40 Processing helix chain 'G' and resid 44 through 47 Processing helix chain 'G' and resid 53 through 61 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: 3.701A 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: 3.595A 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: 3.508A pdb=" N HIS A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 4.209A 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: 3.842A pdb=" N VAL A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Proline residue: A 124 - end of helix removed outlier: 3.846A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 156 removed outlier: 4.011A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 4.026A 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: 3.591A 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: 3.526A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.995A pdb=" N ARG A 315 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'A' and resid 359 through 375 removed outlier: 3.658A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 395 removed outlier: 3.546A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.374A 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: 3.634A pdb=" N ASP A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.968A 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: 3.623A pdb=" N LYS B 116 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU B 117 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 129 through 141 Processing helix chain 'B' and resid 144 through 157 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 200 through 210 removed outlier: 3.525A pdb=" N THR B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.707A pdb=" N LEU B 263 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 311 through 330 Processing helix chain 'B' and resid 334 through 353 Processing helix chain 'B' and resid 355 through 367 removed outlier: 3.711A 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: 3.544A pdb=" N PHE D 215 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 282 Processing helix chain 'D' and resid 286 through 319 Proline residue: D 317 - end of helix Processing helix chain 'H' and resid 40 through 80 removed outlier: 4.321A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.754A 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: 5.124A pdb=" N HIS I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 49 removed outlier: 3.534A pdb=" N LYS J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 3.568A 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: 3.917A pdb=" N PHE N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY N 33 " --> pdb=" O TRP N 30 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR N 46 " --> pdb=" O GLN N 43 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE N 48 " --> pdb=" O ALA N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 70 Processing helix chain 'N' and resid 75 through 102 removed outlier: 3.756A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 135 removed outlier: 4.171A pdb=" N VAL N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 138 through 153 removed outlier: 4.119A pdb=" N VAL N 151 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER N 152 " --> pdb=" O CYS N 148 " (cutoff:3.500A) removed outlier: 4.326A 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: 4.155A pdb=" N THR N 203 " --> pdb=" O ILE N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 246 removed outlier: 6.851A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.786A 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: 3.812A pdb=" N ILE N 299 " --> pdb=" O MET N 295 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU N 302 " --> pdb=" O ALA N 298 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU N 303 " --> pdb=" O ILE N 299 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE N 304 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 3.985A 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: 4.117A pdb=" N PHE N 363 " --> pdb=" O TYR N 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 366 through 382 Processing helix chain 'E' and resid 59 through 91 removed outlier: 3.647A pdb=" N SER E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 4.852A 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 61 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: 3.700A 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: 3.594A pdb=" N VAL Q 145 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 72 through 79 Processing helix chain 'L' and resid 89 through 99 Processing helix chain 'L' and resid 120 through 135 removed outlier: 3.839A pdb=" N VAL L 123 " --> pdb=" O LYS L 120 " (cutoff:3.500A) Proline residue: L 124 - end of helix removed outlier: 3.848A pdb=" N VAL L 127 " --> pdb=" O PRO L 124 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA L 131 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU L 134 " --> pdb=" O ALA L 131 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN L 135 " --> pdb=" O ASP L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 156 removed outlier: 4.009A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU L 156 " --> pdb=" O THR L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 160 No H-bonds generated for 'chain 'L' and resid 158 through 160' Processing helix chain 'L' and resid 162 through 174 Processing helix chain 'L' and resid 179 through 181 No H-bonds generated for 'chain 'L' and resid 179 through 181' Processing helix chain 'L' and resid 188 through 193 removed outlier: 3.584A pdb=" N THR L 193 " --> pdb=" O GLU L 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 206 Processing helix chain 'L' and resid 209 through 211 No H-bonds generated for 'chain 'L' and resid 209 through 211' Processing helix chain 'L' and resid 222 through 232 Processing helix chain 'L' and resid 294 through 304 removed outlier: 3.516A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 312 through 316 removed outlier: 3.971A 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: 3.666A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 395 removed outlier: 3.702A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.366A 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: 3.637A pdb=" N ASP L 468 " --> pdb=" O ARG L 464 " (cutoff:3.500A) removed outlier: 3.966A 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: 3.571A pdb=" N VAL M 108 " --> pdb=" O PRO M 105 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS M 116 " --> pdb=" O ASN M 113 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU M 117 " --> pdb=" O VAL M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 127 Processing helix chain 'M' and resid 129 through 141 Processing helix chain 'M' and resid 144 through 157 Processing helix chain 'M' and resid 160 through 162 No H-bonds generated for 'chain 'M' and resid 160 through 162' Processing helix chain 'M' and resid 175 through 185 Processing helix chain 'M' and resid 188 through 190 No H-bonds generated for 'chain 'M' and resid 188 through 190' Processing helix chain 'M' and resid 200 through 210 removed outlier: 3.519A pdb=" N THR M 209 " --> pdb=" O GLN M 205 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 263 removed outlier: 3.705A 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 367 removed outlier: 3.853A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 375 through 377 No H-bonds generated for 'chain 'M' and resid 375 through 377' Processing helix chain 'M' and resid 383 through 394 Processing helix chain 'M' and resid 407 through 409 No H-bonds generated for 'chain 'M' and resid 407 through 409' Processing helix chain 'M' and resid 413 through 415 No H-bonds generated for 'chain 'M' and resid 413 through 415' Processing helix chain 'O' and resid 87 through 90 No H-bonds generated for 'chain 'O' and resid 87 through 90' Processing helix chain 'O' and resid 110 through 122 Processing helix chain 'O' and resid 124 through 126 No H-bonds generated for 'chain 'O' and resid 124 through 126' Processing helix chain 'O' and resid 135 through 138 Processing helix chain 'O' and resid 145 through 153 Processing helix chain 'O' and resid 185 through 192 Processing helix chain 'O' and resid 210 through 218 removed outlier: 3.543A pdb=" N PHE O 215 " --> pdb=" O ASP O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 267 through 282 Processing helix chain 'O' and resid 286 through 319 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 40 through 80 removed outlier: 4.319A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.748A 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: 5.105A pdb=" N HIS T 55 " --> pdb=" O LYS T 51 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS T 56 " --> pdb=" O ASP T 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 49 removed outlier: 3.559A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.586A 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 removed outlier: 3.528A pdb=" N VAL P 103 " --> pdb=" O ILE P 224 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'P' and resid 114 through 120 removed outlier: 3.910A pdb=" N LYS P 114 " --> pdb=" O HIS P 129 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'P' and resid 185 through 187 Processing sheet with id= E, first strand: chain 'A' and resid 31 through 34 Processing sheet with id= F, first strand: chain 'A' and resid 266 through 271 Processing sheet with id= G, first strand: chain 'B' and resid 16 through 20 removed outlier: 4.124A 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: 3.621A 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: 4.108A 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: 3.600A 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. 4332 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.38 Time building geometry restraints manager: 14.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 13595 1.41 - 1.61: 19562 1.61 - 1.82: 172 1.82 - 2.03: 19 2.03 - 2.24: 19 Bond restraints: 33367 Sorted by residual: bond pdb=" N ALA T 4 " pdb=" CA ALA T 4 " ideal model delta sigma weight residual 1.458 1.572 -0.114 1.90e-02 2.77e+03 3.60e+01 bond pdb=" N ALA I 4 " pdb=" CA ALA I 4 " ideal model delta sigma weight residual 1.458 1.571 -0.113 1.90e-02 2.77e+03 3.53e+01 bond pdb=" C2A HEC O 401 " pdb=" C3A HEC O 401 " ideal model delta sigma weight residual 1.334 1.452 -0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" C2B HEC D 401 " pdb=" C3B HEC D 401 " ideal model delta sigma weight residual 1.334 1.450 -0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" C2C HEC O 401 " pdb=" C3C HEC O 401 " ideal model delta sigma weight residual 1.334 1.446 -0.112 2.00e-02 2.50e+03 3.13e+01 ... (remaining 33362 not shown) Histogram of bond angle deviations from ideal: 84.88 - 103.78: 672 103.78 - 122.68: 39430 122.68 - 141.58: 5238 141.58 - 160.48: 0 160.48 - 179.38: 12 Bond angle restraints: 45352 Sorted by residual: angle pdb=" S1 FES P 301 " pdb="FE2 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 92.24 12.09 1.14e+00 7.69e-01 1.12e+02 angle pdb=" S1 FES P 301 " pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " ideal model delta sigma weight residual 104.33 92.36 11.97 1.20e+00 6.94e-01 9.95e+01 angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.14 97.55 13.59 1.56e+00 4.11e-01 7.59e+01 angle pdb="FE1 FES P 301 " pdb=" S2 FES P 301 " pdb="FE2 FES P 301 " ideal model delta sigma weight residual 75.66 85.18 -9.52 1.14e+00 7.69e-01 6.98e+01 angle pdb=" C GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta sigma weight residual 111.27 99.09 12.18 1.47e+00 4.63e-01 6.87e+01 ... (remaining 45347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.72: 18892 32.72 - 65.45: 976 65.45 - 98.17: 91 98.17 - 130.89: 1 130.89 - 163.62: 3 Dihedral angle restraints: 19963 sinusoidal: 8344 harmonic: 11619 Sorted by residual: dihedral pdb=" C GLN B 215 " pdb=" N GLN B 215 " pdb=" CA GLN B 215 " pdb=" CB GLN B 215 " ideal model delta harmonic sigma weight residual -122.60 -105.65 -16.95 0 2.50e+00 1.60e-01 4.60e+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 -105.96 -16.64 0 2.50e+00 1.60e-01 4.43e+01 dihedral pdb=" C ARG S 51 " pdb=" N ARG S 51 " pdb=" CA ARG S 51 " pdb=" CB ARG S 51 " ideal model delta harmonic sigma weight residual -122.60 -139.08 16.48 0 2.50e+00 1.60e-01 4.34e+01 ... (remaining 19960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.192: 4546 0.192 - 0.384: 396 0.384 - 0.576: 14 0.576 - 0.768: 2 0.768 - 0.960: 4 Chirality restraints: 4962 Sorted by residual: chirality pdb=" CB4 CDL C 505 " pdb=" CB3 CDL C 505 " pdb=" CB6 CDL C 505 " pdb=" OB6 CDL C 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.61 -0.96 2.00e-01 2.50e+01 2.31e+01 chirality pdb=" CB4 CDL N 506 " pdb=" CB3 CDL N 506 " pdb=" CB6 CDL N 506 " pdb=" OB6 CDL N 506 " both_signs ideal model delta sigma weight residual False -2.57 -1.64 -0.94 2.00e-01 2.50e+01 2.19e+01 chirality pdb=" CB4 CDL S 101 " pdb=" CB3 CDL S 101 " pdb=" CB6 CDL S 101 " pdb=" OB6 CDL S 101 " both_signs ideal model delta sigma weight residual False -2.57 -1.66 -0.91 2.00e-01 2.50e+01 2.09e+01 ... (remaining 4959 not shown) Planarity restraints: 5700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A HEC O 401 " 0.008 2.00e-02 2.50e+03 2.80e-02 1.77e+01 pdb=" C2A HEC O 401 " 0.026 2.00e-02 2.50e+03 pdb=" C3A HEC O 401 " 0.020 2.00e-02 2.50e+03 pdb=" C4A HEC O 401 " 0.043 2.00e-02 2.50e+03 pdb=" CAA HEC O 401 " -0.040 2.00e-02 2.50e+03 pdb=" CHA HEC O 401 " -0.007 2.00e-02 2.50e+03 pdb=" CHB HEC O 401 " -0.049 2.00e-02 2.50e+03 pdb=" CMA HEC O 401 " 0.003 2.00e-02 2.50e+03 pdb=" NA HEC O 401 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEC O 401 " -0.005 2.00e-02 2.50e+03 2.67e-02 1.60e+01 pdb=" C1B HEC O 401 " -0.011 2.00e-02 2.50e+03 pdb=" C2B HEC O 401 " -0.022 2.00e-02 2.50e+03 pdb=" C3B HEC O 401 " -0.008 2.00e-02 2.50e+03 pdb=" C4B HEC O 401 " -0.012 2.00e-02 2.50e+03 pdb=" CAB HEC O 401 " 0.050 2.00e-02 2.50e+03 pdb=" CHB HEC O 401 " 0.047 2.00e-02 2.50e+03 pdb=" CHC HEC O 401 " -0.013 2.00e-02 2.50e+03 pdb=" CMB HEC O 401 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS N 96 " -0.039 2.00e-02 2.50e+03 3.20e-02 1.54e+01 pdb=" CG HIS N 96 " 0.055 2.00e-02 2.50e+03 pdb=" ND1 HIS N 96 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS N 96 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 HIS N 96 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS N 96 " -0.036 2.00e-02 2.50e+03 ... (remaining 5697 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 10 2.33 - 2.97: 15596 2.97 - 3.61: 48924 3.61 - 4.26: 85024 4.26 - 4.90: 134264 Nonbonded interactions: 283818 Sorted by model distance: nonbonded pdb=" O CYS P 189 " pdb=" CE MET D 235 " model vdw 1.683 3.460 nonbonded pdb=" NE2 HIS C 183 " pdb="FE HEM C 501 " model vdw 2.039 3.080 nonbonded pdb=" NE2 HIS N 183 " pdb="FE HEM N 501 " model vdw 2.047 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.092 2.520 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.125 3.080 ... (remaining 283813 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' and (resid 26 through 474 or resid 3001 through 3002)) selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = (chain 'C' and (resid 1 through 383 or resid 501 through 503)) selection = (chain 'N' and (resid 1 through 383 or resid 501 through 503)) } ncs_group { reference = chain 'D' selection = chain 'O' } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = (chain 'H' and (resid 9 through 93 or (resid 701 and (name CB2 or name OB2 or na \ me CB3 or name OB3 or name C1 or name C11 or name C12 or name C31 or name C71 or \ name C72 or name CA2 or name CA3 or name CA4 or name CA5 or name CA6 or name CA \ 7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or name OA2 or name \ OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 or name OA9 or \ name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name OB9 or name PA1 \ or name PB2)))) selection = (chain 'S' and (resid 9 through 93 or (resid 101 and (name CB2 or name OB2 or na \ me CB3 or name OB3 or name C1 or name C11 or name C12 or name C31 or name C71 or \ name C72 or name CA2 or name CA3 or name CA4 or name CA5 or name CA6 or name CA \ 7 or name CB4 or name CB5 or name CB6 or name CB7 or name O1 or name OA2 or name \ OA3 or name OA4 or name OA5 or name OA6 or name OA7 or name OA8 or name OA9 or \ name OB4 or name OB5 or name OB6 or name OB7 or name OB8 or name OB9 or name PA1 \ or name PB2)))) } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = (chain 'J' and resid 8 through 82) selection = (chain 'U' and resid 8 through 82) } 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: 2.530 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: 11.690 Check model and map are aligned: 0.490 Set scattering table: 0.290 Process input model: 89.100 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.320 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9272 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 0.206 33367 Z= 0.685 Angle : 1.730 16.417 45352 Z= 1.077 Chirality : 0.115 0.960 4962 Planarity : 0.007 0.049 5700 Dihedral : 18.271 163.616 12462 Min Nonbonded Distance : 1.683 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.58 % Favored : 97.37 % Rotamer: Outliers : 3.76 % Allowed : 7.43 % Favored : 88.81 % Cbeta Deviations : 1.02 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.12), residues: 3955 helix: -1.11 (0.09), residues: 2118 sheet: 0.08 (0.25), residues: 356 loop : -0.77 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.008 TRP P 120 HIS 0.024 0.004 HIS Q 92 PHE 0.049 0.006 PHE B 107 TYR 0.045 0.007 TYR D 237 ARG 0.029 0.002 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 349 time to evaluate : 3.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 287 ASP cc_start: 0.8601 (t0) cc_final: 0.8341 (t0) REVERT: C 288 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8010 (ttpt) REVERT: P 182 PHE cc_start: 0.7450 (m-80) cc_final: 0.7024 (m-80) REVERT: P 186 PHE cc_start: 0.9131 (t80) cc_final: 0.8850 (t80) REVERT: P 202 ARG cc_start: 0.9082 (ttm170) cc_final: 0.8862 (ttp-110) REVERT: P 213 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8453 (tm-30) REVERT: G 12 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8980 (mm-30) REVERT: G 116 LYS cc_start: 0.8983 (tttm) cc_final: 0.8710 (ttmm) REVERT: B 251 GLU cc_start: 0.9343 (mt-10) cc_final: 0.9077 (pm20) REVERT: B 377 ASN cc_start: 0.9561 (m-40) cc_final: 0.9348 (m-40) REVERT: H 35 ARG cc_start: 0.9016 (mtm-85) cc_final: 0.8787 (mtm-85) REVERT: H 78 GLU cc_start: 0.9327 (tt0) cc_final: 0.9040 (tm-30) REVERT: N 250 LYS cc_start: 0.9283 (ttmt) cc_final: 0.9078 (tptp) REVERT: N 369 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8819 (mtp) REVERT: E 55 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8672 (p0) REVERT: Q 84 GLU cc_start: 0.9232 (tt0) cc_final: 0.8930 (tp30) REVERT: Q 88 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8484 (mm-30) REVERT: Q 109 GLN cc_start: 0.9507 (mt0) cc_final: 0.9222 (mt0) REVERT: Q 122 ASP cc_start: 0.8734 (p0) cc_final: 0.8512 (p0) REVERT: L 87 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8437 (ptp90) REVERT: M 19 GLU cc_start: 0.9424 (OUTLIER) cc_final: 0.9121 (mm-30) REVERT: M 31 GLN cc_start: 0.8783 (mt0) cc_final: 0.8577 (mm110) REVERT: M 236 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8775 (mtp85) REVERT: M 341 TYR cc_start: 0.9340 (t80) cc_final: 0.8953 (t80) REVERT: S 78 GLU cc_start: 0.9276 (tt0) cc_final: 0.9033 (pp20) REVERT: U 80 ASN cc_start: 0.9322 (t0) cc_final: 0.8966 (t0) outliers start: 125 outliers final: 16 residues processed: 442 average time/residue: 1.6631 time to fit residues: 854.4372 Evaluate side-chains 300 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 277 time to evaluate : 3.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain N residue 178 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 369 MET Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain Q residue 100 GLU Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 236 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 7.9990 chunk 297 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 200 optimal weight: 0.6980 chunk 158 optimal weight: 5.9990 chunk 307 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 chunk 186 optimal weight: 0.9980 chunk 228 optimal weight: 7.9990 chunk 355 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN C 22 GLN C 173 ASN C 202 HIS C 332 ASN P 85 GLN G 54 ASN G 84 HIS F 109 GLN F 132 HIS A 74 HIS A 192 GLN A 222 HIS A 332 ASN A 371 ASN B 87 HIS B 92 HIS B 197 ASN B 215 GLN B 316 GLN N 14 ASN N 202 HIS N 332 ASN E 90 ASN R 84 HIS Q 132 HIS L 332 ASN L 371 ASN M 87 HIS M 92 HIS M 197 ASN M 215 GLN ** M 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 316 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9200 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33367 Z= 0.206 Angle : 0.587 14.226 45352 Z= 0.290 Chirality : 0.041 0.237 4962 Planarity : 0.004 0.043 5700 Dihedral : 13.960 156.072 5317 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.80 % Allowed : 10.98 % Favored : 87.22 % 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: 0.79 (0.13), residues: 3955 helix: 0.94 (0.11), residues: 2126 sheet: 0.47 (0.26), residues: 369 loop : 0.11 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 156 HIS 0.005 0.001 HIS M 92 PHE 0.020 0.002 PHE L 334 TYR 0.016 0.001 TYR Q 114 ARG 0.010 0.001 ARG P 199 *********************** 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 345 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 285 time to evaluate : 3.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 287 ASP cc_start: 0.8399 (t0) cc_final: 0.8189 (t0) REVERT: C 288 LYS cc_start: 0.8237 (tttp) cc_final: 0.8015 (ttpp) REVERT: P 182 PHE cc_start: 0.7866 (m-80) cc_final: 0.7359 (m-80) REVERT: P 202 ARG cc_start: 0.9082 (ttm170) cc_final: 0.8823 (ttp-110) REVERT: P 213 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8371 (tm-30) REVERT: G 97 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8991 (mt-10) REVERT: G 115 GLU cc_start: 0.9233 (tt0) cc_final: 0.8989 (tt0) REVERT: F 114 TYR cc_start: 0.8757 (t80) cc_final: 0.8437 (t80) REVERT: B 251 GLU cc_start: 0.9351 (mt-10) cc_final: 0.9078 (pm20) REVERT: H 78 GLU cc_start: 0.9352 (tt0) cc_final: 0.8966 (tm-30) REVERT: E 55 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8611 (p0) REVERT: Q 84 GLU cc_start: 0.9235 (tt0) cc_final: 0.9004 (tp30) REVERT: Q 88 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8612 (mm-30) REVERT: Q 109 GLN cc_start: 0.9496 (mt0) cc_final: 0.9213 (mt0) REVERT: Q 115 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8454 (p0) REVERT: Q 116 HIS cc_start: 0.8821 (m-70) cc_final: 0.8450 (m90) REVERT: Q 122 ASP cc_start: 0.8685 (p0) cc_final: 0.8451 (p0) REVERT: S 78 GLU cc_start: 0.9307 (tt0) cc_final: 0.9035 (tm-30) REVERT: U 67 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8727 (pt) REVERT: U 73 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7536 (ptt-90) REVERT: U 80 ASN cc_start: 0.9351 (t0) cc_final: 0.8996 (t0) outliers start: 60 outliers final: 11 residues processed: 321 average time/residue: 1.6692 time to fit residues: 623.3284 Evaluate side-chains 272 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 256 time to evaluate : 3.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 84 VAL Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain Q residue 115 ASP Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 296 optimal weight: 8.9990 chunk 242 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 356 optimal weight: 0.0060 chunk 385 optimal weight: 0.4980 chunk 317 optimal weight: 0.7980 chunk 353 optimal weight: 6.9990 chunk 121 optimal weight: 0.0980 chunk 286 optimal weight: 8.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 157 GLN A 50 GLN A 364 HIS B 377 ASN M 241 ASN M 408 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9162 moved from start: 0.2281 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= 0.143 Angle : 0.501 11.588 45352 Z= 0.243 Chirality : 0.039 0.148 4962 Planarity : 0.004 0.049 5700 Dihedral : 12.639 149.934 5276 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.53 % Allowed : 11.43 % Favored : 87.04 % 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: 1.48 (0.14), residues: 3955 helix: 1.51 (0.11), residues: 2150 sheet: 0.85 (0.27), residues: 367 loop : 0.37 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 142 HIS 0.005 0.001 HIS M 87 PHE 0.016 0.001 PHE L 334 TYR 0.011 0.001 TYR D 117 ARG 0.009 0.000 ARG F 104 *********************** 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 327 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 276 time to evaluate : 3.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 288 LYS cc_start: 0.8181 (tttp) cc_final: 0.7953 (ttpt) REVERT: P 128 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8607 (mmm160) REVERT: P 182 PHE cc_start: 0.7831 (m-80) cc_final: 0.6661 (m-80) REVERT: P 213 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8391 (tm-30) REVERT: G 115 GLU cc_start: 0.9188 (tt0) cc_final: 0.8981 (tt0) REVERT: G 123 GLU cc_start: 0.9239 (tt0) cc_final: 0.8878 (pt0) REVERT: F 109 GLN cc_start: 0.9241 (mt0) cc_final: 0.9041 (mm110) REVERT: F 110 GLU cc_start: 0.9266 (OUTLIER) cc_final: 0.9002 (pp20) REVERT: F 114 TYR cc_start: 0.8771 (t80) cc_final: 0.8399 (t80) REVERT: F 122 ASP cc_start: 0.8731 (p0) cc_final: 0.8481 (p0) REVERT: B 251 GLU cc_start: 0.9323 (mt-10) cc_final: 0.9122 (pm20) REVERT: H 78 GLU cc_start: 0.9370 (tt0) cc_final: 0.8993 (tm-30) REVERT: J 13 SER cc_start: 0.9147 (t) cc_final: 0.8915 (p) REVERT: J 69 GLU cc_start: 0.8479 (pm20) cc_final: 0.8242 (pm20) REVERT: Q 84 GLU cc_start: 0.9245 (tt0) cc_final: 0.9025 (tp30) REVERT: Q 88 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8642 (mm-30) REVERT: Q 109 GLN cc_start: 0.9483 (mt0) cc_final: 0.9200 (mt0) REVERT: Q 122 ASP cc_start: 0.8626 (p0) cc_final: 0.8422 (p0) REVERT: S 57 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8640 (tp) REVERT: S 78 GLU cc_start: 0.9299 (tt0) cc_final: 0.9008 (tm-30) REVERT: U 73 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.7844 (ptt-90) REVERT: U 80 ASN cc_start: 0.9335 (t0) cc_final: 0.9002 (t0) outliers start: 51 outliers final: 8 residues processed: 308 average time/residue: 1.6386 time to fit residues: 591.1492 Evaluate side-chains 272 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 259 time to evaluate : 3.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 9.9990 chunk 268 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 170 optimal weight: 6.9990 chunk 239 optimal weight: 0.8980 chunk 357 optimal weight: 7.9990 chunk 378 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 339 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 96 HIS N 14 ASN L 323 ASN M 197 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9256 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 33367 Z= 0.463 Angle : 0.621 16.134 45352 Z= 0.297 Chirality : 0.045 0.156 4962 Planarity : 0.004 0.055 5700 Dihedral : 12.689 149.804 5272 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.59 % Allowed : 12.21 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.13), residues: 3955 helix: 1.56 (0.11), residues: 2126 sheet: 0.91 (0.27), residues: 365 loop : 0.47 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 142 HIS 0.017 0.001 HIS C 197 PHE 0.022 0.002 PHE C 240 TYR 0.021 0.002 TYR C 225 ARG 0.007 0.001 ARG M 236 *********************** 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 309 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 256 time to evaluate : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 263 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.9004 (mtm) REVERT: C 288 LYS cc_start: 0.8376 (tttp) cc_final: 0.8067 (ttpp) REVERT: P 128 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8581 (mmm160) REVERT: P 213 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8417 (tm-30) REVERT: G 12 GLU cc_start: 0.9270 (mm-30) cc_final: 0.9048 (mm-30) REVERT: G 50 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8944 (pt0) REVERT: G 112 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8600 (tm-30) REVERT: G 115 GLU cc_start: 0.9223 (tt0) cc_final: 0.8971 (tt0) REVERT: F 114 TYR cc_start: 0.8833 (t80) cc_final: 0.8510 (t80) REVERT: B 251 GLU cc_start: 0.9327 (mt-10) cc_final: 0.9119 (pm20) REVERT: H 78 GLU cc_start: 0.9393 (tt0) cc_final: 0.9008 (tm-30) REVERT: J 13 SER cc_start: 0.9205 (t) cc_final: 0.8973 (p) REVERT: J 69 GLU cc_start: 0.8509 (pm20) cc_final: 0.8222 (pm20) REVERT: Q 84 GLU cc_start: 0.9252 (tt0) cc_final: 0.9030 (tp30) REVERT: Q 88 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8720 (mm-30) REVERT: Q 100 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8496 (mt-10) REVERT: Q 109 GLN cc_start: 0.9487 (mt0) cc_final: 0.9194 (mt0) REVERT: S 78 GLU cc_start: 0.9328 (tt0) cc_final: 0.9035 (tm-30) REVERT: U 73 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.7894 (ptt-90) REVERT: U 80 ASN cc_start: 0.9379 (t0) cc_final: 0.9019 (t0) outliers start: 53 outliers final: 18 residues processed: 290 average time/residue: 1.6689 time to fit residues: 564.9571 Evaluate side-chains 271 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 247 time to evaluate : 3.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 213 GLU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 50 GLU 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 137 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain S residue 57 LEU Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain S residue 74 SER Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 282 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 323 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 193 optimal weight: 1.9990 chunk 340 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 GLN A 323 ASN L 91 GLN O 236 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9230 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33367 Z= 0.275 Angle : 0.537 14.616 45352 Z= 0.258 Chirality : 0.041 0.146 4962 Planarity : 0.004 0.055 5700 Dihedral : 12.285 149.893 5270 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.20 % Allowed : 13.26 % Favored : 85.53 % 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: 1.65 (0.14), residues: 3955 helix: 1.64 (0.11), residues: 2132 sheet: 0.94 (0.27), residues: 365 loop : 0.46 (0.17), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 142 HIS 0.009 0.001 HIS C 197 PHE 0.019 0.001 PHE L 334 TYR 0.015 0.001 TYR C 225 ARG 0.007 0.000 ARG Q 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 255 time to evaluate : 3.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 263 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.8649 (mmm) REVERT: C 288 LYS cc_start: 0.8321 (tttp) cc_final: 0.8023 (ttpp) REVERT: P 128 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8629 (mmm160) REVERT: G 50 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8876 (pt0) REVERT: G 115 GLU cc_start: 0.9213 (tt0) cc_final: 0.8961 (tt0) REVERT: G 123 GLU cc_start: 0.9317 (tt0) cc_final: 0.9085 (pt0) REVERT: F 114 TYR cc_start: 0.8768 (t80) cc_final: 0.8523 (t80) REVERT: H 78 GLU cc_start: 0.9398 (tt0) cc_final: 0.8996 (tm-30) REVERT: J 13 SER cc_start: 0.9194 (t) cc_final: 0.8991 (p) REVERT: J 69 GLU cc_start: 0.8491 (pm20) cc_final: 0.8172 (pm20) REVERT: Q 84 GLU cc_start: 0.9249 (tt0) cc_final: 0.9026 (tp30) REVERT: Q 88 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8684 (mm-30) REVERT: Q 100 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8559 (mt-10) REVERT: Q 109 GLN cc_start: 0.9399 (mt0) cc_final: 0.9044 (mt0) REVERT: S 57 LEU cc_start: 0.9044 (mm) cc_final: 0.8714 (tp) REVERT: S 78 GLU cc_start: 0.9328 (tt0) cc_final: 0.9017 (tm-30) REVERT: U 73 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.7882 (ptt-90) REVERT: U 80 ASN cc_start: 0.9370 (t0) cc_final: 0.9034 (t0) outliers start: 40 outliers final: 16 residues processed: 281 average time/residue: 1.6364 time to fit residues: 536.6906 Evaluate side-chains 267 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 247 time to evaluate : 3.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 0.9990 chunk 341 optimal weight: 9.9990 chunk 74 optimal weight: 0.5980 chunk 222 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 379 optimal weight: 5.9990 chunk 314 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 31 optimal weight: 0.0970 chunk 125 optimal weight: 0.7980 chunk 199 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9182 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 33367 Z= 0.150 Angle : 0.490 11.842 45352 Z= 0.236 Chirality : 0.039 0.142 4962 Planarity : 0.004 0.053 5700 Dihedral : 11.639 149.411 5267 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.93 % Allowed : 13.65 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.14), residues: 3955 helix: 1.83 (0.11), residues: 2133 sheet: 1.04 (0.27), residues: 365 loop : 0.49 (0.17), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 142 HIS 0.004 0.001 HIS B 87 PHE 0.016 0.001 PHE A 334 TYR 0.012 0.001 TYR R 31 ARG 0.005 0.000 ARG Q 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 260 time to evaluate : 3.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 263 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.8696 (mmm) REVERT: C 288 LYS cc_start: 0.8281 (tttp) cc_final: 0.7980 (ttpp) REVERT: P 128 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8720 (mmm160) REVERT: P 193 HIS cc_start: 0.9001 (m-70) cc_final: 0.7926 (m-70) REVERT: P 214 TYR cc_start: 0.7268 (p90) cc_final: 0.6839 (p90) REVERT: G 50 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8845 (pt0) REVERT: G 112 GLU cc_start: 0.9210 (OUTLIER) cc_final: 0.8528 (tm-30) REVERT: G 115 GLU cc_start: 0.9211 (tt0) cc_final: 0.8952 (tt0) REVERT: F 114 TYR cc_start: 0.8767 (t80) cc_final: 0.8443 (t80) REVERT: B 392 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8565 (mp10) REVERT: H 78 GLU cc_start: 0.9395 (tt0) cc_final: 0.9011 (tm-30) REVERT: J 69 GLU cc_start: 0.8485 (pm20) cc_final: 0.8141 (pm20) REVERT: Q 84 GLU cc_start: 0.9247 (tt0) cc_final: 0.9015 (tp30) REVERT: Q 88 GLU cc_start: 0.9108 (mm-30) cc_final: 0.8693 (mm-30) REVERT: Q 109 GLN cc_start: 0.9348 (mt0) cc_final: 0.8919 (mt0) REVERT: L 461 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8437 (p0) REVERT: S 57 LEU cc_start: 0.8977 (mm) cc_final: 0.8677 (tp) REVERT: S 78 GLU cc_start: 0.9319 (tt0) cc_final: 0.9023 (tm-30) REVERT: T 34 GLU cc_start: 0.9105 (tt0) cc_final: 0.8796 (pt0) REVERT: U 73 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8070 (ptt-90) REVERT: U 80 ASN cc_start: 0.9357 (t0) cc_final: 0.9020 (t0) outliers start: 31 outliers final: 12 residues processed: 277 average time/residue: 1.6357 time to fit residues: 529.1525 Evaluate side-chains 264 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 245 time to evaluate : 3.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 128 ARG Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 276 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 chunk 319 optimal weight: 0.9990 chunk 211 optimal weight: 1.9990 chunk 377 optimal weight: 4.9990 chunk 236 optimal weight: 0.0670 chunk 230 optimal weight: 0.0970 chunk 174 optimal weight: 8.9990 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 109 GLN I 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9187 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 33367 Z= 0.166 Angle : 0.496 12.050 45352 Z= 0.236 Chirality : 0.039 0.144 4962 Planarity : 0.004 0.054 5700 Dihedral : 11.383 149.068 5267 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.05 % Allowed : 13.71 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.14), residues: 3955 helix: 1.91 (0.11), residues: 2135 sheet: 1.01 (0.27), residues: 369 loop : 0.55 (0.17), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 142 HIS 0.007 0.001 HIS C 197 PHE 0.017 0.001 PHE A 334 TYR 0.013 0.001 TYR B 170 ARG 0.005 0.000 ARG Q 144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 253 time to evaluate : 3.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 288 LYS cc_start: 0.8286 (tttp) cc_final: 0.7981 (ttpp) REVERT: P 214 TYR cc_start: 0.7228 (p90) cc_final: 0.6808 (p90) REVERT: G 16 LYS cc_start: 0.8913 (mmpt) cc_final: 0.8657 (pptt) REVERT: G 50 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8860 (pt0) REVERT: G 112 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8537 (tm-30) REVERT: G 115 GLU cc_start: 0.9209 (tt0) cc_final: 0.8953 (tt0) REVERT: H 78 GLU cc_start: 0.9401 (tt0) cc_final: 0.9016 (tm-30) REVERT: J 15 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8691 (ptmt) REVERT: J 69 GLU cc_start: 0.8524 (pm20) cc_final: 0.8195 (pm20) REVERT: Q 84 GLU cc_start: 0.9246 (tt0) cc_final: 0.9012 (tp30) REVERT: Q 88 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8698 (mm-30) REVERT: Q 107 LYS cc_start: 0.9483 (ttmm) cc_final: 0.9240 (mppt) REVERT: L 461 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8384 (p0) REVERT: S 57 LEU cc_start: 0.8986 (mm) cc_final: 0.8657 (tp) REVERT: S 78 GLU cc_start: 0.9327 (tt0) cc_final: 0.9019 (tm-30) REVERT: T 34 GLU cc_start: 0.9108 (tt0) cc_final: 0.8821 (pt0) REVERT: U 80 ASN cc_start: 0.9352 (t0) cc_final: 0.9004 (t0) outliers start: 35 outliers final: 16 residues processed: 274 average time/residue: 1.6911 time to fit residues: 539.3852 Evaluate side-chains 265 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 246 time to evaluate : 3.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain U residue 13 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 240 optimal weight: 0.4980 chunk 257 optimal weight: 0.8980 chunk 186 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 296 optimal weight: 10.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- 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** I 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9236 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 33367 Z= 0.330 Angle : 0.569 15.255 45352 Z= 0.268 Chirality : 0.042 0.147 4962 Planarity : 0.004 0.054 5700 Dihedral : 11.572 148.929 5267 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.99 % Allowed : 13.80 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.14), residues: 3955 helix: 1.81 (0.11), residues: 2138 sheet: 1.07 (0.27), residues: 365 loop : 0.54 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 142 HIS 0.014 0.001 HIS C 197 PHE 0.019 0.001 PHE C 240 TYR 0.035 0.001 TYR F 114 ARG 0.008 0.000 ARG M 236 *********************** 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 282 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 249 time to evaluate : 4.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 288 LYS cc_start: 0.8335 (tttp) cc_final: 0.7989 (ttpp) REVERT: P 214 TYR cc_start: 0.7397 (p90) cc_final: 0.6809 (p90) REVERT: G 16 LYS cc_start: 0.8976 (mmpt) cc_final: 0.8692 (pptt) REVERT: G 50 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8866 (pt0) REVERT: G 97 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8771 (mp0) REVERT: G 112 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8559 (tm-30) REVERT: G 115 GLU cc_start: 0.9227 (tt0) cc_final: 0.8940 (tt0) REVERT: F 99 ASP cc_start: 0.9300 (m-30) cc_final: 0.9055 (p0) REVERT: B 373 ILE cc_start: 0.9282 (tp) cc_final: 0.9053 (pp) REVERT: H 78 GLU cc_start: 0.9408 (tt0) cc_final: 0.9006 (tm-30) REVERT: J 69 GLU cc_start: 0.8557 (pm20) cc_final: 0.8214 (pm20) REVERT: Q 84 GLU cc_start: 0.9246 (tt0) cc_final: 0.9023 (tp30) REVERT: Q 88 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8721 (mm-30) REVERT: Q 107 LYS cc_start: 0.9490 (ttmm) cc_final: 0.9236 (mppt) REVERT: Q 109 GLN cc_start: 0.9314 (mt0) cc_final: 0.8845 (mt0) REVERT: L 461 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8398 (p0) REVERT: S 57 LEU cc_start: 0.9040 (mm) cc_final: 0.8731 (tp) REVERT: S 78 GLU cc_start: 0.9320 (tt0) cc_final: 0.9018 (tm-30) REVERT: T 31 MET cc_start: 0.8767 (mmm) cc_final: 0.7984 (mmm) REVERT: T 34 GLU cc_start: 0.9134 (tt0) cc_final: 0.8830 (pt0) REVERT: U 73 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.7916 (ptt-90) REVERT: U 80 ASN cc_start: 0.9368 (t0) cc_final: 0.9025 (t0) outliers start: 33 outliers final: 18 residues processed: 270 average time/residue: 1.6401 time to fit residues: 517.4407 Evaluate side-chains 268 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 245 time to evaluate : 3.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 339 ARG Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 5.9990 chunk 361 optimal weight: 0.9980 chunk 330 optimal weight: 8.9990 chunk 352 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 153 optimal weight: 7.9990 chunk 276 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 318 optimal weight: 1.9990 chunk 332 optimal weight: 0.9980 chunk 350 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 193 HIS I 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9197 moved from start: 0.2694 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= 0.177 Angle : 0.508 12.700 45352 Z= 0.242 Chirality : 0.039 0.142 4962 Planarity : 0.004 0.054 5700 Dihedral : 11.193 148.969 5267 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.90 % Allowed : 14.08 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.14), residues: 3955 helix: 1.91 (0.11), residues: 2135 sheet: 1.07 (0.27), residues: 365 loop : 0.57 (0.17), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 142 HIS 0.005 0.001 HIS N 96 PHE 0.016 0.001 PHE A 334 TYR 0.031 0.001 TYR F 114 ARG 0.006 0.000 ARG Q 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 252 time to evaluate : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 288 LYS cc_start: 0.8290 (tttp) cc_final: 0.7945 (ttpp) REVERT: P 214 TYR cc_start: 0.7413 (p90) cc_final: 0.6781 (p90) REVERT: G 16 LYS cc_start: 0.8987 (mmpt) cc_final: 0.8686 (pptt) REVERT: G 50 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8827 (pt0) REVERT: G 112 GLU cc_start: 0.9210 (OUTLIER) cc_final: 0.8528 (tm-30) REVERT: G 115 GLU cc_start: 0.9204 (tt0) cc_final: 0.8924 (tt0) REVERT: G 123 GLU cc_start: 0.9315 (pt0) cc_final: 0.8924 (pp20) REVERT: F 99 ASP cc_start: 0.9285 (m-30) cc_final: 0.9035 (p0) REVERT: F 107 LYS cc_start: 0.9175 (mmmt) cc_final: 0.8874 (tppt) REVERT: B 373 ILE cc_start: 0.9279 (tp) cc_final: 0.9053 (pp) REVERT: H 78 GLU cc_start: 0.9399 (tt0) cc_final: 0.9012 (tm-30) REVERT: J 69 GLU cc_start: 0.8535 (pm20) cc_final: 0.8245 (pm20) REVERT: Q 84 GLU cc_start: 0.9241 (tt0) cc_final: 0.9009 (tp30) REVERT: Q 88 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8718 (mm-30) REVERT: Q 107 LYS cc_start: 0.9505 (ttmm) cc_final: 0.9254 (mppt) REVERT: Q 109 GLN cc_start: 0.9326 (mt0) cc_final: 0.8852 (mt0) REVERT: L 461 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8450 (p0) REVERT: S 57 LEU cc_start: 0.8992 (mm) cc_final: 0.8693 (tp) REVERT: S 78 GLU cc_start: 0.9326 (tt0) cc_final: 0.9024 (tm-30) REVERT: T 30 ASP cc_start: 0.9219 (t70) cc_final: 0.8778 (t0) REVERT: T 34 GLU cc_start: 0.9121 (tt0) cc_final: 0.8824 (pt0) REVERT: U 15 LYS cc_start: 0.9422 (pptt) cc_final: 0.9181 (pptt) REVERT: U 80 ASN cc_start: 0.9358 (t0) cc_final: 0.9025 (t0) outliers start: 30 outliers final: 17 residues processed: 270 average time/residue: 1.6139 time to fit residues: 509.1829 Evaluate side-chains 270 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 250 time to evaluate : 3.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 116 VAL Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 339 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 2.9990 chunk 372 optimal weight: 3.9990 chunk 227 optimal weight: 0.6980 chunk 176 optimal weight: 10.0000 chunk 258 optimal weight: 0.9980 chunk 390 optimal weight: 7.9990 chunk 359 optimal weight: 5.9990 chunk 310 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 240 optimal weight: 8.9990 chunk 190 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9216 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33367 Z= 0.242 Angle : 0.536 13.829 45352 Z= 0.254 Chirality : 0.040 0.145 4962 Planarity : 0.004 0.053 5700 Dihedral : 11.145 148.769 5267 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.69 % Allowed : 14.38 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.14), residues: 3955 helix: 1.89 (0.11), residues: 2140 sheet: 1.08 (0.27), residues: 365 loop : 0.58 (0.17), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 142 HIS 0.011 0.001 HIS C 197 PHE 0.019 0.001 PHE A 334 TYR 0.031 0.001 TYR F 114 ARG 0.009 0.000 ARG Q 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7910 Ramachandran restraints generated. 3955 Oldfield, 0 Emsley, 3955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 250 time to evaluate : 3.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 288 LYS cc_start: 0.8329 (tttp) cc_final: 0.7976 (ttpp) REVERT: P 214 TYR cc_start: 0.7460 (p90) cc_final: 0.6833 (p90) REVERT: G 16 LYS cc_start: 0.8994 (mmpt) cc_final: 0.8678 (pptt) REVERT: G 50 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8828 (pt0) REVERT: G 112 GLU cc_start: 0.9218 (OUTLIER) cc_final: 0.8539 (tm-30) REVERT: G 115 GLU cc_start: 0.9222 (tt0) cc_final: 0.8986 (tt0) REVERT: F 99 ASP cc_start: 0.9293 (m-30) cc_final: 0.9053 (p0) REVERT: F 107 LYS cc_start: 0.9191 (mmmt) cc_final: 0.8914 (tppt) REVERT: B 373 ILE cc_start: 0.9279 (tp) cc_final: 0.9034 (pp) REVERT: D 248 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8341 (ttm) REVERT: H 78 GLU cc_start: 0.9399 (tt0) cc_final: 0.9005 (tm-30) REVERT: J 69 GLU cc_start: 0.8534 (pm20) cc_final: 0.8236 (pm20) REVERT: Q 84 GLU cc_start: 0.9242 (tt0) cc_final: 0.9015 (tp30) REVERT: Q 88 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8727 (mm-30) REVERT: Q 109 GLN cc_start: 0.9328 (mt0) cc_final: 0.8848 (mt0) REVERT: L 461 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8398 (p0) REVERT: S 57 LEU cc_start: 0.9026 (mm) cc_final: 0.8679 (tp) REVERT: S 78 GLU cc_start: 0.9329 (tt0) cc_final: 0.9029 (tm-30) REVERT: T 30 ASP cc_start: 0.9230 (t70) cc_final: 0.8812 (t0) REVERT: T 31 MET cc_start: 0.8732 (mmm) cc_final: 0.8031 (mmm) REVERT: T 34 GLU cc_start: 0.9122 (tt0) cc_final: 0.8862 (pt0) REVERT: U 80 ASN cc_start: 0.9366 (t0) cc_final: 0.9036 (t0) outliers start: 23 outliers final: 16 residues processed: 266 average time/residue: 1.7099 time to fit residues: 531.0145 Evaluate side-chains 271 residues out of total 3325 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 251 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain P residue 115 ASN Chi-restraints excluded: chain P residue 143 VAL Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 112 GLU Chi-restraints excluded: chain F residue 93 ASP Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 239 MET Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain Q residue 93 ASP Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 461 ASP Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 339 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 8.9990 chunk 331 optimal weight: 6.9990 chunk 95 optimal weight: 0.5980 chunk 286 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 311 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 319 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.063922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.046945 restraints weight = 79062.818| |-----------------------------------------------------------------------------| r_work (start): 0.2658 rms_B_bonded: 2.19 r_work: 0.2530 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2398 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9140 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33367 Z= 0.209 Angle : 0.526 12.941 45352 Z= 0.250 Chirality : 0.040 0.144 4962 Planarity : 0.004 0.053 5700 Dihedral : 11.004 148.886 5267 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.66 % Allowed : 14.47 % Favored : 84.87 % 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: 1.90 (0.11), residues: 2141 sheet: 1.09 (0.27), residues: 365 loop : 0.58 (0.17), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 142 HIS 0.008 0.001 HIS C 197 PHE 0.017 0.001 PHE A 334 TYR 0.030 0.001 TYR B 170 ARG 0.010 0.000 ARG Q 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10295.37 seconds wall clock time: 186 minutes 21.47 seconds (11181.47 seconds total)